From 834ad10010566ed7b91153fa26ac4d858fc3a620 Mon Sep 17 00:00:00 2001 From: Colin Date: Mon, 6 Nov 2023 08:45:22 -0500 Subject: [PATCH] Volatile-ize spreadsheet view Remove [skip ci] Volatile [skip ci] Parse out INFO field [skip ci] Misc Misc Restyling Refactoring More misc Misc Misc Misc Misc New Refname renaming fix for breakpoint split view Breakpoint split view Misc [skip ci] Refactors Use 7.0.0 Updates Misc Misc Misc SV inspector working Wow Misc More notifyError --- eslint.config.mjs | 1 + packages/core/assemblyManager/assembly.ts | 6 + .../core/assemblyManager/assemblyManager.ts | 4 +- packages/core/configuration/util.ts | 2 +- .../renderers/RpcRenderedSvgGroup.tsx | 3 + .../renderers/ServerSideRenderedContent.tsx | 3 + packages/core/ui/ResizeHandle.tsx | 7 +- packages/core/util/index.ts | 1 + .../src/BreakendMultiLevelOptionDialog.tsx | 69 +- .../src/BreakendSingleLevelOptionDialog.tsx | 39 +- .../src/AlignmentsFeatureDetail/util.ts | 2 +- .../SharedLinearPileupDisplayMixin.ts | 4 +- .../BreakpointSplitView.ts | 51 +- .../components/Breakends.tsx | 14 +- .../components/PairedFeatures.tsx | 12 +- .../components/Translocations.tsx | 26 +- .../src/BreakpointSplitView/util.ts | 7 +- .../breakpoint-split-view/src/index.test.ts | 3 - .../CircularView/components/CircularView.tsx | 8 +- .../src/CircularView/components/Controls.tsx | 56 +- .../src/CircularView/models/model.ts | 8 +- plugins/jobs-management/src/index.test.ts | 3 - .../AutocompleteTextField.tsx | 1 + .../components/SearchResultsTable.tsx | 2 +- .../src/LaunchSpreadsheetView/index.ts | 12 +- .../SpreadsheetView/components/CellData.tsx | 34 - .../components/ColumnFilterControls.tsx | 81 - .../SpreadsheetView/components/ColumnMenu.tsx | 185 - .../SpreadsheetView/components/DataRow.tsx | 127 - .../SpreadsheetView/components/DataTable.tsx | 91 - .../components/DataTableHeader.tsx | 128 - .../components/GlobalFilterControls.tsx | 73 - .../components/ImportWizard.tsx | 184 +- .../components/NumberEditor.tsx | 54 - .../components/RowCountMessage.tsx | 42 - .../SpreadsheetView/components/RowMenu.tsx | 65 - .../components/SortIndicator.tsx | 36 - .../components/Spreadsheet.test.ts | 17 - .../components/Spreadsheet.tsx | 49 - .../components/SpreadsheetDataGrid.tsx | 38 + .../components/SpreadsheetView.tsx | 130 +- .../SpreadsheetView/components/StatusBar.tsx | 75 - .../src/SpreadsheetView/components/util.ts | 62 +- .../importAdapters/BedImport.test.ts | 14 - .../importAdapters/BedImport.ts | 217 +- .../importAdapters/BedpeImport.ts | 81 + .../importAdapters/ImportUtils.test.ts | 25 - .../importAdapters/ImportUtils.ts | 154 - .../importAdapters/STARFusionImport.test.ts | 27 - .../importAdapters/STARFusionImport.ts | 84 +- .../importAdapters/VcfImport.test.ts | 42 - .../importAdapters/VcfImport.ts | 166 +- .../__snapshots__/ImportUtils.test.ts.snap | 6555 ------- .../STARFusionImport.test.ts.snap | 2354 --- .../__snapshots__/VcfImport.test.ts.snap | 16329 ---------------- .../BreakendMultiLevelOptionDialog.tsx | 2 + .../BreakendSingleLevelOptionDialog.tsx | 2 + .../importAdapters/components/FeatureMenu.tsx | 96 + .../importAdapters/components/LocString.tsx | 40 + .../SpreadsheetView/importAdapters/util.ts | 11 + .../src/SpreadsheetView/index.ts | 4 +- .../models/ColumnDataTypes/LocEnd.ts | 21 - .../models/ColumnDataTypes/LocRef.ts | 21 - .../models/ColumnDataTypes/LocStart.ts | 21 - .../models/ColumnDataTypes/LocString.tsx | 324 - .../MakeSpreadsheetColumnType.tsx | 37 - .../models/ColumnDataTypes/Number.tsx | 175 - .../models/ColumnDataTypes/Text.tsx | 171 - .../models/ColumnDataTypes/index.ts | 34 - .../SpreadsheetView/models/FilterControls.ts | 94 - .../SpreadsheetView/models/ImportWizard.ts | 338 +- .../src/SpreadsheetView/models/Row.ts | 45 - .../src/SpreadsheetView/models/Spreadsheet.ts | 209 - .../SpreadsheetView/models/Spreadsheet.tsx | 167 + .../models/SpreadsheetView.test.ts | 8 - .../SpreadsheetView/models/SpreadsheetView.ts | 345 +- .../SpreadsheetView/models/StaticRowSet.ts | 64 - plugins/sv-inspector/index.test.ts | 3 - .../src/LaunchSvInspectorView/index.ts | 12 +- .../components/SvInspectorView.tsx | 64 +- .../sv-inspector/src/SvInspectorView/index.ts | 12 +- .../SvInspectorView/models/SvInspectorView.ts | 375 +- .../models/adhocFeatureUtils.ts | 153 - .../models/breakpointSplitViewFromTableRow.ts | 85 - plugins/text-indexing/index.test.ts | 3 - .../src/LinearVariantDisplay/configSchema.ts | 9 +- .../src/LinearVariantDisplay/model.ts | 3 +- .../LaunchBreakendPanel.tsx | 6 +- .../saved-sessions/jbrowse_analytics.js | 2 +- .../jbrowse-desktop/src/indexJobsModel.ts | 15 +- products/jbrowse-web/src/SessionLoader.ts | 2 +- .../jbrowse-web/src/components/JBrowse.tsx | 3 +- .../src/tests/SVInspector.test.tsx | 3 - 93 files changed, 1428 insertions(+), 29414 deletions(-) delete mode 100644 plugins/breakpoint-split-view/src/index.test.ts delete mode 100644 plugins/jobs-management/src/index.test.ts delete mode 100644 plugins/spreadsheet-view/src/SpreadsheetView/components/CellData.tsx delete mode 100644 plugins/spreadsheet-view/src/SpreadsheetView/components/ColumnFilterControls.tsx delete mode 100644 plugins/spreadsheet-view/src/SpreadsheetView/components/ColumnMenu.tsx delete mode 100644 plugins/spreadsheet-view/src/SpreadsheetView/components/DataRow.tsx delete mode 100644 plugins/spreadsheet-view/src/SpreadsheetView/components/DataTable.tsx delete mode 100644 plugins/spreadsheet-view/src/SpreadsheetView/components/DataTableHeader.tsx delete mode 100644 plugins/spreadsheet-view/src/SpreadsheetView/components/GlobalFilterControls.tsx delete mode 100644 plugins/spreadsheet-view/src/SpreadsheetView/components/NumberEditor.tsx delete mode 100644 plugins/spreadsheet-view/src/SpreadsheetView/components/RowCountMessage.tsx delete mode 100644 plugins/spreadsheet-view/src/SpreadsheetView/components/RowMenu.tsx delete mode 100644 plugins/spreadsheet-view/src/SpreadsheetView/components/SortIndicator.tsx delete mode 100644 plugins/spreadsheet-view/src/SpreadsheetView/components/Spreadsheet.test.ts delete mode 100644 plugins/spreadsheet-view/src/SpreadsheetView/components/Spreadsheet.tsx create mode 100644 plugins/spreadsheet-view/src/SpreadsheetView/components/SpreadsheetDataGrid.tsx delete mode 100644 plugins/spreadsheet-view/src/SpreadsheetView/components/StatusBar.tsx delete mode 100644 plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/BedImport.test.ts create mode 100644 plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/BedpeImport.ts delete mode 100644 plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/ImportUtils.test.ts delete mode 100644 plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/ImportUtils.ts delete mode 100644 plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/STARFusionImport.test.ts delete mode 100644 plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/VcfImport.test.ts delete mode 100644 plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/__snapshots__/ImportUtils.test.ts.snap delete mode 100644 plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/__snapshots__/STARFusionImport.test.ts.snap delete mode 100644 plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/__snapshots__/VcfImport.test.ts.snap create mode 100644 plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/components/BreakendMultiLevelOptionDialog.tsx create mode 100644 plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/components/BreakendSingleLevelOptionDialog.tsx create mode 100644 plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/components/FeatureMenu.tsx create mode 100644 plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/components/LocString.tsx create mode 100644 plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/util.ts delete mode 100644 plugins/spreadsheet-view/src/SpreadsheetView/models/ColumnDataTypes/LocEnd.ts delete mode 100644 plugins/spreadsheet-view/src/SpreadsheetView/models/ColumnDataTypes/LocRef.ts delete mode 100644 plugins/spreadsheet-view/src/SpreadsheetView/models/ColumnDataTypes/LocStart.ts delete mode 100644 plugins/spreadsheet-view/src/SpreadsheetView/models/ColumnDataTypes/LocString.tsx delete mode 100644 plugins/spreadsheet-view/src/SpreadsheetView/models/ColumnDataTypes/MakeSpreadsheetColumnType.tsx delete mode 100644 plugins/spreadsheet-view/src/SpreadsheetView/models/ColumnDataTypes/Number.tsx delete mode 100644 plugins/spreadsheet-view/src/SpreadsheetView/models/ColumnDataTypes/Text.tsx delete mode 100644 plugins/spreadsheet-view/src/SpreadsheetView/models/ColumnDataTypes/index.ts delete mode 100644 plugins/spreadsheet-view/src/SpreadsheetView/models/FilterControls.ts delete mode 100644 plugins/spreadsheet-view/src/SpreadsheetView/models/Row.ts delete mode 100644 plugins/spreadsheet-view/src/SpreadsheetView/models/Spreadsheet.ts create mode 100644 plugins/spreadsheet-view/src/SpreadsheetView/models/Spreadsheet.tsx delete mode 100644 plugins/spreadsheet-view/src/SpreadsheetView/models/SpreadsheetView.test.ts delete mode 100644 plugins/spreadsheet-view/src/SpreadsheetView/models/StaticRowSet.ts delete mode 100644 plugins/sv-inspector/index.test.ts delete mode 100644 plugins/sv-inspector/src/SvInspectorView/models/adhocFeatureUtils.ts delete mode 100644 plugins/sv-inspector/src/SvInspectorView/models/breakpointSplitViewFromTableRow.ts delete mode 100644 plugins/text-indexing/index.test.ts diff --git a/eslint.config.mjs b/eslint.config.mjs index c2561ea652..d89c549b53 100644 --- a/eslint.config.mjs +++ b/eslint.config.mjs @@ -141,6 +141,7 @@ export default tseslint.config( '@typescript-eslint/no-unsafe-member-access': 'off', '@typescript-eslint/no-unsafe-argument': 'off', '@typescript-eslint/no-unsafe-assignment': 'off', + '@typescript-eslint/no-deprecated': 'off', '@typescript-eslint/restrict-plus-operands': 'off', '@typescript-eslint/no-unsafe-call': 'off', '@typescript-eslint/no-unsafe-return': 'off', diff --git a/packages/core/assemblyManager/assembly.ts b/packages/core/assemblyManager/assembly.ts index 3e6ff3b895..09a816c0cc 100644 --- a/packages/core/assemblyManager/assembly.ts +++ b/packages/core/assemblyManager/assembly.ts @@ -294,6 +294,12 @@ export default function assemblyFactory( self.refNameAliases[refName] || self.lowerCaseRefNameAliases[refName] ) }, + /** + * #method + */ + getCanonicalRefNameOrDefault(refName: string) { + return this.getCanonicalRefName(refName) || refName + }, /** * #method */ diff --git a/packages/core/assemblyManager/assemblyManager.ts b/packages/core/assemblyManager/assemblyManager.ts index 11a04830a0..6970a265f6 100644 --- a/packages/core/assemblyManager/assemblyManager.ts +++ b/packages/core/assemblyManager/assemblyManager.ts @@ -153,9 +153,7 @@ function assemblyManagerFactory(conf: IAnyType, pm: PluginManager) { if (assembly) { return assembly.isValidRefName(refName) } - throw new Error( - `Failed to look up refName ${refName} on ${assemblyName} because assembly does not exist`, - ) + throw new Error(`assembly "${assemblyName}" not found`) }, })) .actions(self => ({ diff --git a/packages/core/configuration/util.ts b/packages/core/configuration/util.ts index ad1794997c..c0aeee92e0 100644 --- a/packages/core/configuration/util.ts +++ b/packages/core/configuration/util.ts @@ -35,7 +35,7 @@ import { * will be sent to each of the slotNames */ export function readConfObject( - confObject: CONFMODEL, + confObject: CONFMODEL | Record, slotPath?: | ConfigurationSlotName> | string[], diff --git a/packages/core/pluggableElementTypes/renderers/RpcRenderedSvgGroup.tsx b/packages/core/pluggableElementTypes/renderers/RpcRenderedSvgGroup.tsx index bc87c695d4..0886d31ff2 100644 --- a/packages/core/pluggableElementTypes/renderers/RpcRenderedSvgGroup.tsx +++ b/packages/core/pluggableElementTypes/renderers/RpcRenderedSvgGroup.tsx @@ -69,6 +69,7 @@ const OldHydrate = observer(function OldHydrate(props: Props) { function doHydrate() { if (domNode && html) { if (domNode.innerHTML) { + unmountComponentAtNode(domNode) } @@ -80,6 +81,7 @@ const OldHydrate = observer(function OldHydrate(props: Props) { // hydration for when we have some free time. helps keep the // framerate up. rIC(() => { + hydrate(, domNode) }) } @@ -87,6 +89,7 @@ const OldHydrate = observer(function OldHydrate(props: Props) { doHydrate() return () => { if (domNode) { + unmountComponentAtNode(domNode) } } diff --git a/packages/core/pluggableElementTypes/renderers/ServerSideRenderedContent.tsx b/packages/core/pluggableElementTypes/renderers/ServerSideRenderedContent.tsx index 235696b940..51bb7d1d06 100644 --- a/packages/core/pluggableElementTypes/renderers/ServerSideRenderedContent.tsx +++ b/packages/core/pluggableElementTypes/renderers/ServerSideRenderedContent.tsx @@ -82,10 +82,12 @@ const OldHydrate = observer(function ({ const domNode = ref.current function doHydrate() { if (domNode) { + unmountComponentAtNode(domNode) domNode.innerHTML = html rIC(() => { + hydrate( @@ -100,6 +102,7 @@ const OldHydrate = observer(function ({ return () => { if (domNode) { + unmountComponentAtNode(domNode) } } diff --git a/packages/core/ui/ResizeHandle.tsx b/packages/core/ui/ResizeHandle.tsx index e3f04586db..b85b11fa75 100644 --- a/packages/core/ui/ResizeHandle.tsx +++ b/packages/core/ui/ResizeHandle.tsx @@ -12,11 +12,14 @@ const useStyles = makeStyles()({ }, flexbox_verticalHandle: { cursor: 'col-resize', - alignSelf: 'stretch', // the height: 100% is actually unable to function inside flexbox + alignSelf: 'stretch', + // uses alignSelf:stretch with flexbox as the height: 100% is actually + // unable to function inside flexbox }, flexbox_horizontalHandle: { cursor: 'row-resize', - alignSelf: 'stretch', // similar to above + alignSelf: 'stretch', + // similar to above }, }) diff --git a/packages/core/util/index.ts b/packages/core/util/index.ts index aadb705758..dcd1fca94e 100644 --- a/packages/core/util/index.ts +++ b/packages/core/util/index.ts @@ -1458,6 +1458,7 @@ export function renderToStaticMarkup( if (createRootFn) { createRootFn(div).render(node) } else { + render(node, div) } }) diff --git a/packages/sv-core/src/BreakendMultiLevelOptionDialog.tsx b/packages/sv-core/src/BreakendMultiLevelOptionDialog.tsx index 75412d5f5c..edaac4b5e0 100644 --- a/packages/sv-core/src/BreakendMultiLevelOptionDialog.tsx +++ b/packages/sv-core/src/BreakendMultiLevelOptionDialog.tsx @@ -4,7 +4,7 @@ import { Button, DialogActions, DialogContent } from '@mui/material' import { getSnapshot } from 'mobx-state-tree' import { Dialog } from '@jbrowse/core/ui' import { when } from 'mobx' -import { getSession, Feature } from '@jbrowse/core/util' +import { Feature, AbstractSessionModel } from '@jbrowse/core/util' import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view' import type { Assembly } from '@jbrowse/core/assemblyManager/assembly' @@ -29,17 +29,17 @@ function stripIds(arr: Track[]) { } const BreakendMultiLevelOptionDialog = observer(function ({ - model, + session, handleClose, feature, assemblyName, viewType, view, }: { - model: unknown + session: AbstractSessionModel handleClose: () => void feature: Feature - view: LinearGenomeViewModel + view?: LinearGenomeViewModel assemblyName: string viewType: { getBreakendCoveringRegions: (arg: { @@ -63,23 +63,28 @@ const BreakendMultiLevelOptionDialog = observer(function ({ title="Multi-level breakpoint split view options" > - { - setCopyTracks(event.target.checked) - }} - /> +
Launch multi-level breakpoint split view
+ {view ? ( + <> + { + setCopyTracks(event.target.checked) + }} + /> - {copyTracks ? ( - { - setMirror(event.target.checked) - }} - /> + {copyTracks ? ( + { + setMirror(event.target.checked) + }} + /> + ) : null} + ) : null} @@ -87,21 +92,23 @@ const BreakendMultiLevelOptionDialog = observer(function ({ onClick={() => { // eslint-disable-next-line @typescript-eslint/no-floating-promises ;(async () => { - const session = getSession(model) try { - const asm = - await session.assemblyManager.waitForAssembly(assemblyName) - if (!asm) { + const { assemblyManager } = session + const assembly = + await assemblyManager.waitForAssembly(assemblyName) + if (!assembly) { throw new Error(`assembly ${assemblyName} not found`) } const { refName, pos, mateRefName, matePos } = viewType.getBreakendCoveringRegions({ feature, - assembly: asm, + assembly: assembly, }) - const viewTracks = getSnapshot(view.tracks) as Track[] + const viewTracks = view + ? (getSnapshot(view.tracks) as Track[]) + : [] const breakpointSplitView = session.addView( 'BreakpointSplitView', { @@ -114,7 +121,7 @@ const BreakendMultiLevelOptionDialog = observer(function ({ { type: 'LinearGenomeView', hideHeader: true, - tracks: stripIds(getSnapshot(view.tracks)), + tracks: stripIds(viewTracks), }, { type: 'LinearGenomeView', @@ -126,8 +133,10 @@ const BreakendMultiLevelOptionDialog = observer(function ({ ], }, ) as unknown as { views: LinearGenomeViewModel[] } - const r1 = asm.regions!.find(r => r.refName === refName) - const r2 = asm.regions!.find(r => r.refName === mateRefName) + const r1 = assembly.regions!.find(r => r.refName === refName) + const r2 = assembly.regions!.find( + r => r.refName === mateRefName, + ) if (!r1 || !r2) { throw new Error("can't find regions") } @@ -172,7 +181,7 @@ const BreakendMultiLevelOptionDialog = observer(function ({ breakpointSplitView.views[0]!.centerAt(pos, refName) } catch (e) { console.error(e) - session.notify(`${e}`) + session.notifyError(`${e}`, e) } })() handleClose() diff --git a/packages/sv-core/src/BreakendSingleLevelOptionDialog.tsx b/packages/sv-core/src/BreakendSingleLevelOptionDialog.tsx index a1a17e2310..18dbbd6785 100644 --- a/packages/sv-core/src/BreakendSingleLevelOptionDialog.tsx +++ b/packages/sv-core/src/BreakendSingleLevelOptionDialog.tsx @@ -4,10 +4,10 @@ import { Button, DialogActions, DialogContent, TextField } from '@mui/material' import { getSnapshot } from 'mobx-state-tree' import { Dialog } from '@jbrowse/core/ui' import { - getSession, Feature, gatherOverlaps, useLocalStorage, + AbstractSessionModel, } from '@jbrowse/core/util' import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view' import type { Assembly } from '@jbrowse/core/assemblyManager/assembly' @@ -33,17 +33,17 @@ function stripIds(arr: Track[]) { } const BreakendSingleLevelOptionDialog = observer(function ({ - model, + session, handleClose, feature, assemblyName, viewType, view, }: { - model: unknown + session: AbstractSessionModel handleClose: () => void feature: Feature - view: LinearGenomeViewModel + view?: LinearGenomeViewModel assemblyName: string viewType: { getBreakendCoveringRegions: (arg: { @@ -70,13 +70,15 @@ const BreakendSingleLevelOptionDialog = observer(function ({ title="Single-level breakpoint split view options" > - { - setCopyTracks(event.target.checked) - }} - /> + {view ? ( + { + setCopyTracks(event.target.checked) + }} + /> + ) : null} - ) : null}{' '} - - + ) }) diff --git a/plugins/spreadsheet-view/src/SpreadsheetView/components/NumberEditor.tsx b/plugins/spreadsheet-view/src/SpreadsheetView/components/NumberEditor.tsx deleted file mode 100644 index 02d6087439..0000000000 --- a/plugins/spreadsheet-view/src/SpreadsheetView/components/NumberEditor.tsx +++ /dev/null @@ -1,54 +0,0 @@ -import React, { useState, useEffect } from 'react' -import { TextField } from '@mui/material' -import { makeStyles } from 'tss-react/mui' -import { observer } from 'mobx-react' - -// locals -import { ImportWizardModel } from '../models/ImportWizard' - -const useStyles = makeStyles()({ - textField: { - width: '2rem', - verticalAlign: 'baseline', - }, -}) - -const NumberEditor = observer(function ({ - model, - disabled, - modelPropName, - modelSetterName, -}: { - model: ImportWizardModel - disabled: boolean - modelPropName: string - modelSetterName: string -}) { - // @ts-expect-error - const [val, setVal] = useState(model[modelPropName]) - const { classes } = useStyles() - useEffect(() => { - const num = Number.parseInt(val, 10) - if (!Number.isNaN(num)) { - if (num > 0) { - // @ts-expect-error - model[modelSetterName](num) - } else { - setVal(1) - } - } - }, [model, modelSetterName, val]) - return ( - { - setVal(evt.target.value) - }} - className={classes.textField} - /> - ) -}) - -export default NumberEditor diff --git a/plugins/spreadsheet-view/src/SpreadsheetView/components/RowCountMessage.tsx b/plugins/spreadsheet-view/src/SpreadsheetView/components/RowCountMessage.tsx deleted file mode 100644 index 36782469d5..0000000000 --- a/plugins/spreadsheet-view/src/SpreadsheetView/components/RowCountMessage.tsx +++ /dev/null @@ -1,42 +0,0 @@ -import React from 'react' -import { observer } from 'mobx-react' - -// locals -import type { SpreadsheetModel } from '../models/Spreadsheet' - -const RowCountMessage = observer(function ({ - spreadsheet, -}: { - spreadsheet: SpreadsheetModel -}) { - // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition - if (spreadsheet.rowSet.isLoaded) { - const { - passingFiltersCount, - count, - selectedCount, - selectedAndPassingFiltersCount, - } = spreadsheet.rowSet - - let rowMessage: string - if (passingFiltersCount !== count) { - rowMessage = `${spreadsheet.rowSet.passingFiltersCount} rows of ${spreadsheet.rowSet.count} total` - if (selectedCount) { - rowMessage += `, ${selectedAndPassingFiltersCount} selected` - const selectedAndNotPassingFiltersCount = - selectedCount - selectedAndPassingFiltersCount - if (selectedAndNotPassingFiltersCount) { - rowMessage += ` (${selectedAndNotPassingFiltersCount} selected rows do not pass filters)` - } - } - } else { - rowMessage = `${spreadsheet.rowSet.count} rows` - if (selectedCount) { - rowMessage += `, ${selectedCount} selected` - } - } - return <>{rowMessage} - } - return null -}) -export default RowCountMessage diff --git a/plugins/spreadsheet-view/src/SpreadsheetView/components/RowMenu.tsx b/plugins/spreadsheet-view/src/SpreadsheetView/components/RowMenu.tsx deleted file mode 100644 index 750ef4d5b5..0000000000 --- a/plugins/spreadsheet-view/src/SpreadsheetView/components/RowMenu.tsx +++ /dev/null @@ -1,65 +0,0 @@ -import React from 'react' -import { observer } from 'mobx-react' -import { Menu, MenuItem } from '@jbrowse/core/ui' -import { Instance } from 'mobx-state-tree' - -// locals -import type SpreadsheetModel from '../models/Spreadsheet' -import type ViewModel from '../models/SpreadsheetView' - -const RowMenu = observer(function ({ - viewModel, - spreadsheetModel, -}: { - viewModel: Instance - spreadsheetModel: Instance -}) { - const currentRowMenu = spreadsheetModel.rowMenuPosition - const { setRowMenuPosition } = spreadsheetModel - - const rowMenuClose = () => { - setRowMenuPosition(null) - } - - const rowNumber = spreadsheetModel.rowMenuPosition?.rowNumber - if (rowNumber === undefined) { - return null - } - - const row = spreadsheetModel.rowSet.rows[+rowNumber - 1] - // eslint-disable-next-line @typescript-eslint/no-unsafe-function-type - function handleMenuItemClick(_event: unknown, callback: Function) { - callback(viewModel, spreadsheetModel, rowNumber, row) - rowMenuClose() - } - - // got through and evaluate all the `disabled` callbacks of the menu items - const menuItems: MenuItem[] = viewModel.rowMenuItems.map(item => { - if (typeof item.disabled === 'function') { - const disabled = item.disabled( - viewModel, - spreadsheetModel, - +rowNumber, - row!, - ) - return { ...item, disabled } - } - return item - }) - - return ( - - ) -}) - -export default RowMenu diff --git a/plugins/spreadsheet-view/src/SpreadsheetView/components/SortIndicator.tsx b/plugins/spreadsheet-view/src/SpreadsheetView/components/SortIndicator.tsx deleted file mode 100644 index 95259aca1b..0000000000 --- a/plugins/spreadsheet-view/src/SpreadsheetView/components/SortIndicator.tsx +++ /dev/null @@ -1,36 +0,0 @@ -import React from 'react' -import { makeStyles } from 'tss-react/mui' - -// icons -import KeyboardArrowUpIcon from '@mui/icons-material/KeyboardArrowUp' -import KeyboardArrowDownIcon from '@mui/icons-material/KeyboardArrowDown' -import { SpreadsheetModel } from '../models/Spreadsheet' - -const useStyles = makeStyles()({ - sortIndicator: { - position: 'relative', - top: '0.2rem', - fontSize: '1rem', - }, -}) - -export default function SortIndicator({ - model, - columnNumber, -}: { - model: SpreadsheetModel - columnNumber: number -}) { - const { classes } = useStyles() - const sortSpec = model.sortColumns.find(c => c.columnNumber === columnNumber) - - if (sortSpec) { - const { descending } = sortSpec - return descending ? ( - - ) : ( - - ) - } - return null -} diff --git a/plugins/spreadsheet-view/src/SpreadsheetView/components/Spreadsheet.test.ts b/plugins/spreadsheet-view/src/SpreadsheetView/components/Spreadsheet.test.ts deleted file mode 100644 index 567f09aa73..0000000000 --- a/plugins/spreadsheet-view/src/SpreadsheetView/components/Spreadsheet.test.ts +++ /dev/null @@ -1,17 +0,0 @@ -import { numToColName } from './util' - -describe('num to col name', () => { - const cases = [ - [10, 'K'], - [26, 'AA'], - [0, 'A'], - [25, 'Z'], - [27 * 26 - 1, 'ZZ'], - ] as const - - cases.forEach(([input, output]) => { - test(`${input} -> ${output}`, () => { - expect(numToColName(input)).toBe(output) - }) - }) -}) diff --git a/plugins/spreadsheet-view/src/SpreadsheetView/components/Spreadsheet.tsx b/plugins/spreadsheet-view/src/SpreadsheetView/components/Spreadsheet.tsx deleted file mode 100644 index 14fd3c53ba..0000000000 --- a/plugins/spreadsheet-view/src/SpreadsheetView/components/Spreadsheet.tsx +++ /dev/null @@ -1,49 +0,0 @@ -import React from 'react' -import { observer } from 'mobx-react' -import { Instance } from 'mobx-state-tree' -import { makeStyles } from 'tss-react/mui' -import { LoadingEllipses } from '@jbrowse/core/ui' - -// locals -import type SpreadsheetStateModel from '../models/Spreadsheet' -import DataTable from './DataTable' - -type SpreadsheetModel = Instance - -const useStyles = makeStyles()(theme => ({ - root: { - position: 'relative', - marginBottom: theme.spacing(1), - background: theme.palette.background.paper, - overflow: 'auto', - }, -})) - -const Spreadsheet = observer(function ({ - model, - height, - page, - rowsPerPage, -}: { - model: SpreadsheetModel - height: number - page: number - rowsPerPage: number -}) { - const { classes } = useStyles() - - return ( -
- { - // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition - model.rowSet.isLoaded && model.initialized ? ( - - ) : ( - - ) - } -
- ) -}) - -export default Spreadsheet diff --git a/plugins/spreadsheet-view/src/SpreadsheetView/components/SpreadsheetDataGrid.tsx b/plugins/spreadsheet-view/src/SpreadsheetView/components/SpreadsheetDataGrid.tsx new file mode 100644 index 0000000000..dbda252f5c --- /dev/null +++ b/plugins/spreadsheet-view/src/SpreadsheetView/components/SpreadsheetDataGrid.tsx @@ -0,0 +1,38 @@ +import React from 'react' +import { observer } from 'mobx-react' +import { DataGrid, GridToolbar } from '@mui/x-data-grid' + +// locals +import { SpreadsheetModel } from '../models/Spreadsheet' + +const SpreadsheetDataGrid = observer(function ({ + model, +}: { + model: SpreadsheetModel +}) { + const { rows, visibleColumns, columns } = model + + return ( + { + model.setVisibleColumns(n) + }} + rowHeight={25} + hideFooter={rows.length < 100} + slots={{ + toolbar: GridToolbar, + }} + slotProps={{ + toolbar: { + showQuickFilter: true, + }, + }} + rows={rows} + columns={columns} + /> + ) +}) + +export default SpreadsheetDataGrid diff --git a/plugins/spreadsheet-view/src/SpreadsheetView/components/SpreadsheetView.tsx b/plugins/spreadsheet-view/src/SpreadsheetView/components/SpreadsheetView.tsx index 1a6c8f0b19..5af036c3ee 100644 --- a/plugins/spreadsheet-view/src/SpreadsheetView/components/SpreadsheetView.tsx +++ b/plugins/spreadsheet-view/src/SpreadsheetView/components/SpreadsheetView.tsx @@ -1,39 +1,25 @@ -import React, { useState } from 'react' -import { Grid } from '@mui/material' +import React, { Suspense, lazy, useState } from 'react' import { makeStyles } from 'tss-react/mui' import { observer } from 'mobx-react' import { ResizeHandle } from '@jbrowse/core/ui' // locals -import ImportWizard from './ImportWizard' -import Spreadsheet from './Spreadsheet' -import GlobalFilterControls from './GlobalFilterControls' -import ColumnFilterControls from './ColumnFilterControls' import { SpreadsheetViewModel } from '../models/SpreadsheetView' -import StatusBar from './StatusBar' +import SpreadsheetDataGrid from './SpreadsheetDataGrid' -const headerHeight = 52 -const colFilterHeight = 46 -const statusBarHeight = 40 +const ImportWizard = lazy(() => import('./ImportWizard')) const useStyles = makeStyles()(theme => ({ - header: { - overflow: 'hidden', - whiteSpace: 'nowrap', - boxSizing: 'border-box', - height: headerHeight, - paddingLeft: theme.spacing(1), - }, contentArea: { overflow: 'auto', + position: 'relative', + marginBottom: theme.spacing(1), + background: theme.palette.background.paper, }, resizeHandle: { - height: 3, - position: 'absolute', - bottom: 0, - left: 0, - background: theme.palette.action.disabled, + height: 5, boxSizing: 'border-box', + background: theme.palette.action.disabled, borderTop: '1px solid #fafafa', }, })) @@ -43,83 +29,41 @@ const SpreadsheetView = observer(function ({ }: { model: SpreadsheetViewModel }) { + const [initialHeight, setInitialHeight] = useState(0) const { classes } = useStyles() - const { - spreadsheet, - filterControls, - hideFilterControls, - hideVerticalResizeHandle, - mode, - height, - } = model - const [page, setPage] = useState(0) - const [rowsPerPage, setRowsPerPage] = useState(100) - - return ( -
- {mode !== 'display' || hideFilterControls ? null : ( - <> - - - - - - {filterControls.columnFilters.map((f, i) => ( - - ))} - - )} - - {mode === 'import' ? ( - - ) : ( -
-
- {spreadsheet ? ( - - ) : null} -
-
- )} - {spreadsheet ? ( - - ) : null} + const { spreadsheet, hideVerticalResizeHandle, height } = model + return spreadsheet ? ( + <> +
+ +
{hideVerticalResizeHandle ? null : ( { + setInitialHeight(height) + }} + onDrag={(_, dist) => model.setHeight(initialHeight - dist)} className={classes.resizeHandle} /> )} -
+ + ) : ( +
Unknown
+ ) +}) + +const SpreadsheetContainer = observer(function ({ + model, +}: { + model: SpreadsheetViewModel +}) { + return !model.initialized ? ( + + + + ) : ( + ) }) -export default SpreadsheetView +export default SpreadsheetContainer diff --git a/plugins/spreadsheet-view/src/SpreadsheetView/components/StatusBar.tsx b/plugins/spreadsheet-view/src/SpreadsheetView/components/StatusBar.tsx deleted file mode 100644 index d6994e7b42..0000000000 --- a/plugins/spreadsheet-view/src/SpreadsheetView/components/StatusBar.tsx +++ /dev/null @@ -1,75 +0,0 @@ -import React from 'react' -import { FormGroup, TablePagination } from '@mui/material' -import { makeStyles } from 'tss-react/mui' - -// locals -import RowCountMessage from './RowCountMessage' -import { SpreadsheetModel } from '../models/Spreadsheet' -import { observer } from 'mobx-react' - -const statusBarHeight = 40 - -const useStyles = makeStyles()(theme => ({ - statusBar: { - height: statusBarHeight, - boxSizing: 'border-box', - borderTop: '1px outset #b1b1b1', - paddingLeft: theme.spacing(1), - }, - verticallyCenter: { - display: 'flex', - justifyContent: 'center', - flexDirection: 'column', - }, - spacer: { - flexGrow: 1, - }, -})) - -const StatusBar = observer(function StatusBar({ - page, - rowsPerPage, - setPage, - setRowsPerPage, - spreadsheet, - mode, -}: { - page: number - mode: string - spreadsheet: SpreadsheetModel - rowsPerPage: number - setPage: (arg: number) => void - setRowsPerPage: (arg: number) => void -}) { - const { classes } = useStyles() - return ( -
- -
- -
-
- { - setPage(newPage) - }} - onRowsPerPageChange={event => { - setRowsPerPage(+event.target.value) - setPage(0) - }} - /> -
- -
- ) -}) - -export default StatusBar diff --git a/plugins/spreadsheet-view/src/SpreadsheetView/components/util.ts b/plugins/spreadsheet-view/src/SpreadsheetView/components/util.ts index fc1bafa1a4..6eefb3508a 100644 --- a/plugins/spreadsheet-view/src/SpreadsheetView/components/util.ts +++ b/plugins/spreadsheet-view/src/SpreadsheetView/components/util.ts @@ -1,16 +1,56 @@ -function letterFor(n: number) { - return String.fromCharCode(n + 65) +import { AbstractSessionModel, FileLocation } from '@jbrowse/core/util' +import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view' + +type LGV = LinearGenomeViewModel +type MaybeLGV = LinearGenomeViewModel | undefined + +export function locationLinkClick({ + assemblyName, + session, + locString, + spreadsheetViewId, +}: { + assemblyName: string + session: AbstractSessionModel + locString: string + spreadsheetViewId: string +}) { + const newViewId = `${spreadsheetViewId}_${assemblyName}` + let view = session.views.find(v => v.id === newViewId) as MaybeLGV + if (!view) { + view = session.addView('LinearGenomeView', { id: newViewId }) as LGV + } + return view.navToLocString(locString, assemblyName) } -export function numToColName(num: number) { - if (num >= 0) { - if (num < 26) { - return letterFor(num) - } - if (num < 27 * 26) { - return letterFor(Math.floor(num / 26 - 1)) + letterFor(num % 26) +export const fileTypes = ['VCF', 'BED', 'BEDPE', 'STAR-Fusion'] + +export const fileTypesRegexp = new RegExp( + `\\.(${fileTypes.join('|')})(\\.gz)?$`, + 'i', +) + +export function getFilename(file?: FileLocation) { + return file + ? // @ts-expect-error + file.uri || + // @ts-expect-error + file.localPath || + // @ts-expect-error + (file.blobId && file.name) + : undefined +} + +export function getFileType(file?: FileLocation) { + const name = getFilename(file) + + if (name) { + const firstMatch = fileTypesRegexp.exec(name)?.[1] + if (firstMatch) { + return firstMatch === 'tsv' && name.includes('star-fusion') + ? 'STAR-Fusion' + : firstMatch.toUpperCase() } } - - throw new RangeError('column number out of range') + return 'VCF' } diff --git a/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/BedImport.test.ts b/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/BedImport.test.ts deleted file mode 100644 index f20f9126be..0000000000 --- a/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/BedImport.test.ts +++ /dev/null @@ -1,14 +0,0 @@ -import { promises as fsPromises } from 'fs' -import path from 'path' - -import { removeBedHeaders } from './BedImport' - -test('bed header trimming', async () => { - const filepath = path.join(__dirname, '..', 'test_data', 'foo.bed') - const buf = await fsPromises.readFile(filepath) - expect(buf[0]).toEqual(98) - expect(buf[1]).toEqual(114) - const trimmedBuffer = removeBedHeaders(buf) - expect(trimmedBuffer[0]).toEqual(99) - expect(trimmedBuffer.length).toBe(275) -}) diff --git a/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/BedImport.ts b/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/BedImport.ts index c67b3ac1c9..e66ef94e14 100644 --- a/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/BedImport.ts +++ b/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/BedImport.ts @@ -1,158 +1,81 @@ -import { ParseOptions, parseTsvBuffer } from './ImportUtils' +import { assembleLocString } from '@jbrowse/core/util' +import { parseStrand } from './util' +import LocString from './components/LocString' import type { Buffer } from 'buffer' -const browserBytes = 'browser '.split('').map(c => c.charCodeAt(0)) -const trackBytes = 'track '.split('').map(c => c.charCodeAt(0)) -const commentBytes = '#'.split('').map(c => c.charCodeAt(0)) - -function bytesAreFoundAt(position: number, buffer: Buffer, bytes: number[]) { - let i = 0 - for (; i < bytes.length; i += 1) { - if (buffer[position + i] !== bytes[i]) { - return false - } - } - return true -} - -export function removeBedHeaders(buffer: Buffer) { - // slice off the first lines of the buffer if it starts with one or more - // header lines +export function parseBedBuffer(buffer: Buffer) { + const data = new TextDecoder('utf8', { fatal: true }).decode(buffer) + const lines = data.split(/\n|\r\n|\r/).filter(f => !!f) + const headerLines = [] let i = 0 - for (; i < buffer.length; i += 1) { - if ( - bytesAreFoundAt(i, buffer, browserBytes) || - bytesAreFoundAt(i, buffer, trackBytes) || - bytesAreFoundAt(i, buffer, commentBytes) - ) { - // consume up to the next newline - do { - i += 1 - } while (buffer[i] !== 10) - } else { - // end of headers, return - break - } + for ( + ; + i < lines.length && + (lines[i]!.startsWith('#') || + lines[i]!.startsWith('browser') || + lines[i]!.startsWith('track')); + i++ + ) { + headerLines.push(lines[i]) } - if (i) { - return buffer.subarray(i) + const header = headerLines.join('\n') + const lastHeaderLine = headerLines.at(-1) + let names = [] as string[] + if (lastHeaderLine?.startsWith('#')) { + names = lastHeaderLine + .slice(1) + .split('\t') + .map(f => f.trim()) } - return buffer -} - -export async function parseBedBuffer(buffer: Buffer, options: ParseOptions) { - const b = removeBedHeaders(buffer) - const data = await parseTsvBuffer(b) - const bedColumns = [ - { name: 'chrom', dataType: { type: 'LocRef' } }, - { name: 'chromStart', dataType: { type: 'LocStart' } }, - { name: 'chromEnd', dataType: { type: 'LocEnd' } }, - { name: 'name', dataType: { type: 'Text' } }, - { name: 'score', dataType: { type: 'Number' } }, - { name: 'strand', dataType: { type: 'Text' } }, - ] as const + const columns = names.length + ? ['refName', 'start', 'end', ...names.slice(3)] + : [ + 'refName', + 'start', + 'end', + 'name', + 'score', + 'strand', + 'thickStart', + 'thickEnd', + 'itemRgb', + 'blockCount', + 'blockSizes', + 'blockStarts', + ] + const rows = [] + for (let j = 0; i < lines.length; i++, j++) { + const line = lines[i]! + const l = line.split('\t') - data.columns.forEach((col, colNumber) => { - const bedColumn = bedColumns[colNumber] - if (bedColumn) { - col.name = bedColumn.name - col.dataType = bedColumn.dataType - } - }) - data.hasColumnNames = true - data.assemblyName = options.selectedAssemblyName + const rest = Object.fromEntries(columns.map((e, idx) => [e, l[idx]])) + const refName = rest.refName! + const start = +rest.start! + const end = +rest.end! + const strand = parseStrand(rest.strand) - data.columnDisplayOrder.push(data.columnDisplayOrder.length) - data.columns.unshift({ - name: 'Location', - dataType: { type: 'LocString' }, - isDerived: true, - derivationFunctionText: `jexl:{text:row.cells[0].text+':'+row.cells[1].text+'..'+row.cells[2].text,\n - extendedData: {refName: row.cells.ref.text, start: parseInt(row.cells.start.text,10), end: parseInt(row.cells.end.text,10)}}`, - }) - return data -} - -export async function parseBedPEBuffer(buffer: Buffer, options: ParseOptions) { - const b = removeBedHeaders(buffer) - const data = await parseTsvBuffer(b) - interface BedColumn { - name: string - dataType: { - type: string - } - featureField: string[] - } - const bedColumns: BedColumn[] = [ - { name: 'chrom1', dataType: { type: 'Text' }, featureField: ['refName'] }, - { name: 'start1', dataType: { type: 'Number' }, featureField: ['start'] }, - { name: 'end1', dataType: { type: 'Number' }, featureField: ['end'] }, - { - name: 'chrom2', - dataType: { type: 'Text' }, - featureField: ['mate', 'refName'], - }, - { - name: 'start2', - dataType: { type: 'Number' }, - featureField: ['mate', 'start'], - }, - { - name: 'end2', - dataType: { type: 'Number' }, - featureField: ['mate', 'end'], - }, - { name: 'name', dataType: { type: 'Text' }, featureField: ['name'] }, - { name: 'score', dataType: { type: 'Number' }, featureField: ['score'] }, - { name: 'strand1', dataType: { type: 'Text' }, featureField: ['strand'] }, - { - name: 'strand2', - dataType: { type: 'Text' }, - featureField: ['mate', 'strand'], - }, - ] as const - data.columns.forEach((col, colNumber) => { - const bedColumn = bedColumns[colNumber] - if (bedColumn) { - col.name = bedColumn.name - col.dataType = bedColumn.dataType - } - }) - data.hasColumnNames = true - - // decorate each row with a feature object in its extendedData - data.rowSet.rows.forEach((row, rowNumber) => { - const featureData: Record = {} - row.cells.forEach(({ text }, columnNumber) => { - const bedColumn = bedColumns[columnNumber] - const val = - bedColumn && bedColumn.dataType.type === 'Number' && text - ? Number.parseFloat(text) - : text - if (bedColumn) { - // a predefined column - if (bedColumn.featureField.length === 2) { - if (!featureData[bedColumn.featureField[0]!]) { - featureData[bedColumn.featureField[0]!] = {} - } - featureData[bedColumn.featureField[0]!][bedColumn.featureField[1]!] = - val - } else { - featureData[bedColumn.featureField[0]!] = val - } - } else { - // some other column - featureData[`column${columnNumber + 1}`] = val - } + rows.push({ + ...rest, + loc: assembleLocString({ + refName, + start, + end, + }), + id: `row_${i}`, + start, + end, + refName, + strand, }) - featureData.uniqueId = `bedpe-${rowNumber}` - row.extendedData = { - feature: featureData, - } - }) - - data.assemblyName = options.selectedAssemblyName + } - return data + return { + header, + rows, + columns, + customComponents: { + loc: LocString, + }, + } } diff --git a/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/BedpeImport.ts b/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/BedpeImport.ts new file mode 100644 index 0000000000..9ac70d39dd --- /dev/null +++ b/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/BedpeImport.ts @@ -0,0 +1,81 @@ +import { parseStrand } from './util' +import type { Buffer } from 'buffer' + +export function parseBedPEBuffer(buffer: Buffer) { + const data = new TextDecoder('utf8', { fatal: true }).decode(buffer) + const lines = data.split(/\n|\r\n|\r/).filter(f => !!f) + const headerLines = [] + let i = 0 + for ( + ; + i < lines.length && + (lines[i]!.startsWith('#') || + lines[i]!.startsWith('browser') || + lines[i]!.startsWith('track')); + i++ + ) { + headerLines.push(lines[i]) + } + const header = headerLines.join('\n') + const lastHeaderLine = headerLines.at(-1) + let names = [] as string[] + if (lastHeaderLine?.startsWith('#')) { + names = lastHeaderLine + .slice(1) + .split('\t') + .map(f => f.trim()) + } + + const columns = [ + 'refName', + 'start', + 'end', + 'mate.refName', + 'mate.start', + 'mate.end', + 'name', + 'score', + 'strand', + 'mate.strand', + ...names.slice(9), + ] + const rows = [] + for (let j = 0; i < lines.length; i++, j++) { + const line = lines[i]! + const l = line.split('\t') + const ref1 = l[0]! + const start1 = +l[1]! + const end1 = +l[2]! + const ref2 = l[3]! + const start2 = +l[4]! + const end2 = +l[5]! + const name = l[6]! + const score = +l[7]! + const strand1 = parseStrand(l[8]) + const strand2 = parseStrand(l[9]) + + const rest = Object.fromEntries( + columns.map((e, idx) => { + const key = columns[idx] || `extra_${idx}` + return [key, e] + }), + ) + + rows.push({ + ...rest, + id: `row_${i}`, + start: start1, + end: end1, + refName: ref1, + strand: strand1, + name, + score, + 'mate.refName': ref2, + 'mate.start': start2, + 'mate.end': end2, + 'mate.strand': strand2, + }) + } + + return { header, rows, columns: [...columns] } +} diff --git a/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/ImportUtils.test.ts b/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/ImportUtils.test.ts deleted file mode 100644 index 3347ef3d77..0000000000 --- a/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/ImportUtils.test.ts +++ /dev/null @@ -1,25 +0,0 @@ -import { promises as fsPromises } from 'fs' -import path from 'path' - -// locals -import { parseCsvBuffer } from './ImportUtils' -import SpreadsheetModel from '../models/Spreadsheet' - -test('csv to spreadsheet snapshot', async () => { - const filepath = path.join( - __dirname, - '..', - 'test_data', - 'breast_cancer.subset.csv', - ) - const buf = await fsPromises.readFile(filepath) - const spreadsheetSnap = await parseCsvBuffer(buf, { - hasColumnNameLine: true, - columnNameLineNumber: 1, - isValidRefName: () => true, - }) - expect(spreadsheetSnap).toMatchSnapshot() - // @ts-expect-error - const spreadsheet = SpreadsheetModel.create(spreadsheetSnap) - expect(spreadsheet.rowSet.rows.length).toBe(49) -}) diff --git a/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/ImportUtils.ts b/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/ImportUtils.ts deleted file mode 100644 index c9cef1f62b..0000000000 --- a/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/ImportUtils.ts +++ /dev/null @@ -1,154 +0,0 @@ -import { ParsedLocString, parseLocString } from '@jbrowse/core/util' -import type { Buffer } from 'buffer' - -export function bufferToString(buffer: Buffer) { - return new TextDecoder('utf8', { fatal: true }).decode(buffer) -} - -async function parseWith(buffer: Buffer, options = {}) { - const csv = await import('csvtojson').then(module => module.default) - return csv({ noheader: true, output: 'csv', ...options }).fromString( - bufferToString(buffer), - ) -} - -export interface Row { - id: string - - extendedData?: any - cells: { - text: string - - extendedData?: any - }[] -} - -export interface RowSet { - isLoaded: boolean - rows: Row[] -} - -export interface ParseOptions { - hasColumnNameLine?: boolean - columnNameLineNumber?: number - selectedAssemblyName?: string - isValidRefName?: (refName: string, assemblyName?: string) => boolean -} - -export interface Column { - name: string - dataType: { type: string } - isDerived?: boolean - derivationFunctionText?: string -} - -function guessColumnType( - rowSet: RowSet, - columnNumber: number, - isValidRefName: (refName: string, assemblyName?: string) => boolean, -) { - const text = rowSet.rows[0]!.cells[columnNumber]!.text || '' - - let guessedType = 'Text' - - let parsedLoc: ParsedLocString | undefined - try { - parsedLoc = parseLocString(text, isValidRefName) - } catch (error) { - // - } - if (parsedLoc?.refName && typeof parsedLoc.start === 'number') { - guessedType = 'LocString' - } else if (/^\d+(\.\d+)?$/.test(text)) { - guessedType = 'Number' - } - - // MAYBE TODO: iterate over the rest of the rows to confirm - // the type for all the rows - - return guessedType -} - -function dataToSpreadsheetSnapshot( - rows: string[][], - options: ParseOptions = {}, -) { - const { - hasColumnNameLine = false, - columnNameLineNumber = 1, - isValidRefName = () => false, - selectedAssemblyName, - } = options - // rows is an array of row objects and columnNames - // is an array of column names (in import order) - let maxCols = 0 - const rowSet: RowSet = { - isLoaded: true, - rows: rows.map((row, rowNumber) => { - const id = rowNumber + (hasColumnNameLine ? 0 : 1) - if (row.length > maxCols) { - maxCols = row.length - } - return { - id: String(id), - cells: row.map((text, columnNumber) => { - return { columnNumber, text } - }), - } - }), - } - - // process the column names row if present - const columnNames: Record = {} - // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition - if (hasColumnNameLine && columnNameLineNumber !== undefined) { - const [colNamesRow] = rowSet.rows.splice(columnNameLineNumber - 1, 1) - - if (colNamesRow) { - colNamesRow.cells.forEach((cell, columnNumber) => { - columnNames[columnNumber] = cell.text || '' - }) - } - } - - // make our column definitions - const columns: Column[] = [] - const columnDisplayOrder = [] - for (let columnNumber = 0; columnNumber < maxCols; columnNumber += 1) { - columnDisplayOrder.push(columnNumber) - const guessedType = guessColumnType(rowSet, columnNumber, isValidRefName) - - // store extendeddata for LocString column - if (guessedType === 'LocString') { - for (const row of rowSet.rows) { - const cell = row.cells[columnNumber]! - cell.extendedData = parseLocString(cell.text, isValidRefName) - } - } - - columns[columnNumber] = { - name: columnNames[columnNumber]!, - dataType: { - type: guessedType, - }, - } - } - - return { - rowSet, - columnDisplayOrder, - hasColumnNames: !!hasColumnNameLine, - columns, - assemblyName: selectedAssemblyName, - } -} - -export async function parseCsvBuffer(buffer: Buffer, options?: ParseOptions) { - const rows = await parseWith(buffer) - return dataToSpreadsheetSnapshot(rows, options) -} - -export async function parseTsvBuffer(buffer: Buffer, options?: ParseOptions) { - const rows = await parseWith(buffer, { delimiter: '\t' }) - return dataToSpreadsheetSnapshot(rows, options) -} diff --git a/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/STARFusionImport.test.ts b/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/STARFusionImport.test.ts deleted file mode 100644 index 22a31768be..0000000000 --- a/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/STARFusionImport.test.ts +++ /dev/null @@ -1,27 +0,0 @@ -import { promises as fsPromises } from 'fs' -import path from 'path' - -// locals -import { parseSTARFusionBuffer } from './STARFusionImport' -import SpreadsheetModel from '../models/Spreadsheet' - -test('starfusion import', async () => { - const filepath = path.join( - __dirname, - '..', - 'test_data', - 'starfusion_example.fusion_predictions.tsv', - ) - const buf = await fsPromises.readFile(filepath) - const spreadsheetSnap = await parseSTARFusionBuffer(buf, { - selectedAssemblyName: 'fogbat', - isValidRefName() { - return true - }, - }) - expect(spreadsheetSnap).toMatchSnapshot() - - // @ts-expect-error - const spreadsheet = SpreadsheetModel.create(spreadsheetSnap) - expect(spreadsheet.rowSet.rows.length).toBe(24) -}) diff --git a/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/STARFusionImport.ts b/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/STARFusionImport.ts index e5356aab0c..54d655f10f 100644 --- a/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/STARFusionImport.ts +++ b/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/STARFusionImport.ts @@ -1,74 +1,14 @@ -import { parseTsvBuffer, ParseOptions } from './ImportUtils' import type { Buffer } from 'buffer' - -function parseSTARFusionBreakpointString(str: string) { - const fields = str.split(':') - const refName = fields[0]! - const pos = Number.parseInt(fields[1]!, 10) - const strand = fields[2] === '-' ? -1 : 1 - return { refName, pos, strand } -} - -const numericColumns: Record = { - SpanningFragCount: true, - FFPM: true, - LeftBreakEntropy: true, - RightBreakEntropy: true, - JunctionReadCount: true, -} - -export async function parseSTARFusionBuffer( - buffer: Buffer, - options: ParseOptions, -) { - const data = await parseTsvBuffer(buffer, { - hasColumnNameLine: true, - columnNameLineNumber: 1, - selectedAssemblyName: options.selectedAssemblyName, - isValidRefName: () => false, - }) - - // remove the # in #FusionName - data.columns[0]!.name = data.columns[0]!.name.replace('#', '') - // set some columns to be numeric - data.columns.forEach(col => { - if (numericColumns[col.name]) { - col.dataType = { type: 'Number' } - } - }) - - // decorate each row with a feature object in its extendedData - data.rowSet.rows.forEach((row, rowNumber) => { - const featureData: Record = {} - row.cells.forEach(({ text }, columnNumber) => { - const column = data.columns[columnNumber]! - if (column.name === 'LeftBreakpoint' && text) { - const { refName, pos, strand } = parseSTARFusionBreakpointString(text) - featureData.refName = refName - featureData.start = pos - featureData.end = pos - featureData.strand = strand - } else if (column.name === 'RightBreakpoint' && text) { - const { refName, pos, strand } = parseSTARFusionBreakpointString(text) - featureData.mate = { - refName, - start: pos, - end: pos, - strand, - } - } else if (text && numericColumns[column.name]) { - // some other column, numeric - featureData[column.name] = Number.parseFloat(text) - } else { - // some other column, text - featureData[column.name] = text - } - }) - featureData.uniqueId = `sf-${rowNumber + 1}` - row.extendedData = { - feature: featureData, - } - }) - - return data +export function parseSTARFusionBuffer(buffer: Buffer) { + const str = new TextDecoder('utf8').decode(buffer) + const lines = str.split(/\n|\r\n/) + const header = lines[0]?.slice(1).split('\t') || [] + return { + rows: lines + .slice(1) + .map(row => + Object.fromEntries(row.split('\t').map((c, i) => [header[i], c])), + ), + columns: header, + } } diff --git a/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/VcfImport.test.ts b/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/VcfImport.test.ts deleted file mode 100644 index 81f5245e8d..0000000000 --- a/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/VcfImport.test.ts +++ /dev/null @@ -1,42 +0,0 @@ -import { promises as fsPromises } from 'fs' -import path from 'path' -import { parseVcfBuffer, splitVcfFileHeaderAndBody } from './VcfImport' -import SpreadsheetModel from '../models/Spreadsheet' - -describe('vcf file splitter', () => { - const cases = [ - [ - '##fileformat=VCFv4.3\nfogbat\n', - { header: '##fileformat=VCFv4.3\n', body: 'fogbat\n' }, - ], - [ - '##fileformat=VCFv4.3\n##zonker\n##deek\n##donk\nfogbat\n', - { - header: '##fileformat=VCFv4.3\n##zonker\n##deek\n##donk\n', - body: 'fogbat\n', - }, - ], - ] as const - - cases.forEach(([input, output], caseNumber) => { - test(`case ${caseNumber}`, () => { - expect(splitVcfFileHeaderAndBody(input)).toEqual(output) - }) - }) -}) - -test('vcf file import', async () => { - const filepath = path.join( - __dirname, - '..', - 'test_data', - '1801160099-N32519_26611_S51_56704.hard-filtered.vcf', - ) - const buf = await fsPromises.readFile(filepath) - const spreadsheetSnap = parseVcfBuffer(buf) - expect(spreadsheetSnap).toMatchSnapshot() - - // @ts-expect-error - const spreadsheet = SpreadsheetModel.create(spreadsheetSnap) - expect(spreadsheet.rowSet.rows.length).toBe(101) -}) diff --git a/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/VcfImport.ts b/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/VcfImport.ts index 016524bad5..d1e6e0b90b 100644 --- a/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/VcfImport.ts +++ b/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/VcfImport.ts @@ -1,121 +1,73 @@ import VCF from '@gmod/vcf' import { VcfFeature } from '@jbrowse/plugin-variants' -import { - bufferToString, - Row, - RowSet, - Column, - ParseOptions, -} from './ImportUtils' -import type { Buffer } from 'buffer' - -const vcfCoreColumns: { name: string; type: string }[] = [ - { name: 'CHROM', type: 'Text' }, // 0 - { name: 'POS', type: 'Number' }, // 1 - { name: 'ID', type: 'Text' }, // 2 - { name: 'REF', type: 'Text' }, // 3 - { name: 'ALT', type: 'Text' }, // 4 - { name: 'QUAL', type: 'Number' }, // 5 - { name: 'FILTER', type: 'Text' }, // 6 - { name: 'INFO', type: 'Text' }, // 7 - { name: 'FORMAT', type: 'Text' }, // 8 -] - -function vcfRecordToRow(vcfParser: any, line: string, lineNumber: number): Row { - const vcfVariant = vcfParser.parseLine(line) - const vcfFeature = new VcfFeature({ - variant: vcfVariant, - parser: vcfParser, - id: `vcf-${lineNumber}`, - }) - - const data = line.split('\t').map(d => (d === '.' ? '' : d)) - // no format column, add blank - if (data.length === 8) { - data.push('') - } - const row: Row = { - id: String(lineNumber + 1), - extendedData: { vcfFeature: vcfFeature.toJSON() }, - cells: data.map((text, columnNumber) => { - return { - columnNumber, - text, - } - }), - } - return row -} -export function parseVcfBuffer(buffer: Buffer, options: ParseOptions = {}) { - const { selectedAssemblyName } = options - let { header, body } = splitVcfFileHeaderAndBody(bufferToString(buffer)) - const rows: Row[] = [] - const vcfParser = new VCF({ header }) - header = '' // garbage collect - body.split(/\n|\r\n|\r/).forEach((line: string, lineNumber) => { - if (/\S/.test(line)) { - rows.push(vcfRecordToRow(vcfParser, line, lineNumber)) - } - }) - body = '' // garbage collect +import type { Buffer } from 'buffer' - const rowSet: RowSet = { - isLoaded: true, - rows, - } - const columnDisplayOrder: number[] = [] - const columns: Column[] = [] - for (let i = 0; i < vcfCoreColumns.length; i += 1) { - columnDisplayOrder.push(i) - columns[i] = { - name: vcfCoreColumns[i]!.name, - dataType: { type: vcfCoreColumns[i]!.type }, - } - } - for (let i = 0; i < vcfParser.samples.length; i += 1) { - const oi = vcfCoreColumns.length + i - columnDisplayOrder.push(oi) - columns[oi] = { - name: vcfParser.samples[i]!, - dataType: { type: 'Text' }, +function getRows(lines: string[], vcfParser: VCF) { + const keys = new Set() + const rows = lines.map((l, id) => { + const [CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO, FORMAT] = l.split('\t') + const ret = Object.fromEntries( + INFO?.split(';') + .map(f => f.trim()) + .map(e => { + const [key, val = 'true'] = e.split('=') + const k = `INFO.${key!.trim()}` + keys.add(k) + return [k, val.trim()] + }) || [], + ) + return { + CHROM, + POS, + ID, + REF, + ALT, + QUAL, + FILTER, + FORMAT, + id, + feature: new VcfFeature({ + parser: vcfParser, + variant: vcfParser.parseLine(l), + id: `${id}`, + }), + ___lineData: l, + ...ret, } - } - - columnDisplayOrder.push(columnDisplayOrder.length) - columns.unshift({ - name: 'Location', - dataType: { type: 'LocString' }, - isDerived: true, - derivationFunctionText: `jexl:{text:row.extendedData.vcfFeature.refName+':'\n - +row.extendedData.vcfFeature.start+'..'+row.extendedData.vcfFeature.end, extendedData:\n - {refName:row.extendedData.vcfFeature.refName,start:row.extendedData.vcfFeature.start,end:row.extendedData.vcfFeature.end}}`, }) - - return { - rowSet, - columnDisplayOrder, - hasColumnNames: true, - columns, - assemblyName: selectedAssemblyName, - } + return { keys, rows } } -export function splitVcfFileHeaderAndBody(wholeFile: string) { - // split into header and the rest of the file - let headerEndIndex = 0 - let prevChar: string | undefined - for (; headerEndIndex < wholeFile.length; headerEndIndex += 1) { - const c = wholeFile[headerEndIndex] - if (prevChar === '\n' && c !== '#') { - break - } - prevChar = c +export function parseVcfBuffer(buffer: Buffer) { + const str = new TextDecoder('utf8').decode(buffer) + const lines = str + .split(/\n|\r\n/) + .map(f => f.trim()) + .filter(f => !!f) + const headerLines = [] + let i = 0 + for (; i < lines.length && lines[i]!.startsWith('#'); i++) { + headerLines.push(lines[i]) } + const header = headerLines.join('\n') + const vcfParser = new VCF({ header }) + const { keys, rows } = getRows(lines.slice(i), vcfParser) return { - header: wholeFile.slice(0, Math.max(0, headerEndIndex)), - body: wholeFile.slice(headerEndIndex), + vcfParser, + rows, + columns: [ + 'CHROM', + 'POS', + 'ID', + 'REF', + 'ALT', + 'QUAL', + 'FILTER', + 'FORMAT', + ...keys, + ], } } diff --git a/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/__snapshots__/ImportUtils.test.ts.snap b/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/__snapshots__/ImportUtils.test.ts.snap deleted file mode 100644 index 143205862e..0000000000 --- a/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/__snapshots__/ImportUtils.test.ts.snap +++ /dev/null @@ -1,6555 +0,0 @@ -// Jest Snapshot v1, https://goo.gl/fbAQLP - -exports[`csv to spreadsheet snapshot 1`] = ` -{ - "assemblyName": undefined, - "columnDisplayOrder": [ - 0, - 1, - 2, - 3, - 4, - 5, - 6, - 7, - 8, - 9, - 10, - 11, - 12, - 13, - 14, - 15, - 16, - 17, - 18, - 19, - 20, - 21, - 22, - 23, - 24, - 25, - 26, - 27, - 28, - 29, - 30, - ], - "columns": [ - { - "dataType": { - "type": "Number", - }, - "name": "one", - }, - { - "dataType": { - "type": "Number", - }, - "name": "two", - }, - { - "dataType": { - "type": "Number", - }, - "name": "three", - }, - { - "dataType": { - "type": "Number", - }, - "name": "four", - }, - { - "dataType": { - "type": "Number", - }, - "name": "", - }, - { - "dataType": { - "type": "Number", - }, - "name": "six", - }, - { - "dataType": { - "type": "Number", - }, - "name": "seven", - }, - { - "dataType": { - "type": "Number", - }, - "name": "eight", - }, - { - "dataType": { - "type": "Number", - }, - "name": "nine", - }, - { - "dataType": { - "type": "Number", - }, - "name": "ten", - }, - { - "dataType": { - "type": "Number", - }, - "name": "eleven", - }, - { - "dataType": { - "type": "Number", - }, - "name": "twelve", - }, - { - "dataType": { - "type": "Number", - }, - "name": "thirteen", - }, - { - "dataType": { - "type": "Number", - }, - "name": "fourteen", - }, - { - "dataType": { - "type": "Number", - }, - "name": "fifteen", - }, - { - "dataType": { - "type": "Number", - }, - "name": "sixteen", - }, - { - "dataType": { - "type": "Number", - }, - "name": "seventeen", - }, - { - "dataType": { - "type": "Number", - }, - "name": "eighteen", - }, - { - "dataType": { - "type": "Number", - }, - "name": "nineteen", - }, - { - "dataType": { - "type": "Number", - }, - "name": "twenty", - }, - { - "dataType": { - "type": "Number", - }, - "name": "twentyone", - }, - { - "dataType": { - "type": "Number", - }, - "name": "twentytwo", - }, - { - "dataType": { - "type": "Number", - }, - "name": "twentythree", - }, - { - "dataType": { - "type": "Number", - }, - "name": "twentyfour", - }, - { - "dataType": { - "type": "Number", - }, - "name": "twentyfive", - }, - { - "dataType": { - "type": "Number", - }, - "name": "twentysix", - }, - { - "dataType": { - "type": "Number", - }, - "name": "twentyseven", - }, - { - "dataType": { - "type": "Number", - }, - "name": "twentyeight", - }, - { - "dataType": { - "type": "Number", - }, - "name": "twentynine", - }, - { - "dataType": { - "type": "Number", - }, - "name": "thirty", - }, - { - "dataType": { - "type": "Number", - }, - "name": undefined, - }, - ], - "hasColumnNames": true, - "rowSet": { - "isLoaded": true, - "rows": [ - { - "cells": [ - { - "columnNumber": 0, - "text": "17.99", - }, - { - "columnNumber": 1, - "text": "10.38", - }, - { - "columnNumber": 2, - "text": "122.8", - }, - { - "columnNumber": 3, - "text": "1001", - }, - { - "columnNumber": 4, - "text": "0.1184", - }, - { - "columnNumber": 5, - "text": "0.2776", - }, - { - "columnNumber": 6, - "text": "0.3001", - }, - { - "columnNumber": 7, - "text": "0.1471", - }, - { - "columnNumber": 8, - "text": "0.2419", - }, - { - "columnNumber": 9, - "text": "0.07871", - }, - { - "columnNumber": 10, - "text": "1.095", - }, - { - "columnNumber": 11, - "text": "0.9053", - }, - { - "columnNumber": 12, - "text": "8.589", - }, - { - "columnNumber": 13, - "text": "153.4", - }, - { - "columnNumber": 14, - "text": "0.006399", - }, - { - "columnNumber": 15, - "text": "0.04904", - }, - { - "columnNumber": 16, - "text": "0.05373", - }, - { - "columnNumber": 17, - "text": "0.01587", - }, - { - "columnNumber": 18, - "text": "0.03003", - }, - { - "columnNumber": 19, - "text": "0.006193", - }, - { - "columnNumber": 20, - "text": "25.38", - }, - { - "columnNumber": 21, - "text": "17.33", - }, - { - "columnNumber": 22, - "text": "184.6", - }, - { - "columnNumber": 23, - "text": "2019", - }, - { - "columnNumber": 24, - "text": "0.1622", - }, - { - "columnNumber": 25, - "text": "0.6656", - }, - { - "columnNumber": 26, - "text": "0.7119", - }, - { - "columnNumber": 27, - "text": "0.2654", - }, - { - "columnNumber": 28, - "text": "0.4601", - }, - { - "columnNumber": 29, - "text": "0.1189", - }, - { - "columnNumber": 30, - "text": "0", - }, - ], - "id": "1", - }, - { - "cells": [ - { - "columnNumber": 0, - "text": "20.57", - }, - { - "columnNumber": 1, - "text": "17.77", - }, - { - "columnNumber": 2, - "text": "132.9", - }, - { - "columnNumber": 3, - "text": "1326", - }, - { - "columnNumber": 4, - "text": "0.08474", - }, - { - "columnNumber": 5, - "text": "0.07864", - }, - { - "columnNumber": 6, - "text": "0.0869", - }, - { - "columnNumber": 7, - "text": "0.07017", - }, - { - "columnNumber": 8, - "text": "0.1812", - }, - { - "columnNumber": 9, - "text": "0.05667", - }, - { - "columnNumber": 10, - "text": "0.5435", - }, - { - "columnNumber": 11, - "text": "0.7339", - }, - { - "columnNumber": 12, - "text": "3.398", - }, - { - "columnNumber": 13, - "text": "74.08", - }, - { - "columnNumber": 14, - "text": "0.005225", - }, - { - "columnNumber": 15, - "text": "0.01308", - }, - { - "columnNumber": 16, - "text": "0.0186", - }, - { - "columnNumber": 17, - "text": "0.0134", - }, - { - "columnNumber": 18, - "text": "0.01389", - }, - { - "columnNumber": 19, - "text": "0.003532", - }, - { - "columnNumber": 20, - "text": "24.99", - }, - { - "columnNumber": 21, - "text": "23.41", - }, - { - "columnNumber": 22, - "text": "158.8", - }, - { - "columnNumber": 23, - "text": "1956", - }, - { - "columnNumber": 24, - "text": "0.1238", - }, - { - "columnNumber": 25, - "text": "0.1866", - }, - { - "columnNumber": 26, - "text": "0.2416", - }, - { - "columnNumber": 27, - "text": "0.186", - }, - { - "columnNumber": 28, - "text": "0.275", - }, - { - "columnNumber": 29, - "text": "0.08902", - }, - { - "columnNumber": 30, - "text": "0", - }, - ], - "id": "2", - }, - { - "cells": [ - { - "columnNumber": 0, - "text": "19.69", - }, - { - "columnNumber": 1, - "text": "21.25", - }, - { - "columnNumber": 2, - "text": "130", - }, - { - "columnNumber": 3, - "text": "1203", - }, - { - "columnNumber": 4, - "text": "0.1096", - }, - { - "columnNumber": 5, - "text": "0.1599", - }, - { - "columnNumber": 6, - "text": "0.1974", - }, - { - "columnNumber": 7, - "text": "0.1279", - }, - { - "columnNumber": 8, - "text": "0.2069", - }, - { - "columnNumber": 9, - "text": "0.05999", - }, - { - "columnNumber": 10, - "text": "0.7456", - }, - { - "columnNumber": 11, - "text": "0.7869", - }, - { - "columnNumber": 12, - "text": "4.585", - }, - { - "columnNumber": 13, - "text": "94.03", - }, - { - "columnNumber": 14, - "text": "0.00615", - }, - { - "columnNumber": 15, - "text": "0.04006", - }, - { - "columnNumber": 16, - "text": "0.03832", - }, - { - "columnNumber": 17, - "text": "0.02058", - }, - { - "columnNumber": 18, - "text": "0.0225", - }, - { - "columnNumber": 19, - "text": "0.004571", - }, - { - "columnNumber": 20, - "text": "23.57", - }, - { - "columnNumber": 21, - "text": "25.53", - }, - { - "columnNumber": 22, - "text": "152.5", - }, - { - "columnNumber": 23, - "text": "1709", - }, - { - "columnNumber": 24, - "text": "0.1444", - }, - { - "columnNumber": 25, - "text": "0.4245", - }, - { - "columnNumber": 26, - "text": "0.4504", - }, - { - "columnNumber": 27, - "text": "0.243", - }, - { - "columnNumber": 28, - "text": "0.3613", - }, - { - "columnNumber": 29, - "text": "0.08758", - }, - { - "columnNumber": 30, - "text": "0", - }, - ], - "id": "3", - }, - { - "cells": [ - { - "columnNumber": 0, - "text": "11.42", - }, - { - "columnNumber": 1, - "text": "20.38", - }, - { - "columnNumber": 2, - "text": "77.58", - }, - { - "columnNumber": 3, - "text": "386.1", - }, - { - "columnNumber": 4, - "text": "0.1425", - }, - { - "columnNumber": 5, - "text": "0.2839", - }, - { - "columnNumber": 6, - "text": "0.2414", - }, - { - "columnNumber": 7, - "text": "0.1052", - }, - { - "columnNumber": 8, - "text": "0.2597", - }, - { - "columnNumber": 9, - "text": "0.09744", - }, - { - "columnNumber": 10, - "text": "0.4956", - }, - { - "columnNumber": 11, - "text": "1.156", - }, - { - "columnNumber": 12, - "text": "3.445", - }, - { - "columnNumber": 13, - "text": "27.23", - }, - { - "columnNumber": 14, - "text": "0.00911", - }, - { - "columnNumber": 15, - "text": "0.07458", - }, - { - "columnNumber": 16, - "text": "0.05661", - }, - { - "columnNumber": 17, - "text": "0.01867", - }, - { - "columnNumber": 18, - "text": "0.05963", - }, - { - "columnNumber": 19, - "text": "0.009208", - }, - { - "columnNumber": 20, - "text": "14.91", - }, - { - "columnNumber": 21, - "text": "26.5", - }, - { - "columnNumber": 22, - "text": "98.87", - }, - { - "columnNumber": 23, - "text": "567.7", - }, - { - "columnNumber": 24, - "text": "0.2098", - }, - { - "columnNumber": 25, - "text": "0.8663", - }, - { - "columnNumber": 26, - "text": "0.6869", - }, - { - "columnNumber": 27, - "text": 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"GT:AD:DP:GQ:PL:SB", - }, - { - "columnNumber": 9, - "text": "0/1:6,13:19:99:452,0,159:2,4,1,12", - }, - ], - "extendedData": { - "vcfFeature": { - "ALT": [ - "G", - ], - "CHROM": "17", - "FILTER": "PASS", - "ID": [ - "rs4988351", - ], - "INFO": { - "AC": [ - 179367, - ], - "AC_OTH": [ - 3973, - ], - "AC_POPMAX": [ - 12810, - ], - "AF": [ - 0.737262, - ], - "AF_OTH": [ - 0.733296, - ], - "AF_POPMAX": [ - 0.856742, - ], - "AN": [ - 243288, - ], - "AN_OTH": [ - 5418, - ], - "AN_POPMAX": [ - 14952, - ], - "AS_FilterStatus": [ - "PASS", - ], - "DB": true, - "DP": [ - 19, - ], - "FS": [ - 6.539, - ], - "FractionInformativeReads": [ - 1, - ], - "Hom": [ - 67544, - ], - "InbreedingCoeff": [ - 0.0545, - ], - "MQ": [ - 60, - ], - "MQRankSum": [ - 1.447, - ], - "POPMAX": [ - "AFR", - ], - "QD": [ - 22.28, - ], - "ReadPosRankSum": [ - 0.219, - ], - "SOR": [ - 2.786, - ], - }, - "POS": 59857809, - "QUAL": 423.4, - "REF": "C", - "aliases": undefined, - "description": "SNV C -> G", - "end": 59857809, - "name": "rs4988351", - "refName": "17", - "samples": { - "1801160099-N32519_26611_S51_56704": { - "AD": [ - 6, - 13, - ], - "DP": [ - 19, - ], - "GQ": [ - 99, - ], - "GT": [ - "0/1", - ], - "PL": [ - 452, - 0, - 159, - ], - "SB": [ - 2, - 4, - 1, - 12, - ], - }, - }, - "start": 59857808, - "type": "SNV", - "uniqueId": "vcf-97", - }, - }, - "id": "98", - }, - { - "cells": [ - { - "columnNumber": 0, - "text": "18", - }, - { - "columnNumber": 1, - "text": "48584855", - }, - { - "columnNumber": 2, - "text": "rs760402978", - }, - { - "columnNumber": 3, - "text": "A", - }, - { - "columnNumber": 4, - "text": "ATT", - }, - { - "columnNumber": 5, - "text": "164.97", - }, - { - "columnNumber": 6, - "text": "PASS", - }, - { - "columnNumber": 7, - "text": "DP=69;FS=1.596;MQ=60.00;MQRankSum=1.611;QD=2.39;ReadPosRankSum=-2.031;SOR=0.387;FractionInformativeReads=0.594;DB", - }, - { - "columnNumber": 8, - "text": "GT:AD:DP:GQ:PL:SB", - }, - { - "columnNumber": 9, - "text": "0/1:28,13:41:99:202,0,707:5,23,3,10", - }, - ], - "extendedData": { - "vcfFeature": { - "ALT": [ - "ATT", - ], - "CHROM": "18", - "FILTER": "PASS", - "ID": [ - "rs760402978", - ], - "INFO": { - "DB": true, - "DP": [ - 69, - ], - "FS": [ - 1.596, - ], - "FractionInformativeReads": [ - 0.594, - ], - "MQ": [ - 60, - ], - "MQRankSum": [ - 1.611, - ], - "QD": [ - 2.39, - ], - "ReadPosRankSum": [ - -2.031, - ], - "SOR": [ - 0.387, - ], - }, - "POS": 48584855, - "QUAL": 164.97, - "REF": "A", - "aliases": undefined, - "description": "insertion A -> ATT", - "end": 48584855, - "name": "rs760402978", - "refName": "18", - "samples": { - "1801160099-N32519_26611_S51_56704": { - "AD": [ - 28, - 13, - ], - "DP": [ - 41, - ], - "GQ": [ - 99, - ], - "GT": [ - "0/1", - ], - "PL": [ - 202, - 0, - 707, - ], - "SB": [ - 5, - 23, - 3, - 10, - ], - }, - }, - "start": 48584854, - "type": "insertion", - "uniqueId": "vcf-98", - }, - }, - "id": "99", - }, - { - "cells": [ - { - "columnNumber": 0, - "text": "19", - }, - { - "columnNumber": 1, - "text": "1219274", - }, - { - "columnNumber": 2, - "text": "rs34928889", - }, - { - "columnNumber": 3, - "text": "G", - }, - { - "columnNumber": 4, - "text": "A", - }, - { - "columnNumber": 5, - "text": "1758.54", - }, - { - "columnNumber": 6, - "text": "PASS", - }, - { - "columnNumber": 7, - "text": "DP=153;FS=3.091;MQ=60.00;MQRankSum=1.482;QD=11.49;ReadPosRankSum=-1.474;SOR=0.457;FractionInformativeReads=1.000;DB;EMV_CLASSIFICATION=Benign;HGVS=NM_000455:c.375-49G>A;AC=71064;AC_OTH=1735;AC_POPMAX=8965;AF=4.67896e-01;AF_OTH=4.46245e-01;AF_POPMAX=8.55276e-01;AN=151880;AN_OTH=3888;AN_POPMAX=10482;AS_FilterStatus=PASS;Hom=17704;InbreedingCoeff=1.13900e-01;POPMAX=EAS", - }, - { - "columnNumber": 8, - "text": "GT:AD:DP:GQ:PL:SB", - }, - { - "columnNumber": 9, - "text": "0/1:85,68:153:99:1787,0,2476:59,26,43,25", - }, - ], - "extendedData": { - "vcfFeature": { - "ALT": [ - "A", - ], - "CHROM": "19", - "FILTER": "PASS", - "ID": [ - "rs34928889", - ], - "INFO": { - "AC": [ - 71064, - ], - "AC_OTH": [ - 1735, - ], - "AC_POPMAX": [ - 8965, - ], - "AF": [ - 0.467896, - ], - "AF_OTH": [ - 0.446245, - ], - "AF_POPMAX": [ - 0.855276, - ], - "AN": [ - 151880, - ], - "AN_OTH": [ - 3888, - ], - "AN_POPMAX": [ - 10482, - ], - "AS_FilterStatus": [ - "PASS", - ], - "DB": true, - "DP": [ - 153, - ], - "EMV_CLASSIFICATION": [ - "Benign", - ], - "FS": [ - 3.091, - ], - "FractionInformativeReads": [ - 1, - ], - "HGVS": [ - "NM_000455:c.375-49G>A", - ], - "Hom": [ - 17704, - ], - "InbreedingCoeff": [ - 0.1139, - ], - "MQ": [ - 60, - ], - "MQRankSum": [ - 1.482, - ], - "POPMAX": [ - "EAS", - ], - "QD": [ - 11.49, - ], - "ReadPosRankSum": [ - -1.474, - ], - "SOR": [ - 0.457, - ], - }, - "POS": 1219274, - "QUAL": 1758.54, - "REF": "G", - "aliases": undefined, - "description": "SNV G -> A", - "end": 1219274, - "name": "rs34928889", - "refName": "19", - "samples": { - "1801160099-N32519_26611_S51_56704": { - "AD": [ - 85, - 68, - ], - "DP": [ - 153, - ], - "GQ": [ - 99, - ], - "GT": [ - "0/1", - ], - "PL": [ - 1787, - 0, - 2476, - ], - "SB": [ - 59, - 26, - 43, - 25, - ], - }, - }, - "start": 1219273, - "type": "SNV", - "uniqueId": "vcf-99", - }, - }, - "id": "100", - }, - { - "cells": [ - { - "columnNumber": 0, - "text": "19", - }, - { - "columnNumber": 1, - "text": "1222012", - }, - { - "columnNumber": 2, - "text": "rs2075607", - }, - { - "columnNumber": 3, - "text": "G", - }, - { - "columnNumber": 4, - "text": "C", - }, - { - "columnNumber": 5, - "text": "2372.25", - }, - { - "columnNumber": 6, - "text": "PASS", - }, - { - "columnNumber": 7, - "text": "DP=193;FS=0.577;MQ=59.94;MQRankSum=-1.285;QD=12.29;ReadPosRankSum=-1.422;SOR=0.780;FractionInformativeReads=1.000;DB;EMV_CLASSIFICATION=Benign;HGVS=NM_000455:c.920+7G>C;AC=30853;AC_OTH=674;AC_POPMAX=3777;AF=1.86351e-01;AF_OTH=1.64712e-01;AF_POPMAX=3.26900e-01;AN=165564;AN_OTH=4092;AN_POPMAX=11554;AS_FilterStatus=PASS;Hom=3149;InbreedingCoeff=8.18000e-02;POPMAX=EAS", - }, - { - "columnNumber": 8, - "text": "GT:AD:DP:GQ:PL:SB", - }, - { - "columnNumber": 9, - "text": "0/1:105,88:193:99:2400,0,2787:33,72,26,62", - }, - ], - "extendedData": { - "vcfFeature": { - "ALT": [ - "C", - ], - "CHROM": "19", - "FILTER": "PASS", - "ID": [ - "rs2075607", - ], - "INFO": { - "AC": [ - 30853, - ], - "AC_OTH": [ - 674, - ], - "AC_POPMAX": [ - 3777, - ], - "AF": [ - 0.186351, - ], - "AF_OTH": [ - 0.164712, - ], - "AF_POPMAX": [ - 0.3269, - ], - "AN": [ - 165564, - ], - "AN_OTH": [ - 4092, - ], - "AN_POPMAX": [ - 11554, - ], - "AS_FilterStatus": [ - "PASS", - ], - "DB": true, - "DP": [ - 193, - ], - "EMV_CLASSIFICATION": [ - "Benign", - ], - "FS": [ - 0.577, - ], - "FractionInformativeReads": [ - 1, - ], - "HGVS": [ - "NM_000455:c.920+7G>C", - ], - "Hom": [ - 3149, - ], - "InbreedingCoeff": [ - 0.0818, - ], - "MQ": [ - 59.94, - ], - "MQRankSum": [ - -1.285, - ], - "POPMAX": [ - "EAS", - ], - "QD": [ - 12.29, - ], - "ReadPosRankSum": [ - -1.422, - ], - "SOR": [ - 0.78, - ], - }, - "POS": 1222012, - "QUAL": 2372.25, - "REF": "G", - "aliases": undefined, - "description": "SNV G -> C", - "end": 1222012, - "name": "rs2075607", - "refName": "19", - "samples": { - "1801160099-N32519_26611_S51_56704": { - "AD": [ - 105, - 88, - ], - "DP": [ - 193, - ], - "GQ": [ - 99, - ], - "GT": [ - "0/1", - ], - "PL": [ - 2400, - 0, - 2787, - ], - "SB": [ - 33, - 72, - 26, - 62, - ], - }, - }, - "start": 1222011, - "type": "SNV", - "uniqueId": "vcf-100", - }, - }, - "id": "101", - }, - ], - }, -} -`; diff --git a/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/components/BreakendMultiLevelOptionDialog.tsx b/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/components/BreakendMultiLevelOptionDialog.tsx new file mode 100644 index 0000000000..f2aedc807b --- /dev/null +++ b/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/components/BreakendMultiLevelOptionDialog.tsx @@ -0,0 +1,2 @@ +// re-exported for react lazy +export { BreakendMultiLevelOptionDialog as default } from '@jbrowse/sv-core' diff --git a/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/components/BreakendSingleLevelOptionDialog.tsx b/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/components/BreakendSingleLevelOptionDialog.tsx new file mode 100644 index 0000000000..e7bdfdc631 --- /dev/null +++ b/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/components/BreakendSingleLevelOptionDialog.tsx @@ -0,0 +1,2 @@ +// re-exported for react lazy +export { BreakendSingleLevelOptionDialog as default } from '@jbrowse/sv-core' diff --git a/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/components/FeatureMenu.tsx b/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/components/FeatureMenu.tsx new file mode 100644 index 0000000000..8c13e8e415 --- /dev/null +++ b/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/components/FeatureMenu.tsx @@ -0,0 +1,96 @@ +import React, { lazy } from 'react' +import { AbstractSessionModel, Feature } from '@jbrowse/core/util' +import CascadingMenuButton from '@jbrowse/core/ui/CascadingMenuButton' + +// icons +import ArrowDropDownIcon from '@mui/icons-material/ArrowDropDown' + +// locals +import { locationLinkClick } from '../../components/util' +import { getEnv } from 'mobx-state-tree' + +// lazies +const BreakendMultiLevelOptionDialog = lazy( + () => import('./BreakendMultiLevelOptionDialog'), +) +const BreakendSingleLevelOptionDialog = lazy( + () => import('./BreakendSingleLevelOptionDialog'), +) + +export default function FeatureMenu({ + assemblyName, + session, + arg, + spreadsheetViewId, +}: { + spreadsheetViewId: string + assemblyName: string + session: AbstractSessionModel + arg: { + value?: string + row: { + feature: Feature + loc: string + } + } +}) { + const { row } = arg + return ( + { + try { + await locationLinkClick({ + spreadsheetViewId, + locString: row.loc, + assemblyName, + session, + }) + } catch (e) { + console.error(e) + session.notifyError(`${e}`, e) + } + }, + }, + { + label: 'Open in single-level split view', + onClick: async () => { + const { pluginManager } = getEnv(session) + const viewType = pluginManager.getViewType('BreakpointSplitView')! + session.queueDialog(handleClose => [ + BreakendSingleLevelOptionDialog, + { + handleClose, + session, + feature: row.feature, + viewType, + assemblyName, + }, + ]) + }, + }, + { + label: 'Open in multi-level split view', + onClick: async () => { + const { pluginManager } = getEnv(session) + const viewType = pluginManager.getViewType('BreakpointSplitView')! + session.queueDialog(handleClose => [ + BreakendMultiLevelOptionDialog, + { + handleClose, + session, + feature: row.feature, + viewType, + assemblyName, + }, + ]) + }, + }, + ]} + > + + + ) +} diff --git a/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/components/LocString.tsx b/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/components/LocString.tsx new file mode 100644 index 0000000000..93d4f9808f --- /dev/null +++ b/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/components/LocString.tsx @@ -0,0 +1,40 @@ +import React from 'react' +import { Link } from '@mui/material' +import { AbstractSessionModel } from '@jbrowse/core/util' + +// locals +import { locationLinkClick } from '../../components/util' + +export default function LocString({ + value, + assemblyName, + session, + spreadsheetViewId, +}: { + value: string + assemblyName: string + session: AbstractSessionModel + spreadsheetViewId: string +}) { + return ( + { + try { + event.preventDefault() + await locationLinkClick({ + spreadsheetViewId, + session, + locString: value, + assemblyName, + }) + } catch (e) { + console.error(e) + session.notifyError(`${e}`, e) + } + }} + > + {value} + + ) +} diff --git a/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/util.ts b/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/util.ts new file mode 100644 index 0000000000..30321439de --- /dev/null +++ b/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/util.ts @@ -0,0 +1,11 @@ +export function parseStrand(strand?: string) { + if (strand === '+') { + return 1 + } else if (strand === '-') { + return -1 + } else if (strand === '.') { + return 0 + } else { + return undefined + } +} diff --git a/plugins/spreadsheet-view/src/SpreadsheetView/index.ts b/plugins/spreadsheet-view/src/SpreadsheetView/index.ts index 9679e550b9..583c766e25 100644 --- a/plugins/spreadsheet-view/src/SpreadsheetView/index.ts +++ b/plugins/spreadsheet-view/src/SpreadsheetView/index.ts @@ -1,10 +1,12 @@ import { lazy } from 'react' import { ViewType } from '@jbrowse/core/pluggableElementTypes' import PluginManager from '@jbrowse/core/PluginManager' -import stateModel from './models/SpreadsheetView' +// locals +import stateModelFactory from './models/SpreadsheetView' export default function SpreadsheetViewF(pluginManager: PluginManager) { pluginManager.addViewType(() => { + const stateModel = stateModelFactory() return new ViewType({ name: 'SpreadsheetView', displayName: 'Spreadsheet view', diff --git a/plugins/spreadsheet-view/src/SpreadsheetView/models/ColumnDataTypes/LocEnd.ts b/plugins/spreadsheet-view/src/SpreadsheetView/models/ColumnDataTypes/LocEnd.ts deleted file mode 100644 index 1cb96305e4..0000000000 --- a/plugins/spreadsheet-view/src/SpreadsheetView/models/ColumnDataTypes/LocEnd.ts +++ /dev/null @@ -1,21 +0,0 @@ -import MakeSpreadsheetColumnType from './MakeSpreadsheetColumnType' -import { FilterModelType as NumberFilterModel } from './Number' -import { types } from 'mobx-state-tree' - -const FilterModelType = types.compose( - NumberFilterModel, - types.model({ - type: types.literal('LocEnd'), - }), -) - -const LocEnd = MakeSpreadsheetColumnType('LocEnd', { - categoryName: 'Location', - displayName: 'End', - compare(cellA: { text: string }, cellB: { text: string }) { - return Number.parseFloat(cellA.text) - Number.parseFloat(cellB.text) - }, - FilterModelType, -}) - -export default LocEnd diff --git a/plugins/spreadsheet-view/src/SpreadsheetView/models/ColumnDataTypes/LocRef.ts b/plugins/spreadsheet-view/src/SpreadsheetView/models/ColumnDataTypes/LocRef.ts deleted file mode 100644 index a9e57037e5..0000000000 --- a/plugins/spreadsheet-view/src/SpreadsheetView/models/ColumnDataTypes/LocRef.ts +++ /dev/null @@ -1,21 +0,0 @@ -import MakeSpreadsheetColumnType from './MakeSpreadsheetColumnType' -import { FilterModelType as NumberFilterModel } from './Text' -import { types } from 'mobx-state-tree' - -const FilterModelType = types.compose( - NumberFilterModel, - types.model({ - type: types.literal('LocRef'), - }), -) - -const LocRef = MakeSpreadsheetColumnType('LocRef', { - categoryName: 'Location', - displayName: 'Reference seq', - compare(cellA: { text: string }, cellB: { text: string }) { - return cellA.text.localeCompare(cellB.text) - }, - FilterModelType, -}) - -export default LocRef diff --git a/plugins/spreadsheet-view/src/SpreadsheetView/models/ColumnDataTypes/LocStart.ts b/plugins/spreadsheet-view/src/SpreadsheetView/models/ColumnDataTypes/LocStart.ts deleted file mode 100644 index 359aeb1919..0000000000 --- a/plugins/spreadsheet-view/src/SpreadsheetView/models/ColumnDataTypes/LocStart.ts +++ /dev/null @@ -1,21 +0,0 @@ -import MakeSpreadsheetColumnType from './MakeSpreadsheetColumnType' -import { types } from 'mobx-state-tree' -import { FilterModelType as NumberFilterModel } from './Number' - -const FilterModelType = types.compose( - NumberFilterModel, - types.model({ - type: types.literal('LocStart'), - }), -) - -const LocStart = MakeSpreadsheetColumnType('LocStart', { - categoryName: 'Location', - displayName: 'Start', - compare(cellA: { text: string }, cellB: { text: string }) { - return Number.parseFloat(cellA.text) - Number.parseFloat(cellB.text) - }, - FilterModelType, -}) - -export default LocStart diff --git a/plugins/spreadsheet-view/src/SpreadsheetView/models/ColumnDataTypes/LocString.tsx b/plugins/spreadsheet-view/src/SpreadsheetView/models/ColumnDataTypes/LocString.tsx deleted file mode 100644 index 7c5c955c76..0000000000 --- a/plugins/spreadsheet-view/src/SpreadsheetView/models/ColumnDataTypes/LocString.tsx +++ /dev/null @@ -1,324 +0,0 @@ -import React from 'react' -import { - IconButton, - TextField, - MenuItem, - InputAdornment, - Select, -} from '@mui/material' -import { makeStyles } from 'tss-react/mui' -import { observer } from 'mobx-react' -import { types, getParent, getPropertyMembers } from 'mobx-state-tree' - -// jbrowse imports -import { - getPropertyType, - getEnumerationValues, - getSubType, -} from '@jbrowse/core/util/mst-reflection' -import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view' -import { - doesIntersect2, - isContainedWithin, - compareLocs, - getSession, - parseLocString, -} from '@jbrowse/core/util' - -// icons -import ClearIcon from '@mui/icons-material/Clear' - -// locals -import MakeSpreadsheetColumnType from './MakeSpreadsheetColumnType' - -type LGV = LinearGenomeViewModel - -const useStyles = makeStyles()({ - textFilterControlAdornment: { marginRight: '-18px' }, - textFilterControl: { - '& .MuiInput-formControl': { - marginTop: 8, - }, - '& .MuiInputLabel-formControl': { - top: '-7px', - '&.MuiInputLabel-shrink': { - top: '-3px', - }, - }, - }, -}) - -// React component for the column filter control -const FilterReactComponent = observer(function ({ - filterModel, -}: { - filterModel: any -}) { - const { classes } = useStyles() - const operationChoices = getEnumerationValues( - getSubType(getPropertyType(getPropertyMembers(filterModel), 'operation')), - ) - return ( - <> - {' '} - filterModel.setLocString(evt.target.value)} - className={classes.textFilterControl} - InputProps={{ - endAdornment: ( - - filterModel.setLocString('')} - > - - - - ), - }} - /> - - ) -}) - -const OPERATIONS = [ - 'overlaps with', - 'contained within', - 'fully contains', - 'does not overlap', - 'not contained within', - 'does not contain', -] as const - -interface Loc { - start: number - end: number - refName: string -} - -// NOTE: assembly names, if present, are ignored in all of these predicates -const OPERATION_PREDICATES = { - 'overlaps with': (cellLocation, specifiedLocation) => { - return ( - cellLocation.refName === specifiedLocation.refName && - doesIntersect2( - cellLocation.start, - cellLocation.end, - specifiedLocation.start, - specifiedLocation.end, - ) - ) - }, - 'contained within': (cellLocation, specifiedLocation) => { - return ( - cellLocation.refName === specifiedLocation.refName && - isContainedWithin( - cellLocation.start, - cellLocation.end, - specifiedLocation.start, - specifiedLocation.end, - ) - ) - }, - 'fully contains': (cellLocation, specifiedLocation) => { - return ( - cellLocation.refName === specifiedLocation.refName && - isContainedWithin( - specifiedLocation.start, - specifiedLocation.end, - cellLocation.start, - cellLocation.end, - ) - ) - }, -} as Record boolean> - -OPERATION_PREDICATES['does not overlap'] = ( - cellLocation, - specifiedLocation, -) => { - return !OPERATION_PREDICATES['overlaps with']!( - cellLocation, - specifiedLocation, - ) -} -OPERATION_PREDICATES['not contained within'] = ( - cellLocation, - specifiedLocation, -) => { - return !OPERATION_PREDICATES['contained within']!( - cellLocation, - specifiedLocation, - ) -} -OPERATION_PREDICATES['does not contain'] = ( - cellLocation, - specifiedLocation, -) => { - return !OPERATION_PREDICATES['fully contains']!( - cellLocation, - specifiedLocation, - ) -} - -// MST model for the column filter control -const FilterModelType = types - .model('ColumnLocStringFilter', { - type: types.literal('LocString'), - columnNumber: types.integer, - locString: '', - operation: types.optional(types.string, OPERATIONS[0]), - }) - .views(self => ({ - get locStringIsInvalid() { - if (self.locString) { - const parsed = this.parsedLocString - return ( - !parsed || - parsed.refName === '' || - typeof parsed.start !== 'number' || - typeof parsed.end !== 'number' || - parsed.start > parsed.end - ) - } - return false - }, - get parsedLocString() { - const session = getSession(self) - - const model = getParent(self, 3).spreadsheet - const { assemblyName } = model - try { - return parseLocString(self.locString, refName => - session.assemblyManager.isValidRefName(refName, assemblyName), - ) - } catch (e) { - return undefined - } - }, - })) - .views(self => ({ - // returns a function that tests the given row - get predicate() { - const { - locString, - locStringIsInvalid, - parsedLocString, - operation, - columnNumber, - } = self // avoid closing over self - if (!locString || locStringIsInvalid || !parsedLocString) { - return function alwaysTrue() { - return true - } - } - - return function stringPredicate(_sheet: any, row: any) { - const { cellsWithDerived: cells } = row - const cell = cells[columnNumber] - - if (!cell?.text || !cell.extendedData) { - return false - } - const parsedCellText = cell.extendedData - if (!parsedCellText.refName) { - return false - } - - const predicate = OPERATION_PREDICATES[operation] - if (!predicate) { - throw new Error(`"${operation}" not implemented in location filter`) - } - - return predicate(parsedCellText, parsedLocString as Loc) - } - }, - })) - .actions(self => ({ - setLocString(s: string) { - self.locString = s - }, - setOperation(op: string) { - self.operation = op - }, - })) - .volatile(() => ({ ReactComponent: FilterReactComponent })) - -// opens a new LGV at the location described in the locString in the cell text - -async function locationLinkClick( - spreadsheet: any, - _columnNumber: number, - - cell: any, -) { - const session = getSession(spreadsheet) - const { assemblyName } = spreadsheet - - const { id } = getParent(spreadsheet) - - const newViewId = `${id}_${assemblyName}` - let view = session.views.find(v => v.id === newViewId) as LGV | undefined - if (!view) { - view = session.addView('LinearGenomeView', { - id: newViewId, - }) as LGV - } - await view.navToLocString(cell.text, assemblyName) -} - -type DataCell = any - -const DataCellReactComponent = observer(function ({ - cell, - columnNumber, - spreadsheet, -}: DataCell) { - return ( - { - evt.preventDefault() - const session = getSession(spreadsheet) - try { - await locationLinkClick(spreadsheet, columnNumber, cell) - } catch (e) { - console.error(e) - session.notifyError(`${e}`, e) - } - }} - title="open a new linear genome view here" - href="#" - > - {cell.text} - - ) -}) - -const LocStringColumnType = MakeSpreadsheetColumnType('LocString', { - categoryName: 'Location', - displayName: 'Full location', - - compare(cellA: { extendedData: any }, cellB: { extendedData: any }) { - return compareLocs(cellA.extendedData, cellB.extendedData) - }, - FilterModelType, - DataCellReactComponent, -}) - -export default LocStringColumnType diff --git a/plugins/spreadsheet-view/src/SpreadsheetView/models/ColumnDataTypes/MakeSpreadsheetColumnType.tsx b/plugins/spreadsheet-view/src/SpreadsheetView/models/ColumnDataTypes/MakeSpreadsheetColumnType.tsx deleted file mode 100644 index adb58aa82d..0000000000 --- a/plugins/spreadsheet-view/src/SpreadsheetView/models/ColumnDataTypes/MakeSpreadsheetColumnType.tsx +++ /dev/null @@ -1,37 +0,0 @@ -import React from 'react' -import { types } from 'mobx-state-tree' - -/** utility function for assembling the MST model of a column data type */ -export default function MakeSpreadsheetColumnType( - name: string, - { - DataCellReactComponent = null, - FilterModelType = null, - compare, - displayName = undefined, - categoryName = undefined, - }: { - compare?: any - DataCellReactComponent?: React.FC | null - FilterModelType?: any - displayName?: string - categoryName?: string - }, -) { - return types - .model(`ColumnDataType${name}`, { - type: types.literal(name), - }) - .volatile(() => ({ - DataCellReactComponent, - FilterModelType: FilterModelType, - displayName: displayName || name, - categoryName, - })) - .views(() => ({ - compare, - get hasFilter() { - return !!FilterModelType - }, - })) -} diff --git a/plugins/spreadsheet-view/src/SpreadsheetView/models/ColumnDataTypes/Number.tsx b/plugins/spreadsheet-view/src/SpreadsheetView/models/ColumnDataTypes/Number.tsx deleted file mode 100644 index af90adcc25..0000000000 --- a/plugins/spreadsheet-view/src/SpreadsheetView/models/ColumnDataTypes/Number.tsx +++ /dev/null @@ -1,175 +0,0 @@ -import React from 'react' -import { types } from 'mobx-state-tree' -import { observer } from 'mobx-react' -import { MenuItem, Select, TextField } from '@mui/material' -import { makeStyles } from 'tss-react/mui' -import MakeSpreadsheetColumnType from './MakeSpreadsheetColumnType' - -const OPERATIONS = [ - 'equals', - 'greater than', - 'less than', - 'between', - 'not between', -] - -// NOTE: assembly names, if present, are ignored in all of these predicates -const OPERATION_PREDICATES = { - equals: (numberInCell, firstNumber) => { - return numberInCell === firstNumber - }, - 'greater than': (numberInCell, firstNumber) => { - return numberInCell > firstNumber - }, - 'less than': (numberInCell, firstNumber) => { - return numberInCell < firstNumber - }, - between: (numberInCell, firstNumber, secondNumber) => { - return ( - numberInCell > firstNumber && - secondNumber !== undefined && - numberInCell < secondNumber - ) - }, -} as Record boolean> - -OPERATION_PREDICATES['not between'] = ( - numberInCell, - firstNumber, - secondNumber, -) => { - return !OPERATION_PREDICATES.between!(numberInCell, firstNumber, secondNumber) -} - -const useStyles = makeStyles()({ - textFilterControlAdornment: { marginRight: '-18px' }, - textFilterControl: { - '& .MuiInput-formControl': { - marginTop: 8, - }, - '& .MuiInputLabel-formControl': { - top: '-7px', - '&.MuiInputLabel-shrink': { - top: '-3px', - }, - }, - }, -}) - -// React component for the column filter control -const FilterReactComponent = observer( - ({ filterModel }: { filterModel: any }) => { - const { classes } = useStyles() - - const operationChoices = OPERATIONS - - return ( - <> - {' '} - { - filterModel.setFirstNumber(Number.parseFloat(evt.target.value)) - }} - className={classes.textFilterControl} - /> - {filterModel.operation !== 'between' && - filterModel.operation !== 'not between' ? null : ( - <> - {' and '} - - filterModel.setSecondNumber(Number.parseFloat(evt.target.value)) - } - className={classes.textFilterControl} - /> - - )} - - ) - }, -) - -// MST model for the column filter control -const FilterModelType = types - .model('ColumnNumberFilter', { - type: types.literal('Number'), - columnNumber: types.integer, - firstNumber: types.maybe(types.number), - secondNumber: types.maybe(types.number), - operation: types.optional(types.enumeration(OPERATIONS), OPERATIONS[0]!), - }) - .views(self => ({ - // returns a function that tests the given row - get predicate() { - if (typeof self.firstNumber !== 'number') { - return function alwaysTrue() { - return true - } - } - - const { firstNumber, secondNumber, operation, columnNumber } = self // avoid closing over self - - return function stringPredicate(_sheet: any, row: any) { - const { cellsWithDerived } = row - const cell = cellsWithDerived[columnNumber] - - if (!cell?.text) { - return false - } - - const parsedCellText = Number.parseFloat(cell.text) - if (typeof parsedCellText !== 'number') { - return false - } - - const predicate = OPERATION_PREDICATES[operation] - if (!predicate) { - throw new Error(`"${operation}" not implemented in location filter`) - } - - return predicate(parsedCellText, firstNumber, secondNumber) - } - }, - })) - .actions(self => ({ - setFirstNumber(n: number) { - self.firstNumber = - Number.isNaN(n) || typeof n !== 'number' ? undefined : n - }, - setSecondNumber(n: number) { - self.secondNumber = - Number.isNaN(n) || typeof n !== 'number' ? undefined : n - }, - setOperation(op: string) { - self.operation = op - }, - })) - .volatile(() => ({ ReactComponent: FilterReactComponent })) - -const NumberColumn = MakeSpreadsheetColumnType('Number', { - compare(cellA: { text: string }, cellB: { text: string }) { - return Number.parseFloat(cellA.text) - Number.parseFloat(cellB.text) - }, - FilterModelType, -}) - -export { NumberColumn, FilterModelType } diff --git a/plugins/spreadsheet-view/src/SpreadsheetView/models/ColumnDataTypes/Text.tsx b/plugins/spreadsheet-view/src/SpreadsheetView/models/ColumnDataTypes/Text.tsx deleted file mode 100644 index 28e385ebab..0000000000 --- a/plugins/spreadsheet-view/src/SpreadsheetView/models/ColumnDataTypes/Text.tsx +++ /dev/null @@ -1,171 +0,0 @@ -import React from 'react' -import { - IconButton, - TextField, - MenuItem, - InputAdornment, - Select, -} from '@mui/material' -import { makeStyles } from 'tss-react/mui' -import MakeSpreadsheetColumnType from './MakeSpreadsheetColumnType' -import { types, getPropertyMembers } from 'mobx-state-tree' -import { observer } from 'mobx-react' -import { - getPropertyType, - getEnumerationValues, - getSubType, -} from '@jbrowse/core/util/mst-reflection' - -// icons -import ClearIcon from '@mui/icons-material/Clear' - -const OPERATIONS = [ - 'equals', - 'contains', - 'does not contain', - 'does not equal', - 'starts with', - 'ends with', -] - -// NOTE: assembly names, if present, are ignored in all of these predicates -const OPERATION_PREDICATES = { - contains: (textInCell, stringToFind) => { - return textInCell.toLowerCase().includes(stringToFind) - }, - equals: (textInCell, stringToFind) => { - return textInCell.toLowerCase() === stringToFind - }, - 'starts with': (textInCell, stringToFind) => { - return textInCell.toLowerCase().startsWith(stringToFind) - }, - 'ends with': (textInCell, stringToFind) => { - const index = textInCell.toLowerCase().indexOf(stringToFind) - if (index === -1) { - return false - } - return index === textInCell.length - stringToFind.length - }, -} as Record boolean> - -OPERATION_PREDICATES['does not contain'] = (textInCell, stringToFind) => { - return !OPERATION_PREDICATES.contains!(textInCell, stringToFind) -} -OPERATION_PREDICATES['does not equal'] = (textInCell, stringToFind) => { - return !OPERATION_PREDICATES.equals!(textInCell, stringToFind) -} - -const useStyles = makeStyles()({ - textFilterControlAdornment: { marginRight: '-18px' }, - textFilterControl: { - margin: 0, - '& .MuiInput-formControl': { - marginTop: 8, - }, - '& .MuiInputLabel-formControl': { - top: '-7px', - '&.MuiInputLabel-shrink': { - top: '-3px', - }, - }, - }, -}) - -// React component for the column filter control -const FilterReactComponent = observer( - ({ filterModel }: { filterModel: any }) => { - const { classes } = useStyles() - const operationChoices = getEnumerationValues( - getSubType(getPropertyType(getPropertyMembers(filterModel), 'operation')), - ) - return ( - <> - {' '} - filterModel.setString(evt.target.value)} - className={classes.textFilterControl} - InputProps={{ - endAdornment: ( - - filterModel.setString('')} - > - - - - ), - }} - /> - - ) - }, -) - -// MST model for the column filter control -const ColumnTextFilter = types - .model('ColumnTextFilter', { - type: types.literal('Text'), - columnNumber: types.integer, - stringToFind: '', - operation: types.optional(types.enumeration(OPERATIONS), OPERATIONS[0]!), - }) - .views(self => ({ - // returns a function that tests the given row - get predicate() { - const { stringToFind, columnNumber, operation } = self // avoid closing over self - if (!stringToFind) { - return function alwaysTrue() { - return true - } - } - const s = stringToFind.toLowerCase() // case insensitive match - - return function stringPredicate(_sheet: any, row: any) { - const { cellsWithDerived } = row - const cell = cellsWithDerived[columnNumber] - if (!cell?.text) { - return false - } - const predicate = OPERATION_PREDICATES[operation] - if (!predicate) { - throw new Error(`"${operation}" not implemented in location filter`) - } - return predicate(cell.text, s) - } - }, - })) - .actions(self => ({ - setString(s: string) { - self.stringToFind = s - }, - setOperation(op: string) { - self.operation = op - }, - })) - .volatile(() => ({ ReactComponent: FilterReactComponent })) - -const TextColumnType = MakeSpreadsheetColumnType('Text', { - compare(cellA: { text: string }, cellB: { text: string }) { - return cellA.text.localeCompare(cellB.text) - }, - FilterModelType: ColumnTextFilter, -}) - -export { TextColumnType as TextColumn, ColumnTextFilter as FilterModelType } diff --git a/plugins/spreadsheet-view/src/SpreadsheetView/models/ColumnDataTypes/index.ts b/plugins/spreadsheet-view/src/SpreadsheetView/models/ColumnDataTypes/index.ts deleted file mode 100644 index 4a4f5b10c3..0000000000 --- a/plugins/spreadsheet-view/src/SpreadsheetView/models/ColumnDataTypes/index.ts +++ /dev/null @@ -1,34 +0,0 @@ -import LocString from './LocString' -import LocRef from './LocRef' -import LocStart from './LocStart' -import LocEnd from './LocEnd' -import { NumberColumn } from './Number' -import { TextColumn as Text } from './Text' -import { types, IAnyModelType } from 'mobx-state-tree' - -const ColumnTypes = { - Number: NumberColumn, - Text, - LocString, - LocRef, - LocStart, - LocEnd, -} - -const allColumnTypes = Object.values(ColumnTypes) -const AnyColumnType = types.union(...allColumnTypes) -const AnyFilterModelType = types.union( - ...allColumnTypes - .map(columnType => { - // just instantiate the blank types to get their filter model types - const { FilterModelType } = columnType.create({ - // @ts-expect-error - type: columnType.properties.type.value, - }) - return FilterModelType as unknown as IAnyModelType | undefined - }) - // some column types might not have filter machinery, filter those out - .filter(t => !!t), -) - -export { ColumnTypes, AnyColumnType, AnyFilterModelType } diff --git a/plugins/spreadsheet-view/src/SpreadsheetView/models/FilterControls.ts b/plugins/spreadsheet-view/src/SpreadsheetView/models/FilterControls.ts deleted file mode 100644 index 07e5dbc631..0000000000 --- a/plugins/spreadsheet-view/src/SpreadsheetView/models/FilterControls.ts +++ /dev/null @@ -1,94 +0,0 @@ -import { types, getParent, SnapshotIn } from 'mobx-state-tree' -import { AnyFilterModelType as AnyColumnFilter } from './ColumnDataTypes' - -// filter that finds a simple string in any of the cells of a row -const RowFullTextFilter = types - .model('RowFullTextFilter', { - type: types.literal('RowFullText'), - stringToFind: '', - }) - .views(self => ({ - // returns a function that tests the given row - get predicate() { - let s = self.stringToFind // avoid closing over self - if (!s) { - return function alwaysTrue() { - return true - } - } - s = s.toLowerCase() - return function stringPredicate( - _sheet: unknown, - row: { cellsWithDerived: { text: string }[] }, - ) { - const { cellsWithDerived } = row - for (const cell of cellsWithDerived) { - // note: case insensitive - if (cell.text.toLowerCase().includes(s)) { - return true - } - } - return false - } - }, - })) - .actions(self => ({ - setString(s: string) { - self.stringToFind = s - }, - clear() { - self.stringToFind = '' - }, - })) - -const model = types - .model('SpreadsheetFilterControls', { - rowFullText: types.optional( - RowFullTextFilter, - () => - ({ - type: 'RowFullText', - stringToFind: '', - }) as SnapshotIn, - ), - columnFilters: types.array(AnyColumnFilter), - }) - .views(self => ({ - get filters() { - return [self.rowFullText, ...self.columnFilters].filter(f => !!f) - }, - setRowFullTextFilter(stringToFind: string) { - // @ts-expect-error - self.rowFullText = { - type: 'RowFullText', - stringToFind, - } - }, - rowPassesFilters(sheet: unknown, row: unknown) { - for (const filter of this.filters) { - if (!filter.predicate(sheet, row)) { - return false - } - } - return true - }, - })) - .actions(self => ({ - addBlankColumnFilter(columnNumber: number) { - const { dataType } = - getParent(self).spreadsheet.columns[columnNumber] - self.columnFilters.push({ - type: dataType.type, - columnNumber, - }) - }, - removeColumnFilter(filter: typeof AnyColumnFilter) { - return self.columnFilters.remove(filter) - }, - clearAllFilters() { - self.columnFilters.clear() - self.rowFullText.clear() - }, - })) - -export default model diff --git a/plugins/spreadsheet-view/src/SpreadsheetView/models/ImportWizard.ts b/plugins/spreadsheet-view/src/SpreadsheetView/models/ImportWizard.ts index 8b5467b2d3..01f434682f 100644 --- a/plugins/spreadsheet-view/src/SpreadsheetView/models/ImportWizard.ts +++ b/plugins/spreadsheet-view/src/SpreadsheetView/models/ImportWizard.ts @@ -1,199 +1,179 @@ -import { types, getParent, Instance } from 'mobx-state-tree' +import { types, getParent, addDisposer, Instance } from 'mobx-state-tree' import { openLocation } from '@jbrowse/core/util/io' -import { getSession, getEnv } from '@jbrowse/core/util' +import { + getSession, + getEnv, + FileLocation as FileLocationType, +} from '@jbrowse/core/util' +import { GenericFilehandle } from 'generic-filehandle' -// 30MB -const IMPORT_SIZE_LIMIT = 30_000_000 +// locals +import { autorun } from 'mobx' +import { getFileType, getFilename } from '../components/util' -const fileTypes = ['CSV', 'TSV', 'VCF', 'BED', 'BEDPE', 'STAR-Fusion'] +const IMPORT_SIZE_LIMIT = 40_000_000 + +const fileTypes = ['VCF', 'BED', 'BEDPE', 'STAR-Fusion'] const fileTypeParsers = { - CSV: () => - import('../importAdapters/ImportUtils').then(r => r.parseCsvBuffer), - TSV: () => - import('../importAdapters/ImportUtils').then(r => r.parseTsvBuffer), VCF: () => import('../importAdapters/VcfImport').then(r => r.parseVcfBuffer), BED: () => import('../importAdapters/BedImport').then(r => r.parseBedBuffer), BEDPE: () => - import('../importAdapters/BedImport').then(r => r.parseBedPEBuffer), + import('../importAdapters/BedpeImport').then(r => r.parseBedPEBuffer), 'STAR-Fusion': () => import('../importAdapters/STARFusionImport').then( r => r.parseSTARFusionBuffer, ), } -// regexp used to guess the type of a file or URL from its file extension -const fileTypesRegexp = new RegExp(`\\.(${fileTypes.join('|')})(\\.gz)?$`, 'i') +async function maybeStat(f: GenericFilehandle) { + let stat: { size: number } | undefined + try { + stat = await f.stat() + } catch (e) { + // not required for stat to succeed to proceed, but it is helpful + console.warn(e) + } + return stat +} /** * #stateModel SpreadsheetImportWizard - * #category view */ -function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars - -const ImportWizard = types - .model('SpreadsheetImportWizard', { - /** - * #property - */ - fileType: types.optional(types.enumeration(fileTypes), 'CSV'), - /** - * #property - */ - hasColumnNameLine: true, - /** - * #property - */ - columnNameLineNumber: 1, - /** - * #property - */ - selectedAssemblyName: types.maybe(types.string), - }) - .volatile(() => ({ - fileTypes, - - fileSource: undefined as any, - error: undefined as unknown, - loading: false, - })) - .views(self => ({ - get isReadyToOpen() { - return ( - !self.error && - self.fileSource && - (self.fileSource.blobId || - self.fileSource.localPath || - self.fileSource.uri) - ) - }, - get canCancel() { - return getParent(self).readyToDisplay - }, - - get fileName() { - return ( - self.fileSource.uri || - self.fileSource.localPath || - (self.fileSource.blobId && self.fileSource.name) - ) - }, - - get requiresUnzip() { - return this.fileName.endsWith('gz') - }, - - isValidRefName(refName: string, assemblyName?: string) { - const { assemblyManager } = getSession(self) - if (!assemblyName) { - return false - } - return assemblyManager.isValidRefName(refName, assemblyName) - }, - })) - .actions(self => ({ - setSelectedAssemblyName(s: string) { - self.selectedAssemblyName = s - }, - setFileSource(newSource: unknown) { - self.fileSource = newSource - self.error = undefined - - if (self.fileSource) { - // try to autodetect the file type, ignore errors - const name = self.fileName - - if (name) { - const firstMatch = fileTypesRegexp.exec(name)?.[1] - if (firstMatch) { - self.fileType = - firstMatch === 'tsv' && name.includes('star-fusion') - ? 'STAR-Fusion' - : firstMatch.toUpperCase() - } - } - } - }, - - toggleHasColumnNameLine() { - self.hasColumnNameLine = !self.hasColumnNameLine - }, - - setColumnNameLineNumber(newnumber: number) { - if (newnumber > 0) { - self.columnNameLineNumber = newnumber - } - }, - - setFileType(typeName: string) { - self.fileType = typeName - }, - - setError(error: unknown) { - console.error(error) - self.loading = false - self.error = error - }, - - setLoaded() { - self.loading = false - self.error = undefined - }, - - cancelButton() { - self.error = undefined - - getParent(self).setDisplayMode() - }, - - // fetch and parse the file, make a new Spreadsheet model for it, - // then set the parent to display it - async import(assemblyName: string) { - if (!self.fileSource) { - return - } - - if (self.loading) { - throw new Error('Cannot import, load already in progress') - } - - self.selectedAssemblyName = assemblyName - self.loading = true - const type = self.fileType as keyof typeof fileTypeParsers - const typeParser = await fileTypeParsers[type]() - - const { unzip } = await import('@gmod/bgzf-filehandle') - const { pluginManager } = getEnv(self) - const filehandle = openLocation(self.fileSource, pluginManager) - try { - const stat = await filehandle.stat() - if (stat.size > IMPORT_SIZE_LIMIT) { - throw new Error( - `File is too big. Tabular files are limited to at most ${( - IMPORT_SIZE_LIMIT / 1000 - ).toLocaleString()}kb.`, - ) +function stateModelFactory() { + return types + .model('SpreadsheetImportWizard', { + /** + * #property + */ + fileTypeOverride: types.maybe(types.string), + /** + * #property + */ + selectedAssemblyName: types.maybe(types.string), + /** + * #property + */ + spreadsheetFilehandle: types.frozen(), + }) + .volatile(() => ({ + fileTypes, + error: undefined as unknown, + loading: false, + })) + .views(self => ({ + /** + * #getter + */ + get fileType() { + if (self.fileTypeOverride) { + return self.fileTypeOverride + } else if (self.spreadsheetFilehandle) { + return getFileType(self.spreadsheetFilehandle) + } else { + return 'VCF' } - } catch (e) { - // not required for stat to succeed to proceed, but it is helpful - console.warn(e) - } - - try { - await filehandle - .readFile() - .then(buffer => (self.requiresUnzip ? unzip(buffer) : buffer)) - .then(buffer => typeParser(buffer, self)) - .then(spreadsheet => { - this.setLoaded() - - getParent(self).displaySpreadsheet(spreadsheet) - }) - } catch (e) { - this.setError(e) - } - }, - })) + }, + + /** + * #getter + */ + get fileName(): string | undefined { + return getFilename(self.spreadsheetFilehandle) + }, + /** + * #getter + */ + get requiresUnzip() { + return this.fileName?.endsWith('gz') + }, + /** + * #method + */ + isValidRefName(refName: string, assemblyName?: string) { + const { assemblyManager } = getSession(self) + return assemblyName + ? assemblyManager.isValidRefName(refName, assemblyName) + : false + }, + })) + .actions(self => ({ + /** + * #action + */ + setSelectedAssemblyName(s: string) { + self.selectedAssemblyName = s + }, + /** + * #action + */ + setSpreadsheetFilehandle(newSource?: FileLocationType) { + self.spreadsheetFilehandle = newSource + self.error = undefined + }, + /** + * #action + */ + setFileType(typeName: string) { + self.fileTypeOverride = typeName + }, + /** + * #action + */ + setError(error: unknown) { + self.error = error + }, + /** + * #action + */ + setLoading(arg: boolean) { + self.loading = arg + }, + afterAttach() { + addDisposer( + self, + autorun(async () => { + try { + const { spreadsheetFilehandle } = self + if (!spreadsheetFilehandle) { + return + } + + this.setLoading(true) + const typeParser = + await fileTypeParsers[ + self.fileType as keyof typeof fileTypeParsers + ]() + + const { unzip } = await import('@gmod/bgzf-filehandle') + const { pluginManager } = getEnv(self) + const f = openLocation(spreadsheetFilehandle, pluginManager) + const stat = await maybeStat(f) + if (stat && stat.size > IMPORT_SIZE_LIMIT) { + throw new Error( + `File is too big. Tabular files are limited to at most ${( + IMPORT_SIZE_LIMIT / 1_000_000 + ).toLocaleString()}Mb.`, + ) + } + const buffer = await f.readFile() + const buf2 = self.requiresUnzip ? await unzip(buffer) : buffer + const spreadsheet = typeParser(buf2) + getParent(self).displaySpreadsheet( + spreadsheet, + self.selectedAssemblyName, + ) + } catch (e) { + console.error(e) + this.setError(e) + } finally { + this.setLoading(false) + } + }), + ) + }, + })) +} -export type ImportWizardStateModel = typeof ImportWizard +export type ImportWizardStateModel = ReturnType export type ImportWizardModel = Instance -export default ImportWizard +export default stateModelFactory diff --git a/plugins/spreadsheet-view/src/SpreadsheetView/models/Row.ts b/plugins/spreadsheet-view/src/SpreadsheetView/models/Row.ts deleted file mode 100644 index 18d97e616e..0000000000 --- a/plugins/spreadsheet-view/src/SpreadsheetView/models/Row.ts +++ /dev/null @@ -1,45 +0,0 @@ -import { types, getParent } from 'mobx-state-tree' - -const CellModel = types.model('SpreadsheetCell', { - text: types.string, - extendedData: types.maybe(types.frozen()), -}) - -const RowModel = types - .model('SpreadsheetRow', { - id: types.identifier, - cells: types.array(CellModel), - extendedData: types.maybe(types.frozen()), - isSelected: false, - }) - .actions(self => ({ - toggleSelect() { - self.isSelected = !self.isSelected - }, - unSelect() { - self.isSelected = false - }, - select() { - self.isSelected = true - }, - setExtendedData(data: unknown) { - self.extendedData = data - }, - })) - .views(self => ({ - get cellsWithDerived() { - const { columns } = getParent(self, 3) - let i = 0 - - return columns.map((column: { isDerived: boolean; expr: any }) => { - if (column.isDerived) { - return column.expr.evalSync({ - row: self, - }) - } - return self.cells[i++] - }) - }, - })) - -export default RowModel diff --git a/plugins/spreadsheet-view/src/SpreadsheetView/models/Spreadsheet.ts b/plugins/spreadsheet-view/src/SpreadsheetView/models/Spreadsheet.ts deleted file mode 100644 index fed5f18a11..0000000000 --- a/plugins/spreadsheet-view/src/SpreadsheetView/models/Spreadsheet.ts +++ /dev/null @@ -1,209 +0,0 @@ -import { stringToJexlExpression } from '@jbrowse/core/util/jexlStrings' -import { getSession, getEnv } from '@jbrowse/core/util' -import { autorun } from 'mobx' -import { - addDisposer, - types, - getParent, - SnapshotIn, - Instance, -} from 'mobx-state-tree' - -// locals -import { ColumnTypes, AnyColumnType } from './ColumnDataTypes' -import StaticRowSetModel from './StaticRowSet' -import type RowModel from './Row' - -type Row = Instance - -const ColumnDefinition = types - .model('ColumnDefinition', { - name: types.maybe(types.string), - dataType: types.optional(AnyColumnType, () => ({ - type: 'Text', - })), - // set to true if column is derived from other columns - // if the column is derived, each cell will have a - // `derivationFunction` that is called to get its value - isDerived: false, - // if this cell is derived from other cells, execute this function to get - // the value - derivationFunctionText: types.maybe(types.string), - }) - .views(self => ({ - get expr() { - if (self.isDerived) { - // compile this as a jexl expression - return stringToJexlExpression( - String(self.derivationFunctionText), - getEnv(self).pluginManager.jexl, - ) - } - return undefined - }, - })) - -type RowMenuPosition = { anchorEl: Element; rowNumber: string } | null - -/** - * #stateModel SpreadsheetViewSpreadsheet - * #category view - */ -function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars - -const Spreadsheet = types - .model('Spreadsheet', { - /** - * #property - */ - rowSet: types.optional(StaticRowSetModel, () => StaticRowSetModel.create()), - /** - * #property - */ - columns: types.array(ColumnDefinition), - /** - * #property - */ - columnDisplayOrder: types.array(types.number), - /** - * #property - */ - hasColumnNames: false, - /** - * #property - */ - sortColumns: types.array( - types - .model('SortColumns', { - columnNumber: types.number, - descending: false, - }) - .actions(self => ({ - switchDirection() { - self.descending = !self.descending - }, - })), - ), - - assemblyName: types.maybe(types.string), - }) - .volatile(() => ({ - defaultDataType: ColumnTypes.Text, - rowMenuPosition: null as RowMenuPosition, - isLoaded: false, - })) - .views(self => ({ - /** - * #getter - */ - get initialized() { - const session = getSession(self) - const name = self.assemblyName - return name ? session.assemblyManager.get(name)?.initialized : false - }, - /** - * #getter - */ - get hideRowSelection() { - // just delegates to parent - - return getParent(self).hideRowSelection - }, - - /** - * #getter - * list of data type names to be made available in the column - * dropdown menu - */ - get dataTypeChoices() { - const typeNames = Object.keys(ColumnTypes) as (keyof typeof ColumnTypes)[] - return typeNames.map(typeName => { - const dataType = ColumnTypes[typeName].create({ type: typeName }) - const { displayName, categoryName } = dataType - return { typeName, displayName, categoryName } - }) - }, - - /** - * #method - */ - rowSortingComparisonFunction(rowA: Row, rowB: Row) { - for (const { columnNumber, descending } of self.sortColumns) { - const { dataType } = self.columns[columnNumber]! - const result = dataType.compare( - rowA.cellsWithDerived[columnNumber], - rowB.cellsWithDerived[columnNumber], - ) - if (result) { - return descending ? -result : result - } - } - return 0 - }, - })) - .actions(self => ({ - afterAttach() { - addDisposer( - self, - autorun(async () => { - const session = getSession(self) - const { assemblyManager } = session - try { - if (self.assemblyName) { - await assemblyManager.waitForAssembly(self.assemblyName) - this.setLoaded(true) - } - } catch (error) { - session.notify( - `failed to load assembly ${self.assemblyName} ${error}`, - 'error', - ) - } - }), - ) - }, - - /** - * #action - */ - setLoaded(flag: boolean) { - self.isLoaded = flag - }, - - /** - * #action - */ - setRowMenuPosition(newPosition: RowMenuPosition) { - self.rowMenuPosition = newPosition - }, - - /** - * #action - */ - setSortColumns(newSort: NonNullable>) { - // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition - if (newSort) { - // @ts-expect-error - self.sortColumns = newSort - } - }, - - /** - * #action - */ - setColumnType(columnNumber: number, newTypeName: string) { - self.columns[columnNumber]!.dataType = { type: newTypeName } - }, - - /** - * #action - */ - unselectAll() { - self.rowSet.unselectAll() - }, - })) - -export type SpreadsheetStateModel = typeof Spreadsheet -export type SpreadsheetModel = Instance - -export default Spreadsheet diff --git a/plugins/spreadsheet-view/src/SpreadsheetView/models/Spreadsheet.tsx b/plugins/spreadsheet-view/src/SpreadsheetView/models/Spreadsheet.tsx new file mode 100644 index 0000000000..3467ee16f3 --- /dev/null +++ b/plugins/spreadsheet-view/src/SpreadsheetView/models/Spreadsheet.tsx @@ -0,0 +1,167 @@ +import React from 'react' +import { + Feature, + assembleLocString, + getSession, + measureGridWidth, +} from '@jbrowse/core/util' +import { autorun } from 'mobx' +import { addDisposer, types, Instance, getParent } from 'mobx-state-tree' +import { GridColDef } from '@mui/x-data-grid' + +// locals +import FeatureMenu from '../importAdapters/components/FeatureMenu' +import LocString from '../importAdapters/components/LocString' + +interface Row { + feature: Feature + [key: string]: unknown +} + +interface ComponentRecord { + Component: React.FC + props: Record +} + +export interface SpreadsheetData { + rows: Row[] + columns: string[] + ColumnComponentMap?: Record +} + +/** + * #stateModel SpreadsheetViewSpreadsheet + * #category view + */ +function stateModelFactory() { + return types + .model('Spreadsheet', { + /** + * #property + */ + assemblyName: types.string, + }) + .volatile(() => ({ + /** + * #volatile + */ + data: undefined as SpreadsheetData | undefined, + /** + * #volatile + */ + visibleColumns: {} as Record, + })) + .views(self => ({ + /** + * #getter + */ + get initialized() { + return !!self.data + }, + })) + .actions(self => ({ + /** + * #action + */ + setVisibleColumns(args: Record) { + self.visibleColumns = args + }, + /** + * #action + */ + setData(data: SpreadsheetData | undefined) { + self.data = data + }, + })) + .views(self => ({ + /** + * #getter + */ + get rows() { + return (self.data?.rows.map(r => ({ + menu: 'a', + loc: assembleLocString({ + refName: r.feature.get('refName'), + start: r.feature.get('start'), + end: r.feature.get('end'), + }), + ...r, + })) || []) as Record[] + }, + /** + * #getter + */ + get features() { + return self.data?.rows.map(r => r.feature) + }, + })) + .views(self => ({ + /** + * #getter + */ + get columns() { + const { data } = self + const session = getSession(self) + return [ + { + field: 'menu', + width: 10, + renderCell: row => ( + (self).id} + assemblyName={self.assemblyName} + arg={row} + /> + ), + }, + { + field: 'loc', + width: measureGridWidth( + self.rows.map(r => r.loc), + { minWidth: 20 }, + ), + renderCell: row => ( + (self).id} + value={row.value} + session={session} + /> + ), + }, + ...(data?.columns.map(m => { + const res = data.ColumnComponentMap?.[m] as any + return { + field: m, + renderCell: res, + width: measureGridWidth( + self.rows.map(r => r[m]), + { minWidth: 20 }, + ), + } + }) || []), + ] satisfies GridColDef[] + }, + })) + .actions(self => ({ + afterAttach() { + addDisposer( + self, + autorun(() => { + const { data } = self + self.setVisibleColumns({ + loc: true, + menu: true, + ...Object.fromEntries(data?.columns.map(c => [c, true]) || []), + }) + }), + ) + }, + })) +} + +export type SpreadsheetStateModel = ReturnType +export type SpreadsheetModel = Instance + +export default stateModelFactory diff --git a/plugins/spreadsheet-view/src/SpreadsheetView/models/SpreadsheetView.test.ts b/plugins/spreadsheet-view/src/SpreadsheetView/models/SpreadsheetView.test.ts deleted file mode 100644 index 6b5b4b395a..0000000000 --- a/plugins/spreadsheet-view/src/SpreadsheetView/models/SpreadsheetView.test.ts +++ /dev/null @@ -1,8 +0,0 @@ -import SpreadsheetView from './SpreadsheetView' - -describe('Spreadsheet View mst model', () => { - it('can instantiate with empty args', () => { - const view = SpreadsheetView.create({ type: 'SpreadsheetView' }) - expect(view).toBeTruthy() - }) -}) diff --git a/plugins/spreadsheet-view/src/SpreadsheetView/models/SpreadsheetView.ts b/plugins/spreadsheet-view/src/SpreadsheetView/models/SpreadsheetView.ts index 784e96ccb0..bf47e00060 100644 --- a/plugins/spreadsheet-view/src/SpreadsheetView/models/SpreadsheetView.ts +++ b/plugins/spreadsheet-view/src/SpreadsheetView/models/SpreadsheetView.ts @@ -1,231 +1,154 @@ -import { types, getEnv, cast, SnapshotIn, Instance } from 'mobx-state-tree' +import { types, Instance } from 'mobx-state-tree' import { BaseViewModel } from '@jbrowse/core/pluggableElementTypes/models' -import { readConfObject } from '@jbrowse/core/configuration' -import { MenuItem } from '@jbrowse/core/ui' import { getSession } from '@jbrowse/core/util' // icons -import DoneIcon from '@mui/icons-material/Done' import FolderOpenIcon from '@mui/icons-material/FolderOpen' -import SpreadsheetModel from './Spreadsheet' -import ImportWizardModel from './ImportWizard' -import FilterControlsModel from './FilterControls' +// locals +import spreadsheetModelFactory, { SpreadsheetData } from './Spreadsheet' +import importWizardFactory from './ImportWizard' -type Spreadsheet = Instance - -export type MenuItemWithDisabledCallback = MenuItem & { - disabled?: - | boolean - | (( - viewModel: unknown, - spreadsheetModel: Spreadsheet, - rowNumber: number, - row: Spreadsheet['rowSet']['rows'][0], - ) => boolean) -} - -const defaultRowMenuItems: MenuItemWithDisabledCallback[] = [ - { - label: 'Toggle select', - icon: DoneIcon, - onClick(_view: unknown, spreadsheet: Spreadsheet) { - const rowNumber = spreadsheet.rowMenuPosition?.rowNumber - if (rowNumber !== undefined) { - spreadsheet.rowSet.rows[+rowNumber - 1]!.toggleSelect() - } - }, - }, -] - -const minHeight = 40 const defaultHeight = 440 /** * #stateModel SpreadsheetView * #category view + * + * extends + * - [BaseViewModel](../baseviewmodel) */ function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars -const model = types - .model('SpreadsheetView', { - /** - * #property - */ - type: types.literal('SpreadsheetView'), - /** - * #property - */ - offsetPx: 0, - /** - * #property - */ - height: types.optional( - types.refinement( - 'SpreadsheetViewHeight', - types.number, - n => n >= minHeight, - ), - defaultHeight, - ), - /** - * #property - */ - hideVerticalResizeHandle: false, - /** - * #property - */ - hideFilterControls: false, - /** - * #property - */ - filterControls: types.optional(FilterControlsModel, () => - FilterControlsModel.create({}), - ), - /** - * #property - * switch specifying whether we are showing the import wizard or the - * spreadsheet in our viewing area - */ - mode: types.optional( - types.enumeration('SpreadsheetViewMode', ['import', 'display']), - 'import', - ), - /** - * #property - */ - importWizard: types.optional(ImportWizardModel, () => - ImportWizardModel.create(), - ), - /** - * #property - */ - spreadsheet: types.maybe(SpreadsheetModel), - }) - .volatile(() => ({ - width: 400, - rowMenuItems: defaultRowMenuItems, - })) - .views(self => ({ - /** - * #getter - */ - get readyToDisplay() { - return !!self.spreadsheet && self.spreadsheet.isLoaded - }, - /** - * #getter - */ - get hideRowSelection() { - return !!getEnv(self).hideRowSelection - }, - /** - * #getter - */ - get outputRows() { - if (self.spreadsheet?.rowSet.isLoaded) { - const selected = self.spreadsheet.rowSet.selectedFilteredRows - if (selected.length) { - return selected - } - return self.spreadsheet.rowSet.sortedFilteredRows - } - return undefined - }, - /** - * #getter - */ - get assembly() { - const name = self.spreadsheet?.assemblyName - if (name) { - const assemblies = getSession(self).assemblies - return assemblies.find(asm => readConfObject(asm, 'name') === name) - } - return undefined - }, - })) - .actions(self => ({ - /** - * #action - */ - setRowMenuItems(newItems: MenuItem[]) { - self.rowMenuItems = newItems - }, - /** - * #action - */ - setWidth(newWidth: number) { - self.width = newWidth - return self.width - }, - /** - * #action - */ - setHeight(newHeight: number) { - self.height = Math.max(newHeight, minHeight) - return self.height - }, - /** - * #action - */ - resizeHeight(distance: number) { - const oldHeight = self.height - const newHeight = this.setHeight(self.height + distance) - return newHeight - oldHeight - }, - /** - * #action - */ - resizeWidth(distance: number) { - const oldWidth = self.width - const newWidth = this.setWidth(self.width + distance) - return newWidth - oldWidth - }, +function stateModelFactory() { + const ImportWizard = importWizardFactory() + const SpreadsheetModelType = spreadsheetModelFactory() + return types + .compose( + BaseViewModel, + types.model('SpreadsheetView', { + /** + * #property + */ + type: types.literal('SpreadsheetView'), + /** + * #property + */ + height: types.optional(types.number, defaultHeight), + /** + * #property + */ + hideVerticalResizeHandle: false, + /** + * #property + */ + importWizard: types.optional(ImportWizard, {}), + /** + * #property + */ + spreadsheet: types.maybe(SpreadsheetModelType), + }), + ) + .volatile(() => ({ + width: 400, + })) + .views(self => ({ + /** + * #getter + */ + get assemblyName() { + return self.spreadsheet?.assemblyName + }, + /** + * #getter + */ + get initialized() { + return self.spreadsheet?.initialized + }, + /** + * #getter + */ + get assembly() { + const name = self.spreadsheet?.assemblyName + return name ? getSession(self).assemblyManager.get(name) : undefined + }, + /** + * #getter + */ + get features() { + return self.spreadsheet?.features + }, + })) + .actions(self => ({ + /** + * #action + */ + setWidth(newWidth: number) { + self.width = newWidth + return self.width + }, + /** + * #action + */ + setHeight(newHeight: number) { + self.height = newHeight + return self.height + }, + /** + * #action + */ + resizeHeight(distance: number) { + const oldHeight = self.height + const newHeight = this.setHeight(self.height + distance) + return newHeight - oldHeight + }, + /** + * #action + */ + resizeWidth(distance: number) { + const oldWidth = self.width + const newWidth = this.setWidth(self.width + distance) + return newWidth - oldWidth + }, - /** - * #action - * load a new spreadsheet and set our mode to display it - */ - displaySpreadsheet(spreadsheet: SnapshotIn) { - self.filterControls.clearAllFilters() - self.spreadsheet = cast(spreadsheet) - self.mode = 'display' - }, - /** - * #action - */ - setImportMode() { - self.mode = 'import' - }, - /** - * #action - */ - setDisplayMode() { - if (self.readyToDisplay) { - self.mode = 'display' - } - }, - })) - .views(self => ({ - /** - * #method - */ - menuItems() { - return [ - { - label: 'Return to import form', - onClick: () => { - self.setImportMode() - }, - icon: FolderOpenIcon, - }, - ] - }, - })) + /** + * #action + * load a new spreadsheet and set our mode to display it + */ + displaySpreadsheet(spreadsheet: SpreadsheetData, assemblyName: string) { + // @ts-expect-error + self.spreadsheet = { assemblyName } + // @ts-expect-error + self.spreadsheet.setData(spreadsheet) + }, -const SpreadsheetView = types.compose(BaseViewModel, model) + /** + * #action + */ + clearData() { + self.spreadsheet = undefined + self.importWizard.setSpreadsheetFilehandle() + }, + })) + .views(self => ({ + /** + * #method + */ + menuItems() { + return [ + { + label: 'Return to import form', + onClick: () => { + self.clearData() + }, + icon: FolderOpenIcon, + }, + ] + }, + })) +} -export type SpreadsheetViewStateModel = typeof SpreadsheetView +export type SpreadsheetViewStateModel = ReturnType export type SpreadsheetViewModel = Instance -export default SpreadsheetView +export default stateModelFactory diff --git a/plugins/spreadsheet-view/src/SpreadsheetView/models/StaticRowSet.ts b/plugins/spreadsheet-view/src/SpreadsheetView/models/StaticRowSet.ts deleted file mode 100644 index 9dcb4608fa..0000000000 --- a/plugins/spreadsheet-view/src/SpreadsheetView/models/StaticRowSet.ts +++ /dev/null @@ -1,64 +0,0 @@ -import RowModel from './Row' -import { types, getParent } from 'mobx-state-tree' - -const StaticRowModel = types - .model('StaticRowSet', { - isLoaded: types.literal(true), - rows: types.array(RowModel), - }) - .views(self => ({ - get count() { - return self.rows.length - }, - - get passingFiltersCount() { - return this.sortedFilteredRows.length - }, - - get selectedCount() { - return this.selectedRows.length - }, - - get selectedAndPassingFiltersCount() { - return this.selectedFilteredRows.length - }, - - get sortedRows() { - const parent = getParent(self) - return [...self.rows].sort(parent.rowSortingComparisonFunction) - }, - - get selectedRows() { - return self.rows.filter(r => r.isSelected) - }, - - get selectedFilteredRows() { - const sheet = getParent(self) - - const view = getParent(sheet) - const { filterControls } = view - return this.selectedRows.filter(row => - filterControls.rowPassesFilters(sheet, row), - ) - }, - - // the set of all rows that pass the filters, sorted - get sortedFilteredRows() { - const sheet = getParent(self) - - const view = getParent(sheet) - const { filterControls } = view - return self.rows - .filter(row => filterControls.rowPassesFilters(sheet, row)) - .sort(sheet.rowSortingComparisonFunction) - }, - })) - .actions(self => ({ - unselectAll() { - self.rows.forEach(row => { - row.unSelect() - }) - }, - })) - -export default StaticRowModel diff --git a/plugins/sv-inspector/index.test.ts b/plugins/sv-inspector/index.test.ts deleted file mode 100644 index c5f4a7f8b2..0000000000 --- a/plugins/sv-inspector/index.test.ts +++ /dev/null @@ -1,3 +0,0 @@ -test('easy', () => { - expect(1).toBe(1) -}) diff --git a/plugins/sv-inspector/src/LaunchSvInspectorView/index.ts b/plugins/sv-inspector/src/LaunchSvInspectorView/index.ts index cf80050d24..834b371a11 100644 --- a/plugins/sv-inspector/src/LaunchSvInspectorView/index.ts +++ b/plugins/sv-inspector/src/LaunchSvInspectorView/index.ts @@ -10,27 +10,17 @@ export default function LaunchSvInspectorViewF(pluginManager: PluginManager) { session, assembly, uri, - fileType, }: { session: AbstractSessionModel assembly: string uri: string - fileType?: string }) => { const view = session.addView('SvInspectorView') as SvInspectorViewModel - const exts = uri.split('.') - let ext = exts.pop()?.toUpperCase() - if (ext === 'GZ') { - ext = exts.pop()?.toUpperCase() - } - - view.spreadsheetView.importWizard.setFileType(fileType || ext || '') view.spreadsheetView.importWizard.setSelectedAssemblyName(assembly) - view.spreadsheetView.importWizard.setFileSource({ + view.spreadsheetView.importWizard.setSpreadsheetFilehandle({ uri, locationType: 'UriLocation', }) - await view.spreadsheetView.importWizard.import(assembly) }, ) } diff --git a/plugins/sv-inspector/src/SvInspectorView/components/SvInspectorView.tsx b/plugins/sv-inspector/src/SvInspectorView/components/SvInspectorView.tsx index 63c1f75bff..a21cc848bc 100644 --- a/plugins/sv-inspector/src/SvInspectorView/components/SvInspectorView.tsx +++ b/plugins/sv-inspector/src/SvInspectorView/components/SvInspectorView.tsx @@ -1,4 +1,4 @@ -import React from 'react' +import React, { Suspense, useState } from 'react' import { observer } from 'mobx-react' import { makeStyles } from 'tss-react/mui' import { ResizeHandle } from '@jbrowse/core/ui' @@ -41,36 +41,42 @@ const SvInspectorView = observer(function ({ const { SpreadsheetViewReactComponent, CircularViewReactComponent, - showCircularView, + spreadsheetView, + circularView, } = model + const [initialCircWidth, setInitialCircWidth] = useState(0) + const [initialSpreadsheetWidth, setInitialSpreadsheetWidth] = useState(0) return (
- +
- {showCircularView ? ( - <> - { - const ret1 = model.circularView.resizeWidth(-distance) - return model.spreadsheetView.resizeWidth(-ret1) - }} - vertical - flexbox - className={classes.resizeHandleVert} - /> -
- - -
- - ) : null} + { + circularView.setWidth(initialCircWidth + total) + spreadsheetView.setWidth(initialSpreadsheetWidth - total) + return undefined + }} + onMouseDown={() => { + setInitialSpreadsheetWidth(spreadsheetView.width) + setInitialCircWidth(circularView.width) + }} + vertical + flexbox + className={classes.resizeHandleVert} + /> +
+ + + + +
+ ) : ( + + ) +}) + +export default SvInspectorViewContainer diff --git a/plugins/sv-inspector/src/SvInspectorView/index.ts b/plugins/sv-inspector/src/SvInspectorView/index.ts index 7cca9df6e1..22cc8c8315 100644 --- a/plugins/sv-inspector/src/SvInspectorView/index.ts +++ b/plugins/sv-inspector/src/SvInspectorView/index.ts @@ -8,7 +8,7 @@ import { IAnyStateTreeNode } from 'mobx-state-tree' import BreakpointSplitViewType from '@jbrowse/plugin-breakpoint-split-view/src/BreakpointSplitView/BreakpointSplitView' import { CircularViewModel } from '@jbrowse/plugin-circular-view' -function defaultOnChordClick( +async function defaultOnChordClick( feature: Feature, chordTrack: IAnyStateTreeNode, pluginManager: PluginManager, @@ -19,7 +19,15 @@ function defaultOnChordClick( const viewType = pluginManager.getViewType( 'BreakpointSplitView', ) as BreakpointSplitViewType - const viewSnapshot = viewType.snapshotFromBreakendFeature(feature, view) + const [assemblyName] = view.assemblyNames + if (!assemblyName) { + throw new Error('error trying to understand what assembly to use') + } + const viewSnapshot = await viewType.snapshotFromBreakendFeature({ + feature, + assemblyName, + session, + }) // try to center the offsetPx viewSnapshot.views[0]!.offsetPx -= view.width / 2 + 100 diff --git a/plugins/sv-inspector/src/SvInspectorView/models/SvInspectorView.ts b/plugins/sv-inspector/src/SvInspectorView/models/SvInspectorView.ts index 58954bfdd6..2917c8d93c 100644 --- a/plugins/sv-inspector/src/SvInspectorView/models/SvInspectorView.ts +++ b/plugins/sv-inspector/src/SvInspectorView/models/SvInspectorView.ts @@ -1,26 +1,17 @@ import clone from 'clone' -import { autorun, reaction } from 'mobx' +import { autorun, trace } from 'mobx' import { types, addDisposer, Instance } from 'mobx-state-tree' import PluginManager from '@jbrowse/core/PluginManager' -import { getSession, Region } from '@jbrowse/core/util' -import { readConfObject } from '@jbrowse/core/configuration' +import { getSession, notEmpty } from '@jbrowse/core/util' import { ElementId } from '@jbrowse/core/util/types/mst' import { BaseViewModel } from '@jbrowse/core/pluggableElementTypes/models' import { SpreadsheetViewStateModel } from '@jbrowse/plugin-spreadsheet-view' import { CircularViewStateModel } from '@jbrowse/plugin-circular-view' // icons -import OpenInNewIcon from '@mui/icons-material/OpenInNew' import FolderOpenIcon from '@mui/icons-material/FolderOpen' -// locals -import { - canOpenBreakpointSplitViewFromTableRow, - openBreakpointSplitViewFromTableRow, - getFeatureForRow, -} from './breakpointSplitViewFromTableRow' - /** * #stateModel SvInspectorView * #category view @@ -41,7 +32,6 @@ function SvInspectorViewF(pluginManager: PluginManager) { const minHeight = 400 const defaultHeight = 550 - const headerHeight = 52 const circularViewOptionsBarHeight = 52 return types .compose( @@ -60,130 +50,148 @@ function SvInspectorViewF(pluginManager: PluginManager) { /** * #property */ - height: types.optional( - types.refinement( - 'SvInspectorViewHeight', - types.number, - n => n >= minHeight, - ), - defaultHeight, - ), + height: types.optional(types.number, defaultHeight), /** * #property */ onlyDisplayRelevantRegionsInCircularView: false, - /** - * #property - * switch specifying whether we are showing the import wizard or the - * spreadsheet in our viewing area - */ - mode: types.optional( - types.enumeration('SvInspectorViewMode', ['import', 'display']), - 'import', - ), + /** * #property */ - spreadsheetView: types.optional(SpreadsheetModel, () => - SpreadsheetModel.create({ - type: 'SpreadsheetView', - hideVerticalResizeHandle: true, - }), - ), + spreadsheetView: types.optional(SpreadsheetModel, { + hideVerticalResizeHandle: true, + type: 'SpreadsheetView', + }), /** * #property */ - circularView: types.optional(CircularModel, () => - CircularModel.create({ - type: 'CircularView', - hideVerticalResizeHandle: true, - hideTrackSelectorButton: true, - disableImportForm: true, - }), - ), + circularView: types.optional(CircularModel, { + type: 'CircularView', + hideVerticalResizeHandle: true, + hideTrackSelectorButton: true, + disableImportForm: true, + }), }), ) .volatile(() => ({ + /** + * #volatile + */ width: 800, + /** + * #volatile + */ + SpreadsheetViewReactComponent: SpreadsheetViewType.ReactComponent, + /** + * #volatile + */ + CircularViewReactComponent: CircularViewType.ReactComponent, + /** + * #volatile + */ + circularViewOptionsBarHeight, })) .views(self => ({ /** * #getter */ - get selectedRows() { - return self.spreadsheetView.spreadsheet?.rowSet.selectedRows + get initialized() { + return self.spreadsheetView.initialized }, /** * #getter */ get assemblyName() { - const { assembly } = self.spreadsheetView - return assembly - ? (readConfObject(assembly, 'name') as string) + return self.spreadsheetView.assemblyName + }, + /** + * #getter + */ + get assembly() { + const { assemblyManager } = getSession(self) + return this.assemblyName + ? assemblyManager.get(this.assemblyName) : undefined }, /** * #getter */ - get showCircularView() { - return self.spreadsheetView.mode === 'display' + get circularViewInitialized() { + return self.spreadsheetView.initialized }, /** * #getter */ get features() { - const session = getSession(self) - const { spreadsheetView } = self - const { outputRows = [] } = spreadsheetView - return outputRows - .map((r, i) => getFeatureForRow(session, spreadsheetView, r, i)) - .filter(f => !!f) + return self.spreadsheetView.features }, /** * #getter */ get featuresAdapterConfigSnapshot() { - return { - type: 'FromConfigAdapter', - features: this.features, - } + return this.features + ? { + type: 'FromConfigAdapter', + features: this.features.map(f => f.toJSON()) || [], + } + : undefined }, /** * #getter */ get featureRefNames() { - const refs = this.features.map(r => r.refName) - const CHR2 = this.features.flatMap(r => r.INFO?.CHR2).filter(f => !!f) - return [...refs, ...CHR2] + if (this.features) { + return [ + ...this.features.map(r => r.get('refName')), + ...this.features + .flatMap(r => r.get('INFO')?.CHR2 as string) + .filter(notEmpty), + ...this.features + .flatMap(r => r.get('mate')?.refName as string) + .filter(notEmpty), + ] + } + return undefined + }, + /** + * #getter + */ + get featureRefSet() { + const a = this.assembly + return a?.initialized + ? new Set( + this.featureRefNames?.map(r => a.getCanonicalRefNameOrDefault(r)), + ) + : undefined }, /** * #getter */ get featuresCircularTrackConfiguration() { - return { - type: 'VariantTrack', - trackId: `sv-inspector-variant-track-${self.id}`, - name: 'features from tabular data', - adapter: this.featuresAdapterConfigSnapshot, - assemblyNames: [this.assemblyName], - displays: [ - { - type: 'ChordVariantDisplay', - displayId: `sv-inspector-variant-track-chord-display-${self.id}`, - onChordClick: - 'jexl:defaultOnChordClick(feature, track, pluginManager)', - renderer: { type: 'StructuralVariantChordRenderer' }, - }, - ], - } + return this.featuresAdapterConfigSnapshot + ? { + type: 'VariantTrack', + trackId: `sv-inspector-variant-track-${self.id}`, + name: 'features from tabular data', + adapter: this.featuresAdapterConfigSnapshot, + assemblyNames: [this.assemblyName], + displays: [ + { + type: 'ChordVariantDisplay', + displayId: `sv-inspector-variant-track-chord-display-${self.id}`, + onChordClick: + 'jexl:defaultOnChordClick(feature, track, pluginManager)', + renderer: { + type: 'StructuralVariantChordRenderer', + }, + }, + ], + } + : undefined }, })) - .volatile(() => ({ - SpreadsheetViewReactComponent: SpreadsheetViewType.ReactComponent, - CircularViewReactComponent: CircularViewType.ReactComponent, - circularViewOptionsBarHeight, - })) .actions(self => ({ /** * #action @@ -198,30 +206,11 @@ function SvInspectorViewF(pluginManager: PluginManager) { self.height = Math.max(newHeight, minHeight) return self.height }, - /** - * #action - */ - setImportMode() { - self.spreadsheetView.setImportMode() - }, - /** - * #action - */ - setDisplayMode() { - self.spreadsheetView.setDisplayMode() - }, - - /** - * #action - */ - setDisplayedRegions(regions: Region[]) { - self.circularView.setDisplayedRegions(regions) - }, /** * #action */ setOnlyDisplayRelevantRegionsInCircularView(val: boolean) { - self.onlyDisplayRelevantRegionsInCircularView = Boolean(val) + self.onlyDisplayRelevantRegionsInCircularView = val }, })) .views(self => ({ @@ -233,7 +222,7 @@ function SvInspectorViewF(pluginManager: PluginManager) { { label: 'Return to import form', onClick: () => { - self.setImportMode() + self.spreadsheetView.clearData() }, icon: FolderOpenIcon, }, @@ -253,147 +242,71 @@ function SvInspectorViewF(pluginManager: PluginManager) { // synchronize subview widths addDisposer( self, - autorun( - () => { - const borderWidth = 1 - if (self.showCircularView) { - const spreadsheetWidth = Math.round(self.width * 0.66) - const circularViewWidth = self.width - spreadsheetWidth - self.spreadsheetView.setWidth(spreadsheetWidth - borderWidth) - self.circularView.setWidth(circularViewWidth) - } else { - self.spreadsheetView.setWidth(self.width) - } - }, - { name: 'SvInspectorView width binding' }, - ), + autorun(() => { + const borderWidth = 1 + if (self.circularViewInitialized) { + const spreadsheetWidth = Math.round(self.width * 0.66) + const circularViewWidth = self.width - spreadsheetWidth + self.spreadsheetView.setWidth(spreadsheetWidth - borderWidth) + self.circularView.setWidth(circularViewWidth) + } else { + self.spreadsheetView.setWidth(self.width) + } + }), ) // synchronize subview heights addDisposer( self, - autorun( - () => { - self.spreadsheetView.setHeight(self.height - headerHeight) - self.circularView.setHeight( - self.height - headerHeight - circularViewOptionsBarHeight, - ) - }, - { name: 'SvInspectorView height binding' }, - ), + autorun(() => { + const { height } = self + self.spreadsheetView.setHeight(height) + self.circularView.setHeight(height - circularViewOptionsBarHeight) + }), ) - - // bind circularview displayedRegions to spreadsheet assembly, mediated - // by the onlyRelevantRegions toggle + // bind CircularView's displayedRegions to spreadsheet assembly, + // mediated by the onlyRelevantRegions toggle addDisposer( self, - autorun( - async () => { - const { - assemblyName, - onlyDisplayRelevantRegionsInCircularView, - circularView, - featureRefNames, - } = self - const { tracks } = circularView - const { assemblyManager } = getSession(self) - if (!assemblyName) { + autorun(async () => { + const { + onlyDisplayRelevantRegionsInCircularView, + circularView, + featureRefSet, + assembly, + } = self + try { + if (circularView.volatileWidth === undefined) { return } - const asm = await assemblyManager.waitForAssembly(assemblyName) - if (!asm) { - return - } - - const { getCanonicalRefName, regions = [] } = asm - if (onlyDisplayRelevantRegionsInCircularView) { - if (tracks.length === 1) { - try { - // canonicalize the store's ref names if necessary - const refSet = new Set( - featureRefNames.map(r => getCanonicalRefName(r) || r), - ) - - circularView.setDisplayedRegions( - clone(regions.filter(r => refSet.has(r.refName))), - ) - } catch (e) { - circularView.setError(e) - } + if (assembly?.regions && featureRefSet) { + if (onlyDisplayRelevantRegionsInCircularView) { + circularView.setDisplayedRegions( + clone( + assembly.regions.filter(r => + featureRefSet.has(r.refName), + ), + ), + ) + } else { + circularView.setDisplayedRegions(assembly.regions) } - } else { - circularView.setDisplayedRegions(regions) } - }, - { name: 'SvInspectorView displayed regions bind' }, - ), - ) - - // bind circularview tracks to our track snapshot view - addDisposer( - self, - reaction( - () => ({ - generatedTrackConf: self.featuresCircularTrackConfiguration, - assemblyName: self.assemblyName, - }), - data => { - const { assemblyName, generatedTrackConf } = data - const { circularView } = self - // hide any visible tracks - circularView.tracks.forEach(t => - circularView.hideTrack(t.configuration.trackId), - ) - - // put our track in as the only track - if (assemblyName) { - // @ts-expect-error - circularView.addTrackConf(generatedTrackConf, { - assemblyName, - }) - } - }, - { - name: 'SvInspectorView track configuration binding', - fireImmediately: true, - }, - ), + } catch (e) { + console.error(e) + circularView.setError(e) + } + }), ) - - // bind spreadsheetView row menu actions to us + // bind CircularView tracks to our track snapshot view addDisposer( self, autorun(() => { - self.spreadsheetView.setRowMenuItems( - // these are the MenuItem entries for the row menu actions in the - // spreadsheet view. these are installed into the child - // SpreadsheetView using an autorun below - [ - { - label: 'Open split detail view', - icon: OpenInNewIcon, - // @ts-expect-error - disabled(spreadsheetView, spreadsheet, rowNumber, row) { - return !canOpenBreakpointSplitViewFromTableRow( - self, - spreadsheetView, - spreadsheet, - row, - rowNumber, - ) - }, - - onClick(spreadsheetView, spreadsheet, rowNumber, row) { - openBreakpointSplitViewFromTableRow( - self, - spreadsheetView, - spreadsheet, - row, - rowNumber, - ) - }, - }, - ], - ) + const { featuresCircularTrackConfiguration } = self + const { circularView } = self + if (featuresCircularTrackConfiguration) { + circularView.clearTracks() + circularView.addTrackConf(featuresCircularTrackConfiguration) + } }), ) }, diff --git a/plugins/sv-inspector/src/SvInspectorView/models/adhocFeatureUtils.ts b/plugins/sv-inspector/src/SvInspectorView/models/adhocFeatureUtils.ts deleted file mode 100644 index a53217bd8b..0000000000 --- a/plugins/sv-inspector/src/SvInspectorView/models/adhocFeatureUtils.ts +++ /dev/null @@ -1,153 +0,0 @@ -// @ts-nocheck -// this file contains the rather verbose functions for -// creating features from CSV/TSV lines -import { parseLocString } from '@jbrowse/core/util' - -export function makeAdHocFeature( - columns, - columnsAlreadyUsedInLocations, - row, - loc1, - loc2, - rowNumber, -) { - // load all the other data in the row into an `otherData` object - const otherData = {} - columns.forEach((column, columnNumber) => { - if (columnsAlreadyUsedInLocations.includes(columnNumber)) { - return - } - let { text } = row.cells[columnNumber] - if (column.dataType.type === 'Number') { - text = Number.parseFloat(text) - } - otherData[column.name] = text - }) - - // make the final feature data out of otherData + the parsed locations - return { - ...otherData, - uniqueId: `sv-inspector-adhoc-${rowNumber}`, - refName: loc1.refName, - start: loc1.start, - end: loc1.end, - mate: { - refName: loc2.refName, - start: loc2.start, - end: loc2.end, - }, - } -} - -export function makeAdHocSvFeatureFromTwoLocations( - columns, - locationColumnNumbers, - row, - rowNumber, - isValidRefName, -) { - // use the first two locations we found (first according to *displayed* order) - const loc1 = parseLocString( - row.cells[locationColumnNumbers[0]].text, - isValidRefName, - ) - const loc2 = parseLocString( - row.cells[locationColumnNumbers[1]].text, - isValidRefName, - ) - - const columnsAlreadyUsedInLocations = [ - locationColumnNumbers[0], - locationColumnNumbers[1], - ] - - return makeAdHocFeature( - columns, - columnsAlreadyUsedInLocations, - row, - loc1, - loc2, - rowNumber, - ) -} - -export function makeAdHocSvFeatureFromTwoRefStartEndSets( - columns, - locRefColumnNumbers, - locStartColumnNumbers, - locEndColumnNumbers, - row, - rowNumber, -) { - const textOf = colno => row.cells[colno].text - const loc1 = { - refName: textOf(locRefColumnNumbers[0]), - start: Number.parseInt(textOf(locStartColumnNumbers[0]), 10) - 1, - end: Number.parseInt(textOf(locEndColumnNumbers[0]), 10), - } - const loc2 = { - refName: textOf(locRefColumnNumbers[1]), - start: Number.parseInt(textOf(locStartColumnNumbers[1]), 10) - 1, - end: Number.parseInt(textOf(locEndColumnNumbers[1]), 10), - } - const columnsAlreadyUsedInLocations = [ - locRefColumnNumbers[0], - locStartColumnNumbers[0], - locEndColumnNumbers[0], - locRefColumnNumbers[1], - locStartColumnNumbers[1], - locEndColumnNumbers[1], - ] - return makeAdHocFeature( - columns, - columnsAlreadyUsedInLocations, - row, - loc1, - loc2, - rowNumber, - ) -} - -// makes a feature data object (passed as `data` to a SimpleFeature constructor) -// out of table row if the row has 2 location columns. undefined if not -export function makeAdHocSvFeature(sheet, rowNumber, row, isValidRefName) { - const { columns, columnDisplayOrder } = sheet - const columnTypes = {} - columnDisplayOrder.forEach(columnNumber => { - const columnDefinition = columns[columnNumber] - if (!columnTypes[columnDefinition.dataType.type]) { - columnTypes[columnDefinition.dataType.type] = [] - } - columnTypes[columnDefinition.dataType.type].push(columnNumber) - }) - const locationColumnNumbers = columnTypes.LocString || [] - const locStartColumnNumbers = columnTypes.LocStart || [] - const locEndColumnNumbers = columnTypes.LocEnd || [] - const locRefColumnNumbers = columnTypes.LocRef || [] - - // if we have 2 or more columns of type location, make a feature from them - if (locationColumnNumbers.length >= 2) { - return makeAdHocSvFeatureFromTwoLocations( - columns, - locationColumnNumbers, - row, - rowNumber, - isValidRefName, - ) - } - if ( - locRefColumnNumbers.length >= 2 && - locStartColumnNumbers.length >= 2 && - locEndColumnNumbers.length >= 2 - ) { - return makeAdHocSvFeatureFromTwoRefStartEndSets( - columns, - locRefColumnNumbers, - locStartColumnNumbers, - locEndColumnNumbers, - row, - rowNumber, - ) - } - return undefined -} diff --git a/plugins/sv-inspector/src/SvInspectorView/models/breakpointSplitViewFromTableRow.ts b/plugins/sv-inspector/src/SvInspectorView/models/breakpointSplitViewFromTableRow.ts deleted file mode 100644 index c28e777182..0000000000 --- a/plugins/sv-inspector/src/SvInspectorView/models/breakpointSplitViewFromTableRow.ts +++ /dev/null @@ -1,85 +0,0 @@ -// @ts-nocheck -import { SimpleFeature, getEnv, getSession } from '@jbrowse/core/util' -import { makeAdHocSvFeature } from './adhocFeatureUtils' - -export function getFeatureForRow(session, spreadsheetView, row, rowNumber) { - return ( - row.extendedData?.vcfFeature || - row.extendedData?.feature || - makeAdHocSvFeature( - spreadsheetView.spreadsheet, - rowNumber, - row, - session.assemblyManager.isValidRefName, - ) - ) -} - -export function breakpointSplitViewSnapshotFromTableRow( - svInspectorView, - spreadsheetView, - spreadsheet, - row, - rowNumber, -) { - const { pluginManager } = getEnv(svInspectorView) - const session = getSession(spreadsheetView) - const featureData = getFeatureForRow(session, spreadsheet, row, rowNumber) - - if (featureData) { - const feature = new SimpleFeature(featureData) - session.setSelection(feature) - return pluginManager - .getViewType('BreakpointSplitView') - .snapshotFromBreakendFeature(feature, svInspectorView.circularView) - } - return undefined -} - -export function openBreakpointSplitViewFromTableRow( - svInspectorView, - spreadsheetView, - spreadsheet, - row, - rowNumber, -) { - const viewSnapshot = breakpointSplitViewSnapshotFromTableRow( - svInspectorView, - spreadsheetView, - spreadsheet, - row, - rowNumber, - ) - if (viewSnapshot) { - // try to center the offsetPx - const { circularView } = svInspectorView - viewSnapshot.views[0].offsetPx -= circularView.width / 2 + 100 - viewSnapshot.views[1].offsetPx -= circularView.width / 2 + 100 - - const session = getSession(spreadsheetView) - session.addView('BreakpointSplitView', viewSnapshot) - } -} - -export function canOpenBreakpointSplitViewFromTableRow( - svInspectorView, - spreadsheetView, - spreadsheet, - row, - rowNumber, -) { - try { - return Boolean( - breakpointSplitViewSnapshotFromTableRow( - svInspectorView, - spreadsheetView, - spreadsheet, - row, - rowNumber, - ), - ) - } catch (e) { - console.error('Unable to open breakpoint split view from table row', e) - return false - } -} diff --git a/plugins/text-indexing/index.test.ts b/plugins/text-indexing/index.test.ts deleted file mode 100644 index c5f4a7f8b2..0000000000 --- a/plugins/text-indexing/index.test.ts +++ /dev/null @@ -1,3 +0,0 @@ -test('easy', () => { - expect(1).toBe(1) -}) diff --git a/plugins/variants/src/LinearVariantDisplay/configSchema.ts b/plugins/variants/src/LinearVariantDisplay/configSchema.ts index 2a80ada3a0..ade30430e1 100644 --- a/plugins/variants/src/LinearVariantDisplay/configSchema.ts +++ b/plugins/variants/src/LinearVariantDisplay/configSchema.ts @@ -5,9 +5,12 @@ import { linearBasicDisplayConfigSchemaFactory } from '@jbrowse/plugin-linear-ge /** * #config LinearVariantDisplay - * mostly empty, this display type is very much - * like a `FeatureTrack` with a `LinearBasicDisplay` except it has a custom - * feature details widget + * + * mostly empty, this display type is very much like a `FeatureTrack` with a + * `LinearBasicDisplay` except it has a custom feature details widget + * + * extends + * - [LinearBasicDisplay](../linearbasicdisplay) */ function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars diff --git a/plugins/variants/src/LinearVariantDisplay/model.ts b/plugins/variants/src/LinearVariantDisplay/model.ts index fc1ea0aab7..f55121a911 100644 --- a/plugins/variants/src/LinearVariantDisplay/model.ts +++ b/plugins/variants/src/LinearVariantDisplay/model.ts @@ -14,9 +14,8 @@ import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration' /** * #stateModel LinearVariantDisplay - * similar to basic display, but provides custom widget on feature click - * extends * + * extends * - [LinearBasicDisplay](../linearbasicdisplay) */ export default function stateModelFactory( diff --git a/plugins/variants/src/VariantFeatureWidget/LaunchBreakendPanel.tsx b/plugins/variants/src/VariantFeatureWidget/LaunchBreakendPanel.tsx index e35e7e361d..88b38c86cc 100644 --- a/plugins/variants/src/VariantFeatureWidget/LaunchBreakendPanel.tsx +++ b/plugins/variants/src/VariantFeatureWidget/LaunchBreakendPanel.tsx @@ -51,7 +51,7 @@ function LocStringList({ } } catch (e) { console.error(e) - session.notify(`${e}`) + session.notifyError(`${e}`, e) } }} > @@ -92,7 +92,7 @@ function LaunchBreakpointSplitViewPanel({ BreakendMultiLevelOptionDialog, { handleClose, - model, + session, feature: simpleFeature, // @ts-expect-error viewType, @@ -112,7 +112,7 @@ function LaunchBreakpointSplitViewPanel({ BreakendSingleLevelOptionDialog, { handleClose, - model, + session, feature: simpleFeature, // @ts-expect-error viewType, diff --git a/products/jbrowse-aws-lambda-functions/saved-sessions/jbrowse_analytics.js b/products/jbrowse-aws-lambda-functions/saved-sessions/jbrowse_analytics.js index c5126413ea..5f7f50a856 100644 --- a/products/jbrowse-aws-lambda-functions/saved-sessions/jbrowse_analytics.js +++ b/products/jbrowse-aws-lambda-functions/saved-sessions/jbrowse_analytics.js @@ -15,7 +15,7 @@ function recordStats(event, context, done) { stats.referer = headers.Referer || headers.referer || null stats.acceptLanguage = headers['Accept-Language'] || null stats.acceptCharset = headers['Accept-Charset'] || null - + stats.host = stats.referer ? url_parser.parse(stats.referer).host : null if (stats.host?.startsWith('www.')) { stats.host = stats.host.slice(4) diff --git a/products/jbrowse-desktop/src/indexJobsModel.ts b/products/jbrowse-desktop/src/indexJobsModel.ts index 02196dd7a5..b672632a58 100644 --- a/products/jbrowse-desktop/src/indexJobsModel.ts +++ b/products/jbrowse-desktop/src/indexJobsModel.ts @@ -317,19 +317,10 @@ export default function jobsModelFactory(_pluginManager: PluginManager) { if (isAbortException(e)) { self.session?.notify('Cancelled job', 'info') } else { - self.session?.notify( - `An error occurred while indexing: ${e}`, - 'error', - { - name: 'Retry', - onClick: () => { - this.queueJob(entry) - }, - }, - ) + self.session?.notifyError(`${e}`, e) } - // remove job from queue but since it was not successful - // do not add to finished list + // remove job from queue but since it was not successful do not add + // to finished list this.dequeueJob() } // clear diff --git a/products/jbrowse-web/src/SessionLoader.ts b/products/jbrowse-web/src/SessionLoader.ts index c53b8568a6..023c86169d 100644 --- a/products/jbrowse-web/src/SessionLoader.ts +++ b/products/jbrowse-web/src/SessionLoader.ts @@ -446,7 +446,7 @@ export function loadSessionSpec( ) } catch (e) { console.error(e) - rootModel.session?.notify(`${e}`) + rootModel.session?.notifyError(`${e}`, e) } } } diff --git a/products/jbrowse-web/src/components/JBrowse.tsx b/products/jbrowse-web/src/components/JBrowse.tsx index c92b744130..586f653f25 100644 --- a/products/jbrowse-web/src/components/JBrowse.tsx +++ b/products/jbrowse-web/src/components/JBrowse.tsx @@ -54,7 +54,8 @@ const JBrowse = observer(function ({ throw new Error(`HTTP ${response.status} (${message})`) } } catch (e) { - session?.notify(`Admin server error: ${e}`) + console.error(e) + session?.notifyError(`Admin server error: ${e}`, e) } }) }, [jbrowse, session, adminKey, adminServer, configPath]) diff --git a/products/jbrowse-web/src/tests/SVInspector.test.tsx b/products/jbrowse-web/src/tests/SVInspector.test.tsx index 0ef50befd8..4e426bc1d5 100644 --- a/products/jbrowse-web/src/tests/SVInspector.test.tsx +++ b/products/jbrowse-web/src/tests/SVInspector.test.tsx @@ -14,7 +14,6 @@ test( 'opens a vcf.gz file in the sv inspector view', () => mockConsoleWarn(async () => { - const consoleMock = jest.spyOn(console, 'warn').mockImplementation() const { session, findByTestId, getByTestId, findByText } = await createView() @@ -36,8 +35,6 @@ test( // confirm breakpoint split view opened expect(session.views.length).toBe(3) expect(session.views[2]!.displayName).toBe('bnd_A split detail') - - consoleMock.mockRestore() }), 60000, )