@apollo-annotation/jbrowse-plugin-apollo 0.1.19 → 0.1.21

package/dist/index.esm.js

@@ -49,7 +49,7 @@ import ExpandMoreIcon from '@mui/icons-material/ExpandMore';
 import ErrorIcon from '@mui/icons-material/Error';
 import SaveIcon from '@mui/icons-material/Save';
 
-var version = "0.1.19";
+var version = "0.1.21";
 
 const ApolloConfigSchema = ConfigurationSchema('ApolloInternetAccount', {
     baseURL: {
@@ -312,7 +312,7 @@ function AddAssembly({ changeManager, handleClose, session, }) {
             const fileUploadChangeBase = {
                 assembly: new ObjectID().toHexString(),
                 assemblyName,
-                fileId,
+                fileIds: { fa: fileId },
             };
             change =
                 fileType === FileType.GFF3 && importFeatures
@@ -2421,7 +2421,26 @@ function ManageUsers({ changeManager, handleClose, session, }) {
             headerName: 'Role',
             width: 140,
             type: 'singleSelect',
-            valueOptions: ['', 'readOnly', 'user', 'admin'],
+            valueOptions: ['readOnly', 'user', 'admin', 'none'],
+            getOptionLabel(value) {
+                switch (value) {
+                    case 'readOnly': {
+                        return 'Read-only';
+                    }
+                    case 'user': {
+                        return 'User';
+                    }
+                    case 'admin': {
+                        return 'Admin';
+                    }
+                    case 'none': {
+                        return 'None';
+                    }
+                    default: {
+                        return 'unknown';
+                    }
+                }
+            },
             editable: true,
         },
         {
@@ -4037,7 +4056,7 @@ class ApolloSequenceAdapter extends BaseSequenceAdapter {
     freeResources( /* { region } */) { }
 }
 
-var configSchema$2 = ConfigurationSchema('ApolloSequenceAdapter', {
+var configSchema$3 = ConfigurationSchema('ApolloSequenceAdapter', {
     assemblyId: {
         type: 'string',
         defaultValue: '',
@@ -4047,7 +4066,7 @@ var configSchema$2 = ConfigurationSchema('ApolloSequenceAdapter', {
 function installApolloSequenceAdapter(pluginManager) {
     pluginManager.addAdapterType(() => new AdapterType({
         name: 'ApolloSequenceAdapter',
-        configSchema: configSchema$2,
+        configSchema: configSchema$3,
         adapterMetadata: {
             category: undefined,
             hiddenFromGUI: true,
@@ -4641,7 +4660,7 @@ class ApolloTextSearchAdapter extends BaseAdapter {
     freeResources() { }
 }
 
-var configSchema$1 = ConfigurationSchema('ApolloTextSearchAdapter', {
+var configSchema$2 = ConfigurationSchema('ApolloTextSearchAdapter', {
     assemblyNames: {
         type: 'stringArray',
         defaultValue: [],
@@ -4664,7 +4683,7 @@ function installApolloTextSearchAdapter(pluginManager) {
     pluginManager.addTextSearchAdapterType(() => new TextSearchAdapterType({
         name: 'ApolloTextSearchAdapter',
         displayName: 'Apollo text search adapter',
-        configSchema: configSchema$1,
+        configSchema: configSchema$2,
         AdapterClass: ApolloTextSearchAdapter,
         description: 'Apollo Text Search adapter',
     }));
@@ -5967,11 +5986,7 @@ const ApolloTranscriptDetailsWidget = observer(function ApolloTranscriptDetails(
         React__default.createElement(TranscriptSequence, { feature: feature, session: apolloSession, assembly: currentAssembly._id || '', refName: refName })));
 });
 
-function configSchemaFactory$1(pluginManager) {
-    const LGVPlugin = pluginManager.getPlugin('LinearGenomeViewPlugin');
-    const { baseLinearDisplayConfigSchema } = LGVPlugin.exports;
-    return ConfigurationSchema('LinearApolloDisplay', { height: { type: 'number', defaultValue: 500 } }, { baseConfiguration: baseLinearDisplayConfigSchema, explicitlyTyped: true });
-}
+const configSchema$1 = ConfigurationSchema('LinearApolloDisplay', {}, { explicitIdentifier: 'displayId', explicitlyTyped: true });
 
 function handleFeatureTypeChange(changeManager, feature, oldType, newType) {
     const featureId = feature._id;
@@ -6215,56 +6230,16 @@ const NumberCell = observer(function NumberCell({ initialValue, notifyError, onC
             } })));
 });
 
-// TODO: get this added to LGV runtime exports so we don't have to duplicate it
 const minDisplayHeight = 20;
-/**
- * #stateModel TrackHeightMixin
- * #category display
- */
-const TrackHeightMixin = types
-    .model({
-    heightPreConfig: types.maybe(types.refinement('displayHeight', types.number, (n) => n >= minDisplayHeight)),
-})
-    .volatile(() => ({
-    scrollTop: 0,
-}))
-    .views((self) => ({
-    get height() {
-        // @ts-expect-error getConf needs self.configuration
-        return self.heightPreConfig ?? getConf(self, 'height');
-    },
-}))
-    .actions((self) => ({
-    setScrollTop(scrollTop) {
-        self.scrollTop = scrollTop;
-    },
-    setHeight(displayHeight) {
-        self.heightPreConfig = Math.max(displayHeight, minDisplayHeight);
-        return self.height;
-    },
-    resizeHeight(distance) {
-        const oldHeight = self.height;
-        const newHeight = this.setHeight(self.height + distance);
-        return newHeight - oldHeight;
-    },
-}));
-
 function baseModelFactory(_pluginManager, configSchema) {
-    // TODO: Restore this when TRackHeightMixin is in LGV runtime exports
-    // const LGVPlugin = pluginManager.getPlugin(
-    //   'LinearGenomeViewPlugin',
-    // ) as LinearGenomeViewPlugin
-    // const { TrackHeightMixin } = LGVPlugin.exports
-    return types
-        .compose(BaseDisplay, TrackHeightMixin)
-        .named('BaseLinearApolloDisplay')
+    return BaseDisplay.named('BaseLinearApolloDisplay')
         .props({
         type: types.literal('LinearApolloDisplay'),
         configuration: ConfigurationReference(configSchema),
+        graphical: true,
+        table: false,
+        heightPreConfig: types.maybe(types.refinement('displayHeight', types.number, (n) => n >= minDisplayHeight)),
     })
-        .volatile((self) => ({
-        lgv: getContainingView(self),
-    }))
         .views((self) => {
         const { configuration, renderProps: superRenderProps } = self;
         return {
@@ -6277,6 +6252,26 @@ function baseModelFactory(_pluginManager, configSchema) {
             },
         };
     })
+        .volatile(() => ({
+        scrollTop: 0,
+    }))
+        .views((self) => ({
+        get lgv() {
+            return getContainingView(self);
+        },
+        get height() {
+            if (self.heightPreConfig) {
+                return self.heightPreConfig;
+            }
+            if (self.graphical && self.table) {
+                return 500;
+            }
+            if (self.graphical) {
+                return 200;
+            }
+            return 300;
+        },
+    }))
         .views((self) => ({
         get rendererTypeName() {
             return self.configuration.renderer.type;
@@ -6333,6 +6328,73 @@ function baseModelFactory(_pluginManager, configSchema) {
                 .apolloSelectedFeature;
         },
     }))
+        .actions((self) => ({
+        setScrollTop(scrollTop) {
+            self.scrollTop = scrollTop;
+        },
+        setHeight(displayHeight) {
+            self.heightPreConfig = Math.max(displayHeight, minDisplayHeight);
+            return self.height;
+        },
+        resizeHeight(distance) {
+            const oldHeight = self.height;
+            const newHeight = this.setHeight(self.height + distance);
+            return newHeight - oldHeight;
+        },
+        showGraphicalOnly() {
+            self.graphical = true;
+            self.table = false;
+        },
+        showTableOnly() {
+            self.graphical = false;
+            self.table = true;
+        },
+        showGraphicalAndTable() {
+            self.graphical = true;
+            self.table = true;
+        },
+    }))
+        .views((self) => {
+        const { trackMenuItems: superTrackMenuItems } = self;
+        return {
+            trackMenuItems() {
+                const { graphical, table } = self;
+                return [
+                    ...superTrackMenuItems(),
+                    {
+                        type: 'subMenu',
+                        label: 'Appearance',
+                        subMenu: [
+                            {
+                                label: 'Show graphical display',
+                                type: 'radio',
+                                checked: graphical && !table,
+                                onClick: () => {
+                                    self.showGraphicalOnly();
+                                },
+                            },
+                            {
+                                label: 'Show table display',
+                                type: 'radio',
+                                checked: table && !graphical,
+                                onClick: () => {
+                                    self.showTableOnly();
+                                },
+                            },
+                            {
+                                label: 'Show both graphical and table display',
+                                type: 'radio',
+                                checked: table && graphical,
+                                onClick: () => {
+                                    self.showGraphicalAndTable();
+                                },
+                            },
+                        ],
+                    },
+                ];
+            },
+        };
+    })
         .actions((self) => ({
         setSelectedFeature(feature) {
             self.session.apolloSetSelectedFeature(feature);
@@ -8346,7 +8408,7 @@ const useStyles$1 = makeStyles()((theme) => ({
 const LinearApolloDisplay = observer(function LinearApolloDisplay(props) {
     const theme = useTheme();
     const { model } = props;
-    const { apolloRowHeight, contextMenuItems: getContextMenuItems, cursor, featuresHeight, isShown, onMouseDown, onMouseLeave, onMouseMove, onMouseUp, regionCannotBeRendered, session, setCanvas, setCollaboratorCanvas, setOverlayCanvas, setSeqTrackCanvas, setSeqTrackOverlayCanvas, setTheme, tabularEditor, } = model;
+    const { apolloRowHeight, contextMenuItems: getContextMenuItems, cursor, featuresHeight, isShown, onMouseDown, onMouseLeave, onMouseMove, onMouseUp, regionCannotBeRendered, session, setCanvas, setCollaboratorCanvas, setOverlayCanvas, setSeqTrackCanvas, setSeqTrackOverlayCanvas, setTheme, } = model;
     const { classes } = useStyles$1();
     const lgv = getContainingView(model);
     useEffect(() => {
@@ -8403,9 +8465,7 @@ const LinearApolloDisplay = observer(function LinearApolloDisplay(props) {
             React__default.createElement("canvas", { ref: async (node) => {
                     await Promise.resolve();
                     setOverlayCanvas(node);
-                }, width: lgv.dynamicBlocks.totalWidthPx, height: featuresHeight, onMouseMove: onMouseMove, onMouseLeave: onMouseLeave, onMouseDown: onMouseDown, onMouseUp: onMouseUp, onClick: () => {
-                    tabularEditor.showPane();
-                }, className: classes.canvas, style: { cursor: cursor ?? 'default' }, "data-testid": "overlayCanvas" }),
+                }, width: lgv.dynamicBlocks.totalWidthPx, height: featuresHeight, onMouseMove: onMouseMove, onMouseLeave: onMouseLeave, onMouseDown: onMouseDown, onMouseUp: onMouseUp, className: classes.canvas, style: { cursor: cursor ?? 'default' }, "data-testid": "overlayCanvas" }),
             lgv.displayedRegions.flatMap((region, idx) => {
                 const assembly = assemblyManager.get(region.assemblyName);
                 return [...session.apolloDataStore.checkResults.values()]
@@ -8541,25 +8601,33 @@ const AccordionControl = observer(function AccordionControl({ onClick, onResize,
 });
 const DisplayComponent = observer(function DisplayComponent({ model, ...other }) {
     const { classes } = useStyles();
-    const { height: overallHeight, isShown, selectedFeature, tabularEditor, toggleShown, } = model;
-    const detailsHeight = tabularEditor.isShown ? model.detailsHeight : 0;
-    const featureAreaHeight = isShown
-        ? overallHeight - detailsHeight - accordionControlHeight * 2
-        : 0;
-    const onDetailsResize = (delta) => {
-        model.setDetailsHeight(model.detailsHeight - delta);
-    };
+    const { detailsHeight, graphical, height: overallHeight, isShown, selectedFeature, table, tabularEditor, toggleShown, } = model;
     const canvasScrollContainerRef = useRef(null);
     useEffect(() => {
         scrollSelectedFeatureIntoView(model, canvasScrollContainerRef);
     }, [model, selectedFeature]);
+    const onDetailsResize = (delta) => {
+        model.setDetailsHeight(detailsHeight - delta);
+    };
+    if (graphical && table) {
+        const tabularHeight = tabularEditor.isShown ? detailsHeight : 0;
+        const featureAreaHeight = isShown
+            ? overallHeight - detailsHeight - accordionControlHeight * 2
+            : 0;
+        return (React__default.createElement("div", { style: { height: overallHeight } },
+            React__default.createElement(AccordionControl, { open: isShown, title: "Graphical", onClick: toggleShown }),
+            React__default.createElement("div", { className: classes.shading, ref: canvasScrollContainerRef, style: { height: featureAreaHeight } },
+                React__default.createElement(LinearApolloDisplay, { model: model, ...other })),
+            React__default.createElement(AccordionControl, { title: "Table", open: tabularEditor.isShown, onClick: tabularEditor.togglePane, onResize: onDetailsResize }),
+            React__default.createElement("div", { className: classes.details, style: { height: tabularHeight } },
+                React__default.createElement(TabularEditorPane, { model: model }))));
+    }
+    if (graphical) {
+        return (React__default.createElement("div", { className: classes.shading, ref: canvasScrollContainerRef, style: { height: overallHeight } },
+            React__default.createElement(LinearApolloDisplay, { model: model, ...other })));
+    }
     return (React__default.createElement("div", { className: classes.details, style: { height: overallHeight } },
-        React__default.createElement(AccordionControl, { open: isShown, title: "Graphical", onClick: toggleShown }),
-        React__default.createElement("div", { className: classes.shading, ref: canvasScrollContainerRef, style: { height: featureAreaHeight } },
-            React__default.createElement(LinearApolloDisplay, { model: model, ...other })),
-        React__default.createElement(AccordionControl, { title: "Table", open: tabularEditor.isShown, onClick: tabularEditor.togglePane, onResize: onDetailsResize }),
-        React__default.createElement("div", { style: { height: detailsHeight } },
-            React__default.createElement(TabularEditorPane, { model: model }))));
+        React__default.createElement(TabularEditorPane, { model: model })));
 });
 function makeSixFrameDisplayComponent(pluginManager) {
     const LGVPlugin = pluginManager.getPlugin('LinearGenomeViewPlugin');
@@ -9680,9 +9748,9 @@ function extendSession(pluginManager, sessionModel) {
                                 if (Object.keys(filteredConfig).length === 0) {
                                     filteredConfig = undefined;
                                 }
-                                let trackConfigSnapshot = getSnapshot(conf);
+                                const trackConfigSnapshot = getSnapshot(conf);
                                 const newTrackId = trackId.slice(0, trackId.length - sessionTrackIdentifier.length);
-                                trackConfigSnapshot = {
+                                const newTrackConfigSnapshot = {
                                     ...trackConfigSnapshot,
                                     trackId: newTrackId,
                                 };
@@ -9697,7 +9765,7 @@ function extendSession(pluginManager, sessionModel) {
                                             ...filteredConfig,
                                             tracks: filteredConfig?.tracks && [
                                                 ...filteredConfig.tracks,
-                                                trackConfigSnapshot,
+                                                newTrackConfigSnapshot,
                                             ],
                                         },
                                     });
@@ -9708,6 +9776,10 @@ function extendSession(pluginManager, sessionModel) {
                                     const { notify } = self;
                                     notify('Track added', 'success');
                                 }
+                                // @ts-expect-error This method is missing in the JB types
+                                self.deleteTrackConf(conf);
+                                // eslint-disable-next-line @typescript-eslint/no-unsafe-call
+                                jbrowse.addTrackConf(newTrackConfigSnapshot);
                             },
                             icon: SaveIcon,
                         },
@@ -9744,6 +9816,10 @@ function extendSession(pluginManager, sessionModel) {
                                     const { notify } = self;
                                     notify('Track removed', 'success');
                                 }
+                                // @ts-expect-error This method is missing in the JB types
+                                self.deleteTrackConf(conf);
+                                // eslint-disable-next-line @typescript-eslint/no-unsafe-call
+                                jbrowse.deleteTrackConf(conf);
                             },
                             icon: SaveIcon,
                         },
@@ -10271,7 +10347,7 @@ class ApolloPlugin extends Plugin {
             });
         });
         pluginManager.addDisplayType(() => {
-            const configSchema = configSchemaFactory$1(pluginManager);
+            const configSchema = configSchema$1;
             return new DisplayType({
                 name: 'LinearApolloDisplay',
                 configSchema,