@jbrowse/plugin-variants 3.7.0 → 4.0.0

package/esm/ChordVariantDisplay/models/stateModelFactory.js

@@ -1,33 +1,171 @@
-import { ConfigurationReference } from '@jbrowse/core/configuration';
-import { getContainingView } from '@jbrowse/core/util';
-import { getParentRenderProps } from '@jbrowse/core/util/tracks';
-import { BaseChordDisplayModel } from '@jbrowse/plugin-circular-view';
-import { types } from 'mobx-state-tree';
+import { ConfigurationReference, getConf } from '@jbrowse/core/configuration';
+import { BaseDisplay } from '@jbrowse/core/pluggableElementTypes/models';
+import { getContainingView, getEnv, getSession, isFeature, makeAbortableReaction, } from '@jbrowse/core/util';
+import { getParentRenderProps, getRpcSessionId, getTrackAssemblyNames, } from '@jbrowse/core/util/tracks';
+import { getParent, isAlive, types } from '@jbrowse/mobx-state-tree';
+import { renderReactionData, renderReactionEffect } from "./renderReaction.js";
 const stateModelFactory = (configSchema) => {
     return types
-        .compose('ChordVariantDisplay', BaseChordDisplayModel, types.model({
+        .compose('ChordVariantDisplay', BaseDisplay, types.model({
         type: types.literal('ChordVariantDisplay'),
+        bezierRadiusRatio: 0.1,
+        assemblyName: types.maybe(types.string),
         configuration: ConfigurationReference(configSchema),
     }))
+        .volatile(() => ({
+        filled: false,
+        reactElement: undefined,
+        data: undefined,
+        html: undefined,
+        message: '',
+        renderingComponent: undefined,
+        refNameMap: undefined,
+    }))
+        .actions(self => {
+        const { pluginManager } = getEnv(self);
+        const track = self;
+        return {
+            onChordClick(feature) {
+                getConf(self, 'onChordClick', { feature, track, pluginManager });
+            },
+        };
+    })
         .views(self => ({
+        get blockDefinitions() {
+            const view = getContainingView(self);
+            const origSlices = view.staticSlices;
+            if (!self.refNameMap) {
+                return origSlices;
+            }
+            const slices = structuredClone(origSlices);
+            for (const slice of slices) {
+                const regions = slice.region.elided
+                    ? slice.region.regions
+                    : [slice.region];
+                for (const region of regions) {
+                    const renamed = self.refNameMap[region.refName];
+                    if (renamed && region.refName !== renamed) {
+                        region.refName = renamed;
+                    }
+                }
+            }
+            return slices;
+        },
         get rendererTypeName() {
             return self.configuration.renderer.type;
         },
+        get rendererType() {
+            return getEnv(self).pluginManager.getRendererType(this.rendererTypeName);
+        },
+        get selectedFeatureId() {
+            if (!isAlive(self)) {
+                return undefined;
+            }
+            const { selection } = getSession(self);
+            return isFeature(selection) ? selection.id() : undefined;
+        },
         renderProps() {
             const view = getContainingView(self);
             return {
                 ...getParentRenderProps(self),
                 rpcDriverName: self.rpcDriverName,
-                displayModel: self,
                 bezierRadius: view.radiusPx * self.bezierRadiusRatio,
                 radius: view.radiusPx,
-                blockDefinitions: self.blockDefinitions,
+                blockDefinitions: this.blockDefinitions,
                 config: self.configuration.renderer,
+                onChordClick: self.onChordClick,
+            };
+        },
+        renderingProps() {
+            return {
+                displayModel: self,
                 onChordClick: (arg) => {
                     self.onChordClick(arg);
                 },
             };
         },
+    }))
+        .actions(self => ({
+        renderStarted() {
+            self.filled = false;
+            self.message = '';
+            self.reactElement = undefined;
+            self.data = undefined;
+            self.html = undefined;
+            self.error = undefined;
+            self.renderingComponent = undefined;
+        },
+        renderSuccess({ message, data, reactElement, html, renderingComponent, }) {
+            if (message) {
+                self.filled = false;
+                self.message = message;
+                self.reactElement = undefined;
+                self.data = undefined;
+                self.html = undefined;
+                self.error = undefined;
+                self.renderingComponent = undefined;
+            }
+            else {
+                self.filled = true;
+                self.message = '';
+                self.reactElement = reactElement;
+                self.data = data;
+                self.html = html;
+                self.error = undefined;
+                self.renderingComponent = renderingComponent;
+            }
+        },
+        renderError(error) {
+            console.error(error);
+            self.filled = false;
+            self.message = '';
+            self.reactElement = undefined;
+            self.html = undefined;
+            self.data = undefined;
+            self.error = error;
+            self.renderingComponent = undefined;
+        },
+        setRefNameMap(refNameMap) {
+            self.refNameMap = refNameMap;
+        },
+    }))
+        .actions(self => ({
+        afterAttach() {
+            makeAbortableReaction(self, renderReactionData, renderReactionEffect, {
+                name: `${self.type} ${self.id} rendering`,
+                fireImmediately: true,
+            }, self.renderStarted, self.renderSuccess, self.renderError);
+            makeAbortableReaction(self, () => {
+                return {
+                    assemblyNames: getTrackAssemblyNames(self.parentTrack),
+                    adapter: getConf(getParent(self, 2), 'adapter'),
+                    assemblyManager: getSession(self).assemblyManager,
+                };
+            }, async (args, stopToken) => {
+                return args
+                    ? args.assemblyManager.getRefNameMapForAdapter(args.adapter, args.assemblyNames[0], {
+                        stopToken,
+                        sessionId: getRpcSessionId(self),
+                    })
+                    : undefined;
+            }, {
+                name: `${self.type} ${self.id} getting refNames`,
+                fireImmediately: true,
+            }, () => { }, refNameMap => {
+                if (refNameMap) {
+                    self.setRefNameMap(refNameMap);
+                }
+            }, error => {
+                console.error(error);
+                self.setError(error);
+            });
+        },
+    }))
+        .views(self => ({
+        async renderSvg(opts) {
+            const { renderSvg } = await import("./renderSvg.js");
+            return renderSvg(self, opts);
+        },
     }));
 };
 export default stateModelFactory;

package/esm/LinearVariantDisplay/configSchema.d.ts

@@ -1,8 +1,8 @@
 import type PluginManager from '@jbrowse/core/PluginManager';
-import type { Instance } from 'mobx-state-tree';
-export default function configSchemaF(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    renderer: import("mobx-state-tree").IAnyModelType;
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+import type { Instance } from '@jbrowse/mobx-state-tree';
+export default function configSchemaF(pluginManager: PluginManager): import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
+    renderer: import("@jbrowse/mobx-state-tree").IAnyModelType;
+}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
     maxFeatureScreenDensity: {
         type: string;
         description: string;
@@ -29,6 +29,6 @@ export default function configSchemaF(pluginManager: PluginManager): import("@jb
         description: string;
         defaultValue: never[];
     };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>, undefined>>;
+}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>, undefined>>;
 export type LinearVariantDisplayConfigModel = ReturnType<typeof configSchemaF>;
 export type LinearVariantDisplayConfig = Instance<LinearVariantDisplayConfigModel>;

package/esm/LinearVariantDisplay/configSchema.js

@@ -1,9 +1,9 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-import { linearBasicDisplayConfigSchemaFactory } from '@jbrowse/plugin-linear-genome-view';
+import { linearFeatureDisplayConfigSchemaFactory } from '@jbrowse/plugin-linear-genome-view';
 function x() { }
 export default function configSchemaF(pluginManager) {
     return ConfigurationSchema('LinearVariantDisplay', {}, {
-        baseConfiguration: linearBasicDisplayConfigSchemaFactory(pluginManager),
+        baseConfiguration: linearFeatureDisplayConfigSchemaFactory(pluginManager),
         explicitlyTyped: true,
     });
 }

package/esm/LinearVariantDisplay/index.js

@@ -1,7 +1,7 @@
+import { lazy } from 'react';
 import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType';
-import { BaseLinearDisplayComponent } from '@jbrowse/plugin-linear-genome-view';
-import configSchemaF from './configSchema';
-import stateModelFactory from './model';
+import configSchemaF from "./configSchema.js";
+import stateModelFactory from "./model.js";
 export default function LinearVariantDisplayF(pluginManager) {
     pluginManager.addDisplayType(() => {
         const configSchema = configSchemaF(pluginManager);
@@ -12,7 +12,9 @@ export default function LinearVariantDisplayF(pluginManager) {
             stateModel: stateModelFactory(configSchema),
             trackType: 'VariantTrack',
             viewType: 'LinearGenomeView',
-            ReactComponent: BaseLinearDisplayComponent,
+            ReactComponent: lazy(() => import('@jbrowse/plugin-linear-genome-view').then(m => ({
+                default: m.LinearBasicDisplayComponent,
+            }))),
         });
     });
 }