@jbrowse/product-core 2.6.1

package/esm/Session/Tracks.js

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+import { types } from 'mobx-state-tree';
+import { BaseSessionModel, isBaseSession } from './BaseSession';
+import { ReferenceManagementSessionMixin } from './ReferenceManagement';
+/**
+ * #stateModel TracksManagerSessionMixin
+ * composed of
+ * - BaseSessionModel
+ * - ReferenceManagementSessionMixin
+ */
+export function TracksManagerSessionMixin(pluginManager) {
+    return types
+        .compose('TracksManagerSessionMixin', BaseSessionModel(pluginManager), ReferenceManagementSessionMixin(pluginManager))
+        .views(self => ({
+        /**
+         * #getter
+         */
+        get tracks() {
+            return self.jbrowse.tracks;
+        },
+    }))
+        .actions(self => ({
+        /**
+         * #action
+         */
+        addTrackConf(trackConf) {
+            return self.jbrowse.addTrackConf(trackConf);
+        },
+        /**
+         * #action
+         */
+        deleteTrackConf(trackConf) {
+            const callbacksToDereferenceTrack = [];
+            const dereferenceTypeCount = {};
+            const referring = self.getReferring(trackConf);
+            self.removeReferring(referring, trackConf, callbacksToDereferenceTrack, dereferenceTypeCount);
+            callbacksToDereferenceTrack.forEach(cb => cb());
+            if (self.adminMode) {
+                return self.jbrowse.deleteTrackConf(trackConf);
+            }
+        },
+    }));
+}
+/** Type guard for SessionWithTracks */
+export function isSessionWithTracks(thing) {
+    return isBaseSession(thing) && 'tracks' in thing;
+}

package/esm/Session/index.d.ts

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+export * from './ReferenceManagement';
+export * from './Connections';
+export * from './DrawerWidgets';
+export * from './DialogQueue';
+export * from './Themes';
+export * from './Tracks';
+export * from './MultipleViews';
+export * from './BaseSession';
+export * from './SessionTracks';
+export * from './BaseSession';

package/esm/Session/index.js

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+export * from './ReferenceManagement';
+export * from './Connections';
+export * from './DrawerWidgets';
+export * from './DialogQueue';
+export * from './Themes';
+export * from './Tracks';
+export * from './MultipleViews';
+export * from './BaseSession';
+export * from './SessionTracks';
+export * from './BaseSession';

package/esm/index.d.ts

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+export * from './RootModel';
+export * from './Session';
+export * from './ui';

package/esm/index.js

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+export * from './RootModel';
+export * from './Session';
+export * from './ui';

package/esm/ui/AboutDialog.d.ts

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+import React from 'react';
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+export declare function AboutDialog({ config, handleClose, }: {
+    config: AnyConfigurationModel;
+    handleClose: () => void;
+}): React.JSX.Element;

package/esm/ui/AboutDialog.js

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+import React from 'react';
+import Dialog from '@jbrowse/core/ui/Dialog';
+import { getSession, getEnv } from '@jbrowse/core/util';
+import { getTrackName } from '@jbrowse/core/util/tracks';
+import AboutContents from './AboutDialogContents';
+export function AboutDialog({ config, handleClose, }) {
+    const session = getSession(config);
+    const trackName = getTrackName(config, session);
+    const { pluginManager } = getEnv(session);
+    const AboutComponent = pluginManager.evaluateExtensionPoint('Core-replaceAbout', AboutContents, { session, config });
+    return (React.createElement(Dialog, { open: true, onClose: handleClose, title: trackName, maxWidth: "xl" },
+        React.createElement(AboutComponent, { config: config })));
+}

package/esm/ui/AboutDialogContents.d.ts

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+import React from 'react';
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+export default function AboutContents({ config, }: {
+    config: AnyConfigurationModel;
+}): React.JSX.Element;

package/esm/ui/AboutDialogContents.js

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+import React, { useState } from 'react';
+import copy from 'copy-to-clipboard';
+import { Button } from '@mui/material';
+import { makeStyles } from 'tss-react/mui';
+import { getConf, readConfObject, } from '@jbrowse/core/configuration';
+import { getSession, getEnv } from '@jbrowse/core/util';
+import { BaseCard, Attributes, } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail';
+import FileInfoPanel from './FileInfoPanel';
+const useStyles = makeStyles()({
+    content: {
+        minWidth: 800,
+    },
+});
+export default function AboutContents({ config, }) {
+    const [copied, setCopied] = useState(false);
+    const conf = readConfObject(config);
+    const session = getSession(config);
+    const { classes } = useStyles();
+    const hideUris = getConf(session, ['formatAbout', 'hideUris']) ||
+        readConfObject(config, ['formatAbout', 'hideUris']);
+    const { pluginManager } = getEnv(session);
+    const confPostExt = pluginManager.evaluateExtensionPoint('Core-customizeAbout', {
+        config: {
+            ...conf,
+            ...getConf(session, ['formatAbout', 'config'], { config: conf }),
+            ...readConfObject(config, ['formatAbout', 'config'], { config: conf }),
+        },
+    }, { session, config });
+    const ExtraPanel = pluginManager.evaluateExtensionPoint('Core-extraAboutPanel', null, { session, config });
+    return (React.createElement("div", { className: classes.content },
+        React.createElement(BaseCard, { title: "Configuration" },
+            !hideUris ? (React.createElement(Button, { variant: "contained", style: { float: 'right' }, onClick: () => {
+                    copy(JSON.stringify(conf, null, 2));
+                    setCopied(true);
+                    setTimeout(() => setCopied(false), 1000);
+                } }, copied ? 'Copied to clipboard!' : 'Copy config')) : null,
+            React.createElement(Attributes, { attributes: confPostExt, omit: ['displays', 'baseUri', 'refNames', 'formatAbout'], hideUris: hideUris })),
+        ExtraPanel ? (React.createElement(BaseCard, { title: ExtraPanel.name },
+            React.createElement(ExtraPanel.Component, { config: config }))) : null,
+        React.createElement(FileInfoPanel, { config: config })));
+}

package/esm/ui/FileInfoPanel.d.ts

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+import React from 'react';
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+export default function FileInfoPanel({ config, }: {
+    config: AnyConfigurationModel;
+}): React.JSX.Element | null;

package/esm/ui/FileInfoPanel.js

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+import React, { useState, useEffect } from 'react';
+import { Typography } from '@mui/material';
+import { readConfObject, } from '@jbrowse/core/configuration';
+import LoadingEllipses from '@jbrowse/core/ui/LoadingEllipses';
+import { getSession } from '@jbrowse/core/util';
+import { BaseCard, Attributes, } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail';
+export default function FileInfoPanel({ config, }) {
+    const [error, setError] = useState();
+    const [info, setInfo] = useState();
+    const session = getSession(config);
+    const { rpcManager } = session;
+    useEffect(() => {
+        const aborter = new AbortController();
+        const { signal } = aborter;
+        let cancelled = false;
+        (async () => {
+            try {
+                const adapterConfig = readConfObject(config, 'adapter');
+                const result = await rpcManager.call(config.trackId, 'CoreGetInfo', {
+                    adapterConfig,
+                    signal,
+                });
+                if (!cancelled) {
+                    setInfo(result);
+                }
+            }
+            catch (e) {
+                if (!cancelled) {
+                    console.error(e);
+                    setError(e);
+                }
+            }
+        })();
+        return () => {
+            aborter.abort();
+            cancelled = true;
+        };
+    }, [config, rpcManager]);
+    const details = typeof info === 'string'
+        ? {
+            header: `<pre>${info
+                .replaceAll('<', '&lt;')
+                .replaceAll('>', '&gt;')}</pre>`,
+        }
+        : info || {};
+    return info !== null ? (React.createElement(BaseCard, { title: "File info" }, error ? (React.createElement(Typography, { color: "error" }, `${error}`)) : info === undefined ? (React.createElement(LoadingEllipses, { message: "Loading file data" })) : (React.createElement(Attributes, { attributes: details })))) : null;
+}

package/esm/ui/index.d.ts

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+export * from './AboutDialog';

package/esm/ui/index.js

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+export * from './AboutDialog';

package/package.json

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+{
+  "name": "@jbrowse/product-core",
+  "version": "2.6.1",
+  "sideEffects": false,
+  "description": "JBrowse 2 code shared between products but not used by plugins",
+  "keywords": [
+    "jbrowse",
+    "jbrowse2",
+    "bionode",
+    "biojs",
+    "genomics"
+  ],
+  "license": "Apache-2.0",
+  "homepage": "https://jbrowse.org",
+  "bugs": "https://github.com/GMOD/jbrowse-components/issues",
+  "repository": {
+    "type": "git",
+    "url": "https://github.com/GMOD/jbrowse-components.git",
+    "directory": "packages/product-core"
+  },
+  "author": "JBrowse Team",
+  "distMain": "dist/index.js",
+  "distModule": "esm/index.js",
+  "srcMain": "src/index.ts",
+  "srcModule": "src/index.ts",
+  "main": "dist/index.js",
+  "module": "esm/index.js",
+  "files": [
+    "dist",
+    "esm",
+    "src"
+  ],
+  "scripts": {
+    "build:esm": "tsc --build tsconfig.build.esm.json",
+    "build:es5": "tsc --build tsconfig.build.es5.json",
+    "build": "npm run build:esm && npm run build:es5",
+    "test": "cd ../..; jest packages/product-core",
+    "clean": "rimraf dist esm *.tsbuildinfo",
+    "prebuild": "yarn clean",
+    "prepack": "yarn build && yarn useDist",
+    "postpack": "yarn useSrc",
+    "useDist": "node ../../scripts/useDist.js",
+    "useSrc": "node ../../scripts/useSrc.js"
+  },
+  "dependencies": {
+    "@babel/runtime": "^7.16.3",
+    "@mui/icons-material": "^5.0.0",
+    "@mui/material": "^5.10.17",
+    "copy-to-clipboard": "^3.3.1",
+    "react-error-boundary": "^4.0.3",
+    "shortid": "^2.2.15"
+  },
+  "peerDependencies": {
+    "mobx": "^6.0.0",
+    "mobx-react": "^7.0.0",
+    "mobx-state-tree": "^5.0.0",
+    "react": "^17.0.0",
+    "react-dom": "^17.0.0",
+    "rxjs": "^7.0.0",
+    "tss-react": "^4.0.0"
+  },
+  "publishConfig": {
+    "access": "public"
+  },
+  "gitHead": "1cbe7ba097fb2d2763c776e5e429e4670cdd583c"
+}

package/src/RootModel/BaseRootModel.ts

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+import PluginManager from '@jbrowse/core/PluginManager'
+import assemblyManagerFactory, {
+  BaseAssemblyConfigSchema,
+} from '@jbrowse/core/assemblyManager'
+import RpcManager from '@jbrowse/core/rpc/RpcManager'
+import {
+  IAnyType,
+  Instance,
+  SnapshotIn,
+  cast,
+  getSnapshot,
+  isStateTreeNode,
+  types,
+} from 'mobx-state-tree'
+import TextSearchManager from '@jbrowse/core/TextSearch/TextSearchManager'
+
+/**
+ * #stateModel BaseRootModel
+ * #category root
+ * factory function for the Base-level root model shared by all products
+ */
+export function BaseRootModelFactory({
+  pluginManager,
+  jbrowseModelType,
+  sessionModelType,
+  assemblyConfigSchema,
+}: {
+  pluginManager: PluginManager
+  jbrowseModelType: IAnyType
+  sessionModelType: IAnyType
+  assemblyConfigSchema: BaseAssemblyConfigSchema
+}) {
+  return types
+    .model('BaseRootModel', {
+      /**
+       * #property
+       * `jbrowse` is a mapping of the config.json into the in-memory state
+       * tree
+       */
+      jbrowse: jbrowseModelType,
+
+      /**
+       * #property
+       * `session` encompasses the currently active state of the app, including
+       * views open, tracks open in those views, etc.
+       */
+      session: types.maybe(sessionModelType),
+      /**
+       * #property
+       */
+      sessionPath: types.optional(types.string, ''),
+
+      /**
+       * #property
+       */
+      assemblyManager: types.optional(
+        assemblyManagerFactory(assemblyConfigSchema, pluginManager),
+        {},
+      ),
+    })
+    .volatile(self => ({
+      rpcManager: new RpcManager(
+        pluginManager,
+        self.jbrowse.configuration.rpc,
+        {
+          MainThreadRpcDriver: {},
+        },
+      ),
+
+      adminMode: false,
+      isAssemblyEditing: false,
+      error: undefined as unknown,
+      textSearchManager: new TextSearchManager(pluginManager),
+      pluginManager,
+    }))
+    .actions(self => ({
+      /**
+       * #action
+       */
+      setError(error: unknown) {
+        self.error = error
+      },
+      /**
+       * #action
+       */
+      setSession(sessionSnapshot?: SnapshotIn<IAnyType>) {
+        self.session = cast(sessionSnapshot)
+      },
+      /**
+       * #action
+       */
+      setDefaultSession() {
+        this.setSession(self.jbrowse.defaultSession)
+      },
+      /**
+       * #action
+       */
+      setSessionPath(path: string) {
+        self.sessionPath = path
+      },
+      /**
+       * #action
+       */
+      renameCurrentSession(newName: string) {
+        if (self.session) {
+          const snapshot = JSON.parse(JSON.stringify(getSnapshot(self.session)))
+          snapshot.name = newName
+          this.setSession(snapshot)
+        }
+      },
+      /**
+       * #action
+       */
+      setAssemblyEditing(flag: boolean) {
+        self.isAssemblyEditing = flag
+      },
+    }))
+}
+
+export type BaseRootModelType = ReturnType<typeof BaseRootModelFactory>
+export type BaseRootModel = Instance<BaseRootModelType>
+
+/** Type guard for checking if something is a JB root model */
+export function isRootModel(thing: unknown): thing is BaseRootModelType {
+  return (
+    isStateTreeNode(thing) &&
+    'session' in thing &&
+    'jbrowse' in thing &&
+    'assemblyManager' in thing
+  )
+}

package/src/RootModel/InternetAccounts.ts

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+import PluginManager from '@jbrowse/core/PluginManager'
+import { AnyConfigurationModel } from '@jbrowse/core/configuration'
+import { UriLocation } from '@jbrowse/core/util'
+import { autorun } from 'mobx'
+import { Instance, addDisposer, types } from 'mobx-state-tree'
+import { BaseRootModel } from './BaseRootModel'
+
+/**
+ * #stateModel InternetAccountsMixin
+ * #category root
+ */
+export function InternetAccountsRootModelMixin(pluginManager: PluginManager) {
+  return types
+    .model({
+      /**
+       * #property
+       */
+      internetAccounts: types.array(
+        pluginManager.pluggableMstType('internet account', 'stateModel'),
+      ),
+    })
+    .actions(self => ({
+      /**
+       * #action
+       */
+      initializeInternetAccount(
+        internetAccountConfig: AnyConfigurationModel,
+        initialSnapshot = {},
+      ) {
+        const internetAccountType = pluginManager.getInternetAccountType(
+          internetAccountConfig.type,
+        )
+        if (!internetAccountType) {
+          throw new Error(
+            `unknown internet account type ${internetAccountConfig.type}`,
+          )
+        }
+
+        const length = self.internetAccounts.push({
+          ...initialSnapshot,
+          type: internetAccountConfig.type,
+          configuration: internetAccountConfig,
+        })
+        return self.internetAccounts[length - 1]
+      },
+
+      /**
+       * #action
+       */
+      createEphemeralInternetAccount(
+        internetAccountId: string,
+        initialSnapshot = {},
+        url: string,
+      ) {
+        let hostUri
+
+        try {
+          hostUri = new URL(url).origin
+        } catch (e) {
+          // ignore
+        }
+        // id of a custom new internaccount is `${type}-${name}`
+        const internetAccountSplit = internetAccountId.split('-')
+        const configuration = {
+          type: internetAccountSplit[0],
+          internetAccountId: internetAccountId,
+          name: internetAccountSplit.slice(1).join('-'),
+          description: '',
+          domains: hostUri ? [hostUri] : [],
+        }
+        const type = pluginManager.getInternetAccountType(configuration.type)
+        const internetAccount = type.stateModel.create({
+          ...initialSnapshot,
+          type: configuration.type,
+          configuration,
+        })
+        self.internetAccounts.push(internetAccount)
+        return internetAccount
+      },
+      /**
+       * #action
+       */
+      findAppropriateInternetAccount(location: UriLocation) {
+        // find the existing account selected from menu
+        const selectedId = location.internetAccountId
+        if (selectedId) {
+          const selectedAccount = self.internetAccounts.find(account => {
+            return account.internetAccountId === selectedId
+          })
+          if (selectedAccount) {
+            return selectedAccount
+          }
+        }
+
+        // if no existing account or not found, try to find working account
+        for (const account of self.internetAccounts) {
+          const handleResult = account.handlesLocation(location)
+          if (handleResult) {
+            return account
+          }
+        }
+
+        // if still no existing account, create ephemeral config to use
+        return selectedId
+          ? this.createEphemeralInternetAccount(selectedId, {}, location.uri)
+          : null
+      },
+    }))
+    .actions(self => ({
+      afterCreate() {
+        addDisposer(
+          self,
+          autorun(() => {
+            const { jbrowse } = self as typeof self & BaseRootModel
+            jbrowse.internetAccounts.forEach(self.initializeInternetAccount)
+          }),
+        )
+      },
+    }))
+}
+
+export type RootModelWithInternetAccountsType = ReturnType<
+  typeof InternetAccountsRootModelMixin
+>
+export type RootModelWithInternetAccounts =
+  Instance<RootModelWithInternetAccountsType>

package/src/RootModel/index.ts

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+export * from './BaseRootModel'
+export * from './InternetAccounts'

package/src/Session/BaseSession.ts

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+import shortid from 'shortid'
+import PluginManager from '@jbrowse/core/PluginManager'
+import {
+  IAnyStateTreeNode,
+  Instance,
+  getParent,
+  isStateTreeNode,
+  types,
+} from 'mobx-state-tree'
+import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration'
+import { BaseAssemblyConfigSchema } from '@jbrowse/core/assemblyManager'
+
+// locals
+import type { BaseRootModelType } from '../RootModel/BaseRootModel'
+
+/**
+ * #stateModel BaseSessionModel
+ * base session shared by **all** JBrowse products. Be careful what you include
+ * here, everything will use it.
+ */
+export function BaseSessionModel<
+  ROOT_MODEL_TYPE extends BaseRootModelType,
+  JB_CONFIG_SCHEMA extends AnyConfigurationSchemaType,
+>(pluginManager: PluginManager) {
+  return types
+    .model({
+      /**
+       * #property
+       */
+      id: types.optional(types.identifier, shortid()),
+      /**
+       * #property
+       */
+      name: types.string,
+      /**
+       * #property
+       */
+      margin: 0,
+    })
+    .volatile(() => ({
+      /**
+       * #volatile
+       * this is the globally "selected" object. can be anything. code that
+       * wants to deal with this should examine it to see what kind of thing it
+       * is.
+       */
+      selection: undefined as unknown,
+    }))
+    .views(self => ({
+      get root() {
+        return getParent<ROOT_MODEL_TYPE>(self)
+      },
+    }))
+    .views(self => ({
+      /**
+       * #getter
+       */
+      get jbrowse() {
+        return self.root.jbrowse
+      },
+      /**
+       * #getter
+       */
+      get rpcManager() {
+        return self.root.rpcManager
+      },
+      /**
+       * #getter
+       */
+      get configuration(): Instance<JB_CONFIG_SCHEMA> {
+        return this.jbrowse.configuration
+      },
+      /**
+       * #getter
+       */
+      get adminMode() {
+        return self.root.adminMode
+      },
+
+      /**
+       * #getter
+       */
+      get textSearchManager() {
+        return self.root.textSearchManager
+      },
+    }))
+    .views(self => ({
+      /**
+       * #getter
+       */
+      get assemblies(): Instance<BaseAssemblyConfigSchema>[] {
+        return self.jbrowse.assemblies
+      },
+    }))
+    .actions(self => ({
+      /**
+       * #action
+       * set the global selection, i.e. the globally-selected object. can be a
+       * feature, a view, just about anything
+       */
+      setSelection(thing: unknown) {
+        self.selection = thing
+      },
+
+      /**
+       * #action
+       * clears the global selection
+       */
+      clearSelection() {
+        self.selection = undefined
+      },
+    }))
+}
+
+/** Session mixin MST type for the most basic session */
+export type BaseSessionType = ReturnType<typeof BaseSessionModel>
+
+/** Instance of the most basic possible session */
+export type BaseSession = Instance<BaseSessionType>
+
+/** Type guard for BaseSession */
+export function isBaseSession(thing: IAnyStateTreeNode): thing is BaseSession {
+  return 'id' in thing && 'name' in thing && 'root' in thing
+}
+
+/** Type guard for whether a thing is JBrowse session */
+export function isSession(thing: unknown): thing is BaseSession {
+  return isStateTreeNode(thing) && isBaseSession(thing)
+}