@jbrowse/core 3.7.0 → 4.0.0

package/assemblyManager/assembly.js

@@ -1,307 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = assemblyFactory;
-const abortable_promise_cache_1 = __importDefault(require("@gmod/abortable-promise-cache"));
-const mobx_1 = require("mobx");
-const mobx_state_tree_1 = require("mobx-state-tree");
-const configuration_1 = require("../configuration");
-const util_1 = require("../data_adapters/util");
-const util_2 = require("../util");
-const QuickLRU_1 = __importDefault(require("../util/QuickLRU"));
-const refNameRegex = new RegExp('[0-9A-Za-z!#$%&+./:;?@^_|~-][0-9A-Za-z!#$%&*+./:;=?@^_|~-]*');
-const refNameColors = [
-    'rgb(153, 102, 0)',
-    'rgb(102, 102, 0)',
-    'rgb(153, 153, 30)',
-    'rgb(204, 0, 0)',
-    'rgb(255, 0, 0)',
-    'rgb(255, 0, 204)',
-    'rgb(165, 132, 132)',
-    'rgb(204, 122, 0)',
-    'rgb(178, 142, 0)',
-    'rgb(153, 153, 0)',
-    'rgb(122, 153, 0)',
-    'rgb(0, 165, 0)',
-    'rgb(53, 128, 0)',
-    'rgb(0, 0, 204)',
-    'rgb(96, 145, 242)',
-    'rgb(107, 142, 178)',
-    'rgb(0, 165, 165)',
-    'rgb(122, 153, 153)',
-    'rgb(153, 0, 204)',
-    'rgb(204, 51, 255)',
-    'rgb(173, 130, 216)',
-    'rgb(102, 102, 102)',
-    'rgb(145, 145, 145)',
-    'rgb(142, 142, 142)',
-    'rgb(142, 142, 107)',
-    'rgb(96, 163, 48)',
-];
-async function loadRefNameMap(assembly, adapterConfig, options, stopToken) {
-    const { sessionId } = options;
-    await (0, util_2.when)(() => !!(assembly.regions && assembly.refNameAliases), {
-        name: 'when assembly ready',
-    });
-    const refNames = (await assembly.rpcManager.call(sessionId || 'assemblyRpc', 'CoreGetRefNames', {
-        adapterConfig,
-        stopToken,
-        ...options,
-    }, { timeout: 1000000 }));
-    const { refNameAliases } = assembly;
-    if (!refNameAliases) {
-        throw new Error(`error loading assembly ${assembly.name}'s refNameAliases`);
-    }
-    const refNameMap = Object.fromEntries(refNames.map(name => {
-        checkRefName(name);
-        return [assembly.getCanonicalRefName(name), name];
-    }));
-    return {
-        forwardMap: refNameMap,
-        reverseMap: Object.fromEntries(Object.entries(refNameMap).map(([canonicalName, adapterName]) => [
-            adapterName,
-            canonicalName,
-        ])),
-    };
-}
-function checkRefName(refName) {
-    if (!refNameRegex.test(refName)) {
-        throw new Error(`Encountered invalid refName: "${refName}"`);
-    }
-}
-function assemblyFactory(assemblyConfigType, pluginManager) {
-    const adapterLoads = new abortable_promise_cache_1.default({
-        cache: new QuickLRU_1.default({ maxSize: 1000 }),
-        async fill(args, _stopToken, statusCallback) {
-            const { adapterConf, self, options } = args;
-            return loadRefNameMap(self, adapterConf, { ...options, statusCallback });
-        },
-    });
-    return mobx_state_tree_1.types
-        .model({
-        configuration: mobx_state_tree_1.types.safeReference(assemblyConfigType),
-    })
-        .volatile(() => ({
-        error: undefined,
-        loadingP: undefined,
-        volatileRegions: undefined,
-        refNameAliases: undefined,
-        cytobands: undefined,
-    }))
-        .views(self => ({
-        getConf(arg) {
-            return self.configuration ? (0, configuration_1.getConf)(self, arg) : undefined;
-        },
-        get lowerCaseRefNameAliases() {
-            return self.refNameAliases
-                ? Object.fromEntries(Object.entries(self.refNameAliases).map(([key, val]) => {
-                    return [key.toLowerCase(), val];
-                }))
-                : undefined;
-        },
-    }))
-        .views(self => ({
-        get initialized() {
-            self.load();
-            return !!self.refNameAliases;
-        },
-        get name() {
-            return self.getConf('name') || '';
-        },
-        get regions() {
-            self.load();
-            return self.volatileRegions;
-        },
-        get aliases() {
-            return self.getConf('aliases') || [];
-        },
-        get displayName() {
-            return self.getConf('displayName') || self.getConf('name') || '';
-        },
-        hasName(name) {
-            return this.allAliases.includes(name);
-        },
-        get allAliases() {
-            return [this.name, ...this.aliases];
-        },
-        get allRefNames() {
-            return !self.refNameAliases
-                ? undefined
-                : Object.keys(self.refNameAliases);
-        },
-        get lowerCaseRefNames() {
-            return !self.lowerCaseRefNameAliases
-                ? undefined
-                : Object.keys(self.lowerCaseRefNameAliases);
-        },
-        get allRefNamesWithLowerCase() {
-            return this.allRefNames && this.lowerCaseRefNames
-                ? [...new Set([...this.allRefNames, ...this.lowerCaseRefNames])]
-                : undefined;
-        },
-        get rpcManager() {
-            return (0, mobx_state_tree_1.getParent)(self, 2).rpcManager;
-        },
-        get refNameColors() {
-            const colors = self.getConf('refNameColors') || [];
-            return colors.length === 0 ? refNameColors : colors;
-        },
-    }))
-        .views(self => ({
-        get refNames() {
-            var _a;
-            return (_a = self.regions) === null || _a === void 0 ? void 0 : _a.map(region => region.refName);
-        },
-    }))
-        .views(self => ({
-        getCanonicalRefName(refName) {
-            if (!self.refNameAliases || !self.lowerCaseRefNameAliases) {
-                throw new Error('aliases not loaded, we expect them to be loaded before getCanonicalRefName can be called');
-            }
-            return (self.refNameAliases[refName] || self.lowerCaseRefNameAliases[refName]);
-        },
-        getCanonicalRefName2(asmName) {
-            return this.getCanonicalRefName(asmName) || asmName;
-        },
-        getRefNameColor(refName) {
-            if (!self.refNames) {
-                return undefined;
-            }
-            const idx = self.refNames.indexOf(refName);
-            return idx === -1
-                ? undefined
-                : self.refNameColors[idx % self.refNameColors.length];
-        },
-        isValidRefName(refName) {
-            if (!self.refNameAliases) {
-                throw new Error('isValidRefName cannot be called yet, the assembly has not finished loading');
-            }
-            return !!this.getCanonicalRefName(refName);
-        },
-    }))
-        .actions(self => ({
-        setLoaded({ regions, refNameAliases, cytobands, }) {
-            this.setRegions(regions);
-            this.setRefNameAliases(refNameAliases);
-            this.setCytobands(cytobands);
-        },
-        setError(e) {
-            self.error = e;
-        },
-        setRegions(regions) {
-            self.volatileRegions = regions;
-        },
-        setRefNameAliases(aliases) {
-            self.refNameAliases = aliases;
-        },
-        setCytobands(cytobands) {
-            self.cytobands = cytobands;
-        },
-        setLoadingP(p) {
-            self.loadingP = p;
-        },
-        load() {
-            if (!self.loadingP) {
-                self.loadingP = this.loadPre().catch((e) => {
-                    this.setLoadingP(undefined);
-                    this.setError(e);
-                });
-            }
-            return self.loadingP;
-        },
-        async loadPre() {
-            var _a, _b;
-            var _c;
-            const conf = self.configuration;
-            const refNameAliasesAdapterConf = (_a = conf === null || conf === void 0 ? void 0 : conf.refNameAliases) === null || _a === void 0 ? void 0 : _a.adapter;
-            const cytobandAdapterConf = (_b = conf === null || conf === void 0 ? void 0 : conf.cytobands) === null || _b === void 0 ? void 0 : _b.adapter;
-            const sequenceAdapterConf = conf === null || conf === void 0 ? void 0 : conf.sequence.adapter;
-            const assemblyName = self.name;
-            const regions = await getAssemblyRegions({
-                config: sequenceAdapterConf,
-                pluginManager,
-            });
-            for (const r of regions) {
-                checkRefName(r.refName);
-            }
-            const refNameAliases = {};
-            const refNameAliasCollection = await getRefNameAliases({
-                config: refNameAliasesAdapterConf,
-                pluginManager,
-            });
-            for (const { refName, aliases, override } of refNameAliasCollection) {
-                for (const alias of aliases) {
-                    checkRefName(alias);
-                    refNameAliases[alias] = refName;
-                }
-                if (override) {
-                    refNameAliases[refName] = refName;
-                }
-            }
-            for (const region of regions) {
-                refNameAliases[_c = region.refName] || (refNameAliases[_c] = region.refName);
-            }
-            this.setLoaded({
-                refNameAliases,
-                regions: regions.map(r => ({
-                    ...r,
-                    refName: refNameAliases[r.refName] || r.refName,
-                    assemblyName,
-                })),
-                cytobands: await getCytobands({
-                    config: cytobandAdapterConf,
-                    pluginManager,
-                }),
-            });
-        },
-    }))
-        .views(self => ({
-        getAdapterMapEntry(adapterConf, options) {
-            const { stopToken, statusCallback, ...rest } = options;
-            if (!options.sessionId) {
-                throw new Error('sessionId is required');
-            }
-            return adapterLoads.get((0, util_1.adapterConfigCacheKey)(adapterConf), {
-                adapterConf,
-                self,
-                options: rest,
-            }, undefined, statusCallback);
-        },
-        async getRefNameMapForAdapter(adapterConf, opts) {
-            if (!opts.sessionId) {
-                throw new Error('sessionId is required');
-            }
-            const map = await this.getAdapterMapEntry(adapterConf, opts);
-            return map.forwardMap;
-        },
-        async getReverseRefNameMapForAdapter(adapterConf, opts) {
-            const map = await this.getAdapterMapEntry(adapterConf, opts);
-            return map.reverseMap;
-        },
-        afterCreate() {
-            (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(() => {
-                self.allRefNamesWithLowerCase;
-            }));
-        },
-    }));
-}
-async function getRefNameAliases({ config, pluginManager, stopToken, }) {
-    const type = pluginManager.getAdapterType(config.type);
-    const CLASS = await type.getAdapterClass();
-    const adapter = new CLASS(config, undefined, pluginManager);
-    return adapter.getRefNameAliases({ stopToken });
-}
-async function getCytobands({ config, pluginManager, }) {
-    const type = pluginManager.getAdapterType(config.type);
-    const CLASS = await type.getAdapterClass();
-    const adapter = new CLASS(config, undefined, pluginManager);
-    return adapter.getData();
-}
-async function getAssemblyRegions({ config, pluginManager, stopToken, }) {
-    const type = pluginManager.getAdapterType(config.type);
-    const CLASS = await type.getAdapterClass();
-    const adapter = new CLASS(config, undefined, pluginManager);
-    return adapter.getRegions({ stopToken });
-}

package/assemblyManager/assemblyConfigSchema.d.ts

@@ -1,27 +0,0 @@
-import type PluginManager from '../PluginManager';
-declare function assemblyConfigSchema(pluginManager: PluginManager): import("../configuration/configurationSchema").ConfigurationSchemaType<{
-    aliases: {
-        type: string;
-        defaultValue: never[];
-        description: string;
-    };
-    sequence: import("../configuration").AnyConfigurationSchemaType;
-    refNameColors: {
-        type: string;
-        defaultValue: never[];
-        description: string;
-    };
-    refNameAliases: import("../configuration/configurationSchema").ConfigurationSchemaType<{
-        adapter: import("mobx-state-tree").IAnyModelType;
-    }, import("../configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-    cytobands: import("../configuration/configurationSchema").ConfigurationSchemaType<{
-        adapter: import("mobx-state-tree").IAnyModelType;
-    }, import("../configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-    displayName: {
-        type: string;
-        defaultValue: string;
-        description: string;
-    };
-}, import("../configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "name">>;
-export default assemblyConfigSchema;
-export type BaseAssemblyConfigSchema = ReturnType<typeof assemblyConfigSchema>;

package/assemblyManager/assemblyConfigSchema.js

@@ -1,53 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const configuration_1 = require("../configuration");
-function assemblyConfigSchema(pluginManager) {
-    return (0, configuration_1.ConfigurationSchema)('BaseAssembly', {
-        aliases: {
-            type: 'stringArray',
-            defaultValue: [],
-            description: 'Other possible names for the assembly',
-        },
-        sequence: pluginManager.getTrackType('ReferenceSequenceTrack')
-            .configSchema,
-        refNameColors: {
-            type: 'stringArray',
-            defaultValue: [],
-            description: 'Define custom colors for each reference sequence. Will cycle through this list if there are not enough colors for every sequence.',
-        },
-        refNameAliases: (0, configuration_1.ConfigurationSchema)('RefNameAliases', {
-            adapter: pluginManager.pluggableConfigSchemaType('adapter'),
-        }, {
-            preProcessSnapshot: snap => {
-                return !snap.adapter
-                    ? {
-                        adapter: {
-                            type: 'RefNameAliasAdapter',
-                        },
-                    }
-                    : snap;
-            },
-        }),
-        cytobands: (0, configuration_1.ConfigurationSchema)('Cytoband', {
-            adapter: pluginManager.pluggableConfigSchemaType('adapter'),
-        }, {
-            preProcessSnapshot: snap => {
-                return !snap.adapter
-                    ? {
-                        adapter: {
-                            type: 'CytobandAdapter',
-                        },
-                    }
-                    : snap;
-            },
-        }),
-        displayName: {
-            type: 'string',
-            defaultValue: '',
-            description: 'A human readable display name for the assembly e.g. "Homo sapiens (hg38)" while the assembly name may just be "hg38"',
-        },
-    }, {
-        explicitIdentifier: 'name',
-    });
-}
-exports.default = assemblyConfigSchema;