@apollo-annotation/jbrowse-plugin-apollo 0.3.12 → 1.0.0

package/dist/BackendDrivers/InMemoryFileDriver.d.ts

@@ -1,162 +0,0 @@
-import type { AssemblySpecificChange, Change } from '@apollo-annotation/common';
-import type { AnnotationFeatureSnapshot, CheckResultSnapshot } from '@apollo-annotation/mst';
-import { ValidationResultSet } from '@apollo-annotation/shared';
-import { type Region } from '@jbrowse/core/util';
-import type { SubmitOpts } from '../ChangeManager';
-import { BackendDriver, type RefNameAliases } from './BackendDriver';
-export declare class InMemoryFileDriver extends BackendDriver {
-    getFeatures(): Promise<[
-        AnnotationFeatureSnapshot[],
-        CheckResultSnapshot[]
-    ]>;
-    getSequence(region: Region): Promise<{
-        seq: string;
-        refSeq: string;
-    }>;
-    getRefNameAliases(assemblyName: string): Promise<RefNameAliases[]>;
-    getRegions(assemblyName: string): Promise<Region[]>;
-    getAssemblies(): ({
-        configuration: any;
-    } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
-        error: unknown;
-        loadingP: Promise<void> | undefined;
-        volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-        refNameAliases: {
-            [x: string]: string;
-        } | undefined;
-        canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
-        cytobands: import("@jbrowse/core/util").Feature[] | undefined;
-    } & {
-        getConf(arg: string): any;
-        readonly lowerCaseRefNameAliases: {
-            [k: string]: string;
-        } | undefined;
-    } & {
-        readonly initialized: boolean;
-        readonly name: string;
-        readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-        readonly aliases: string[];
-        readonly displayName: string;
-        hasName(name: string): boolean;
-        readonly allAliases: string[];
-        readonly allRefNames: string[] | undefined;
-        readonly lowerCaseRefNames: string[] | undefined;
-        readonly allRefNamesWithLowerCase: string[] | undefined;
-        readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
-        readonly refNameColors: string[];
-    } & {
-        readonly refNames: string[] | undefined;
-    } & {
-        getCanonicalRefName(refName: string): string | undefined;
-        getCanonicalRefName2(refName: string): string;
-        getRefNameColor(refName: string): string | undefined;
-        isValidRefName(refName: string): boolean;
-        getSeqAdapterRefName(canonicalRefName: string): string;
-    } & {
-        setLoaded({ regions, refNameAliases, cytobands, }: {
-            regions: import("@jbrowse/core/util").Region[];
-            refNameAliases: {
-                [x: string]: string;
-            };
-            cytobands: import("@jbrowse/core/util").Feature[];
-        }): void;
-        setError(e: unknown): void;
-        setRegions(regions: import("@jbrowse/core/util").Region[]): void;
-        setRefNameAliases(aliases: {
-            [x: string]: string;
-        }): void;
-        setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
-        setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
-        setLoadingP(p?: Promise<void>): void;
-        load(): Promise<void>;
-        loadPre(): Promise<void>;
-    } & {
-        getAdapterMapEntry(adapterConf: {
-            [x: string]: unknown;
-        }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
-        getRefNameMapForAdapter(adapterConf: {
-            [x: string]: unknown;
-        }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
-            [x: string]: string;
-        }>;
-        getReverseRefNameMapForAdapter(adapterConf: {
-            [x: string]: unknown;
-        }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
-            [x: string]: string;
-        }>;
-        afterCreate(): void;
-    } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
-        configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
-    }, {
-        error: unknown;
-        loadingP: Promise<void> | undefined;
-        volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-        refNameAliases: {
-            [x: string]: string;
-        } | undefined;
-        canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
-        cytobands: import("@jbrowse/core/util").Feature[] | undefined;
-    } & {
-        getConf(arg: string): any;
-        readonly lowerCaseRefNameAliases: {
-            [k: string]: string;
-        } | undefined;
-    } & {
-        readonly initialized: boolean;
-        readonly name: string;
-        readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-        readonly aliases: string[];
-        readonly displayName: string;
-        hasName(name: string): boolean;
-        readonly allAliases: string[];
-        readonly allRefNames: string[] | undefined;
-        readonly lowerCaseRefNames: string[] | undefined;
-        readonly allRefNamesWithLowerCase: string[] | undefined;
-        readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
-        readonly refNameColors: string[];
-    } & {
-        readonly refNames: string[] | undefined;
-    } & {
-        getCanonicalRefName(refName: string): string | undefined;
-        getCanonicalRefName2(refName: string): string;
-        getRefNameColor(refName: string): string | undefined;
-        isValidRefName(refName: string): boolean;
-        getSeqAdapterRefName(canonicalRefName: string): string;
-    } & {
-        setLoaded({ regions, refNameAliases, cytobands, }: {
-            regions: import("@jbrowse/core/util").Region[];
-            refNameAliases: {
-                [x: string]: string;
-            };
-            cytobands: import("@jbrowse/core/util").Feature[];
-        }): void;
-        setError(e: unknown): void;
-        setRegions(regions: import("@jbrowse/core/util").Region[]): void;
-        setRefNameAliases(aliases: {
-            [x: string]: string;
-        }): void;
-        setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
-        setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
-        setLoadingP(p?: Promise<void>): void;
-        load(): Promise<void>;
-        loadPre(): Promise<void>;
-    } & {
-        getAdapterMapEntry(adapterConf: {
-            [x: string]: unknown;
-        }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
-        getRefNameMapForAdapter(adapterConf: {
-            [x: string]: unknown;
-        }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
-            [x: string]: string;
-        }>;
-        getReverseRefNameMapForAdapter(adapterConf: {
-            [x: string]: unknown;
-        }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
-            [x: string]: string;
-        }>;
-        afterCreate(): void;
-    }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>)[];
-    submitChange(_change: Change | AssemblySpecificChange, _opts?: SubmitOpts): Promise<ValidationResultSet>;
-    searchFeatures(_term: string, _assemblies: string[]): Promise<AnnotationFeatureSnapshot[]>;
-}
-//# sourceMappingURL=InMemoryFileDriver.d.ts.map

package/dist/BackendDrivers/InMemoryFileDriver.d.ts.map

@@ -1 +0,0 @@
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package/dist/LinearApolloDisplay/glyphs/index.d.ts

@@ -1,4 +0,0 @@
-export * from './BoxGlyph';
-export * from './GeneGlyph';
-export * from './GenericChildGlyph';
-//# sourceMappingURL=index.d.ts.map

package/dist/LinearApolloDisplay/glyphs/index.d.ts.map

@@ -1 +0,0 @@
-{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../src/LinearApolloDisplay/glyphs/index.ts"],"names":[],"mappings":"AAAA,cAAc,YAAY,CAAA;AAC1B,cAAc,aAAa,CAAA;AAC3B,cAAc,qBAAqB,CAAA"}

package/dist/components/OpenLocalFile.d.ts

@@ -1,15 +0,0 @@
-import type { InMemoryFileDriver } from '../BackendDrivers';
-import type { ApolloSessionModel } from '../session';
-interface OpenLocalFileProps {
-    session: ApolloSessionModel;
-    handleClose(): void;
-    inMemoryFileDriver: InMemoryFileDriver;
-}
-export interface RefSeqInterface {
-    refName: string;
-    uniqueId: string;
-    aliases?: string[];
-}
-export declare function OpenLocalFile({ handleClose, session }: OpenLocalFileProps): import("react/jsx-runtime").JSX.Element;
-export {};
-//# sourceMappingURL=OpenLocalFile.d.ts.map

package/dist/components/OpenLocalFile.d.ts.map

@@ -1 +0,0 @@
-{"version":3,"file":"OpenLocalFile.d.ts","sourceRoot":"","sources":["../../src/components/OpenLocalFile.tsx"],"names":[],"mappings":"AAkBA,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,mBAAmB,CAAA;AAC3D,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,YAAY,CAAA;AAKpD,UAAU,kBAAkB;IAC1B,OAAO,EAAE,kBAAkB,CAAA;IAC3B,WAAW,IAAI,IAAI,CAAA;IACnB,kBAAkB,EAAE,kBAAkB,CAAA;CACvC;AAED,MAAM,WAAW,eAAe;IAC9B,OAAO,EAAE,MAAM,CAAA;IACf,QAAQ,EAAE,MAAM,CAAA;IAChB,OAAO,CAAC,EAAE,MAAM,EAAE,CAAA;CACnB;AAED,wBAAgB,aAAa,CAAC,EAAE,WAAW,EAAE,OAAO,EAAE,EAAE,kBAAkB,2CAwJzE"}

package/dist/util/loadAssemblyIntoClient.d.ts

@@ -1,5 +0,0 @@
-import { type ClientDataStore } from '@apollo-annotation/common';
-import type { ApolloAssemblyI, CheckResultSnapshot } from '@apollo-annotation/mst';
-export declare function loadAssemblyIntoClient(assemblyId: string, gff3FileText: string, apolloDataStore: ClientDataStore): Promise<ApolloAssemblyI>;
-export declare function checkFeatures(assembly: ApolloAssemblyI): Promise<CheckResultSnapshot[]>;
-//# sourceMappingURL=loadAssemblyIntoClient.d.ts.map

package/dist/util/loadAssemblyIntoClient.d.ts.map

@@ -1 +0,0 @@
-{"version":3,"file":"loadAssemblyIntoClient.d.ts","sourceRoot":"","sources":["../../src/util/loadAssemblyIntoClient.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,eAAe,EAAiB,MAAM,2BAA2B,CAAA;AAC/E,OAAO,KAAK,EACV,eAAe,EACf,mBAAmB,EACpB,MAAM,wBAAwB,CAAA;AAU/B,wBAAsB,sBAAsB,CAC1C,UAAU,EAAE,MAAM,EAClB,YAAY,EAAE,MAAM,EACpB,eAAe,EAAE,eAAe,4BAyDjC;AAED,wBAAsB,aAAa,CACjC,QAAQ,EAAE,eAAe,GACxB,OAAO,CAAC,mBAAmB,EAAE,CAAC,CAehC"}

package/src/BackendDrivers/DesktopFileDriver.ts

@@ -1,184 +0,0 @@
-/* eslint-disable @typescript-eslint/require-await */
-import {
-  type AssemblySpecificChange,
-  type Change,
-  isAssemblySpecificChange,
-} from '@apollo-annotation/common'
-import type {
-  AnnotationFeatureSnapshot,
-  CheckResultSnapshot,
-} from '@apollo-annotation/mst'
-import {
-  ValidationResultSet,
-  annotationFeatureToGFF3,
-  splitStringIntoChunks,
-} from '@apollo-annotation/shared'
-import { type GFF3Item, formatSync } from '@gmod/gff'
-import { getConf } from '@jbrowse/core/configuration'
-import { type Region, getSession } from '@jbrowse/core/util'
-import { getSnapshot } from '@jbrowse/mobx-state-tree'
-
-import { checkFeatures, loadAssemblyIntoClient } from '../util'
-
-import { BackendDriver, type RefNameAliases } from './BackendDriver'
-
-export class DesktopFileDriver extends BackendDriver {
-  async loadAssembly(assemblyName: string) {
-    const { assemblyManager } = getSession(this.clientStore)
-    const assembly = assemblyManager.get(assemblyName)
-    if (!assembly) {
-      throw new Error(`Assembly ${assemblyName} not found`)
-    }
-    const { file } = getConf(assembly, ['sequence', 'metadata']) as {
-      file: string
-    }
-
-    // eslint-disable-next-line @typescript-eslint/no-require-imports, @typescript-eslint/consistent-type-imports
-    const fs = require('node:fs') as typeof import('fs')
-    const fileContents = await fs.promises.readFile(file, 'utf8')
-    return loadAssemblyIntoClient(assemblyName, fileContents, this.clientStore)
-  }
-
-  async getAssembly(assemblyName: string) {
-    let assembly = this.clientStore.assemblies.get(assemblyName)
-    if (!assembly) {
-      assembly = await this.loadAssembly(assemblyName)
-    }
-    return assembly
-  }
-
-  async getRefNameAliases(assemblyName: string): Promise<RefNameAliases[]> {
-    const assembly = await this.getAssembly(assemblyName)
-    const refNameAliases: RefNameAliases[] = []
-    for (const [, refSeq] of assembly.refSeqs) {
-      refNameAliases.push({
-        refName: refSeq.name,
-        aliases: [refSeq._id],
-        uniqueId: `alias-${refSeq._id}`,
-      })
-    }
-    return refNameAliases
-  }
-
-  async getFeatures(
-    region: Region,
-  ): Promise<[AnnotationFeatureSnapshot[], CheckResultSnapshot[]]> {
-    await this.getAssembly(region.assemblyName)
-    return [[], []]
-  }
-
-  async getSequence(region: Region) {
-    const { assemblyName, end, refName, start } = region
-    const assembly = await this.getAssembly(assemblyName)
-    const refSeq = assembly.refSeqs.get(refName)
-    if (!refSeq) {
-      throw new Error(`refSeq ${refName} not found in client data store`)
-    }
-    const seq = refSeq.getSequence(start, end)
-    return { seq, refSeq: refName }
-  }
-
-  async getRegions(assemblyName: string): Promise<Region[]> {
-    const assembly = await this.getAssembly(assemblyName)
-    const regions: Region[] = []
-    for (const [, refSeq] of assembly.refSeqs) {
-      regions.push({
-        assemblyName,
-        refName: refSeq.name,
-        start: refSeq.sequence[0].start,
-        end: refSeq.sequence[0].stop,
-      })
-    }
-    return regions
-  }
-
-  getAssemblies() {
-    const { assemblyManager } = getSession(this.clientStore)
-    return assemblyManager.assemblies.filter((assembly) => {
-      const sequenceMetadata = getConf(assembly, ['sequence', 'metadata']) as
-        | { apollo: boolean; internetAccountConfigId?: string; file?: string }
-        | undefined
-      return Boolean(
-        sequenceMetadata &&
-          sequenceMetadata.apollo &&
-          !sequenceMetadata.internetAccountConfigId &&
-          sequenceMetadata.file,
-      )
-    })
-  }
-
-  async submitChange(change: Change | AssemblySpecificChange) {
-    if (!isAssemblySpecificChange(change)) {
-      throw new Error(
-        `Cannot use this type of change with local file: "${change.typeName}"`,
-      )
-    }
-    const { assemblyManager } = getSession(this.clientStore)
-    const assembly = assemblyManager.get(change.assembly)
-    if (!assembly) {
-      throw new Error(`Could not find assembly with name "${change.assembly}"`)
-    }
-    const { file } = getConf(assembly, ['sequence', 'metadata']) as {
-      file: string
-    }
-    const clientAssembly = this.clientStore.assemblies.get(change.assembly)
-    if (!clientAssembly) {
-      throw new Error(
-        `Could not find assembly in client with name "${change.assembly}"`,
-      )
-    }
-    const refSeqs = new Set(...clientAssembly.refSeqs.keys())
-    const { checkResults } = this.clientStore
-    for (const checkResult of checkResults.values()) {
-      if (refSeqs.has(checkResult.refSeq)) {
-        checkResults.delete(checkResult._id)
-      }
-    }
-    const newCheckResults = await checkFeatures(clientAssembly)
-    this.clientStore.addCheckResults(newCheckResults)
-    const gff3Items: GFF3Item[] = [{ directive: 'gff-version', value: '3' }]
-    for (const [, refSeq] of clientAssembly.refSeqs) {
-      gff3Items.push({
-        directive: 'sequence-region',
-        value: `${refSeq.name} 1 ${refSeq.sequence[0].stop}`,
-      })
-    }
-    for (const comment of clientAssembly.comments) {
-      gff3Items.push({ comment })
-    }
-    for (const [, refSeq] of clientAssembly.refSeqs) {
-      const { features } = refSeq
-      for (const [, feature] of features) {
-        gff3Items.push(annotationFeatureToGFF3(getSnapshot(feature)))
-      }
-    }
-    for (const [, refSeq] of clientAssembly.refSeqs) {
-      const [sequence] = refSeq.sequence
-      const formattedSequence = splitStringIntoChunks(
-        sequence.sequence,
-        80,
-      ).join('\n')
-      gff3Items.push({
-        id: refSeq.name,
-        description: refSeq.description,
-        sequence: formattedSequence,
-      })
-    }
-
-    const gff3Contents = formatSync(gff3Items)
-
-    // eslint-disable-next-line @typescript-eslint/no-require-imports, @typescript-eslint/consistent-type-imports
-    const fs = require('node:fs') as typeof import('fs')
-    await fs.promises.writeFile(file, gff3Contents, 'utf8')
-
-    const results = new ValidationResultSet()
-    return results
-  }
-
-  async searchFeatures(
-    _term: string,
-    _assemblies: string[],
-  ): Promise<AnnotationFeatureSnapshot[]> {
-    return []
-  }
-}

package/src/BackendDrivers/InMemoryFileDriver.ts

@@ -1,107 +0,0 @@
-/* eslint-disable @typescript-eslint/require-await */
-import type { AssemblySpecificChange, Change } from '@apollo-annotation/common'
-import type {
-  AnnotationFeatureSnapshot,
-  CheckResultSnapshot,
-} from '@apollo-annotation/mst'
-import { ValidationResultSet } from '@apollo-annotation/shared'
-import { getConf } from '@jbrowse/core/configuration'
-import { type Region, getSession } from '@jbrowse/core/util'
-
-import type { SubmitOpts } from '../ChangeManager'
-import { checkFeatures } from '../util'
-
-import { BackendDriver, type RefNameAliases } from './BackendDriver'
-
-export class InMemoryFileDriver extends BackendDriver {
-  async getFeatures(): Promise<
-    [AnnotationFeatureSnapshot[], CheckResultSnapshot[]]
-  > {
-    return [[], []]
-  }
-
-  async getSequence(region: Region) {
-    const { assemblyName, end, refName, start } = region
-    const assembly = this.clientStore.assemblies.get(assemblyName)
-    if (!assembly) {
-      return { seq: '', refSeq: refName }
-    }
-    const refSeq = assembly.refSeqs.get(refName)
-    if (!refSeq) {
-      return { seq: '', refSeq: refName }
-    }
-    const seq = refSeq.getSequence(start, end)
-    return { seq, refSeq: refName }
-  }
-
-  async getRefNameAliases(assemblyName: string): Promise<RefNameAliases[]> {
-    const assembly = this.clientStore.assemblies.get(assemblyName)
-    const refNameAliases: RefNameAliases[] = []
-    if (!assembly) {
-      return refNameAliases
-    }
-    for (const [, refSeq] of assembly.refSeqs) {
-      refNameAliases.push({
-        refName: refSeq.name,
-        aliases: [refSeq._id],
-        uniqueId: `alias-${refSeq._id}`,
-      })
-    }
-    return refNameAliases
-  }
-
-  async getRegions(assemblyName: string): Promise<Region[]> {
-    const assembly = this.clientStore.assemblies.get(assemblyName)
-    if (!assembly) {
-      return []
-    }
-    const regions: Region[] = []
-    for (const [, refSeq] of assembly.refSeqs) {
-      regions.push({
-        assemblyName,
-        refName: refSeq.name,
-        start: refSeq.sequence[0].start,
-        end: refSeq.sequence[0].stop,
-      })
-    }
-    return regions
-  }
-
-  getAssemblies() {
-    const { assemblyManager } = getSession(this.clientStore)
-    return assemblyManager.assemblies.filter((assembly) => {
-      const sequenceMetadata = getConf(assembly, ['sequence', 'metadata']) as
-        | { apollo: boolean; internetAccountConfigId?: string; file?: string }
-        | undefined
-      return Boolean(
-        sequenceMetadata &&
-          sequenceMetadata.apollo &&
-          !sequenceMetadata.file &&
-          !sequenceMetadata.internetAccountConfigId,
-      )
-    })
-  }
-
-  async submitChange(
-    _change: Change | AssemblySpecificChange,
-    _opts: SubmitOpts = {},
-  ) {
-    const { clientStore } = this
-    const { assemblies } = clientStore
-    clientStore.clearCheckResults()
-    for (const [, assembly] of assemblies) {
-      if (assembly.backendDriverType === 'InMemoryFileDriver') {
-        const checkResults = await checkFeatures(assembly)
-        clientStore.addCheckResults(checkResults)
-      }
-    }
-    return new ValidationResultSet()
-  }
-
-  async searchFeatures(
-    _term: string,
-    _assemblies: string[],
-  ): Promise<AnnotationFeatureSnapshot[]> {
-    return []
-  }
-}

package/src/LinearApolloDisplay/glyphs/index.ts

@@ -1,3 +0,0 @@
-export * from './BoxGlyph'
-export * from './GeneGlyph'
-export * from './GenericChildGlyph'