@apollo-annotation/shared 0.1.19 → 0.1.20

package/dist/Changes/TypeChange.js

@@ -0,0 +1,114 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.TypeChange = void 0;
+/* eslint-disable @typescript-eslint/restrict-template-expressions */
+/* eslint-disable @typescript-eslint/require-await */
+/* eslint-disable @typescript-eslint/no-unnecessary-condition */
+const common_1 = require("@apollo-annotation/common");
+class TypeChange extends common_1.FeatureChange {
+    typeName = 'TypeChange';
+    changes;
+    constructor(json, options) {
+        super(json, options);
+        this.changes = 'changes' in json ? json.changes : [json];
+    }
+    toJSON() {
+        const { assembly, changedIds, changes, typeName } = this;
+        if (changes.length === 1) {
+            const [{ featureId, newType, oldType }] = changes;
+            return { typeName, changedIds, assembly, featureId, oldType, newType };
+        }
+        return { typeName, changedIds, assembly, changes };
+    }
+    /**
+     * Applies the required change to database
+     * @param backend - parameters from backend
+     * @returns
+     */
+    async executeOnServer(backend) {
+        const { featureModel, session } = backend;
+        const { changes, logger } = this;
+        const featuresForChanges = [];
+        // Let's first check that all features are found and those old values match with expected ones. We do this just to be sure that all changes can be done.
+        for (const entry of changes) {
+            const { featureId, oldType } = entry;
+            // Search correct feature
+            const topLevelFeature = await featureModel
+                .findOne({ allIds: featureId })
+                .session(session)
+                .exec();
+            if (!topLevelFeature) {
+                const errMsg = `*** ERROR: The following featureId was not found in database ='${featureId}'`;
+                logger.error(errMsg);
+                throw new Error(errMsg);
+                // throw new NotFoundException(errMsg)  -- This is causing runtime error because Exception comes from @nestjs/common!!!
+            }
+            logger.debug?.(`*** Feature found: ${JSON.stringify(topLevelFeature)}`);
+            const foundFeature = this.getFeatureFromId(topLevelFeature, featureId);
+            if (!foundFeature) {
+                const errMsg = 'ERROR when searching feature by featureId';
+                logger.error(errMsg);
+                throw new Error(errMsg);
+            }
+            logger.debug?.(`*** Found feature: ${JSON.stringify(foundFeature)}`);
+            if (foundFeature.type !== oldType) {
+                const errMsg = `*** ERROR: Feature's current type "${topLevelFeature.type}" doesn't match with expected value "${oldType}"`;
+                logger.error(errMsg);
+                throw new Error(errMsg);
+            }
+            featuresForChanges.push({ feature: foundFeature, topLevelFeature });
+        }
+        // Let's update objects.
+        for (const [idx, change] of changes.entries()) {
+            const { newType } = change;
+            const { feature, topLevelFeature } = featuresForChanges[idx];
+            feature.type = newType;
+            if (topLevelFeature._id.equals(feature._id)) {
+                topLevelFeature.markModified('type'); // Mark as modified. Without this save() -method is not updating data in database
+            }
+            else {
+                topLevelFeature.markModified('children'); // Mark as modified. Without this save() -method is not updating data in database
+            }
+            try {
+                await topLevelFeature.save();
+            }
+            catch (error) {
+                logger.debug?.(`*** FAILED: ${error}`);
+                throw error;
+            }
+            logger.debug?.(`*** Object updated in Mongo. New object: ${JSON.stringify(topLevelFeature)}`);
+        }
+    }
+    async executeOnLocalGFF3(_backend) {
+        throw new Error('executeOnLocalGFF3 not implemented');
+    }
+    async executeOnClient(dataStore) {
+        if (!dataStore) {
+            throw new Error('No data store');
+        }
+        for (const [idx, changedId] of this.changedIds.entries()) {
+            const feature = dataStore.getFeature(changedId);
+            if (!feature) {
+                throw new Error(`Could not find feature with identifier "${changedId}"`);
+            }
+            feature.setType(this.changes[idx].newType);
+        }
+    }
+    getInverse() {
+        const { assembly, changedIds, changes, logger, typeName } = this;
+        const inverseChangedIds = [...changedIds].reverse();
+        const inverseChanges = [...changes].reverse().map((endChange) => ({
+            featureId: endChange.featureId,
+            oldType: endChange.newType,
+            newType: endChange.oldType,
+        }));
+        return new TypeChange({
+            changedIds: inverseChangedIds,
+            typeName,
+            changes: inverseChanges,
+            assembly,
+        }, { logger });
+    }
+}
+exports.TypeChange = TypeChange;
+//# sourceMappingURL=TypeChange.js.map

package/dist/Changes/TypeChange.js.map

@@ -0,0 +1 @@
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package/dist/Changes/UserChange.d.ts

@@ -0,0 +1,25 @@
+import { Change, ChangeOptions, ClientDataStore, LocalGFF3DataStore, SerializedChange, ServerDataStore } from '@apollo-annotation/common';
+export interface SerializedUserChangeBase extends SerializedChange {
+    typeName: 'UserChange';
+    userId: string;
+}
+export interface UserChangeDetails {
+    role: 'admin' | 'user' | 'readOnly';
+}
+export interface SerializedUserChangeSingle extends SerializedUserChangeBase, UserChangeDetails {
+}
+export interface SerializedUserChangeMultiple extends SerializedUserChangeBase {
+    changes: UserChangeDetails[];
+}
+export type SerializedUserChange = SerializedUserChangeSingle | SerializedUserChangeMultiple;
+export declare class UserChange extends Change {
+    typeName: "UserChange";
+    changes: UserChangeDetails[];
+    userId: string;
+    constructor(json: SerializedUserChange, options?: ChangeOptions);
+    toJSON(): SerializedUserChange;
+    executeOnServer(backend: ServerDataStore): Promise<void>;
+    executeOnLocalGFF3(_backend: LocalGFF3DataStore): Promise<void>;
+    executeOnClient(_dataStore: ClientDataStore): Promise<void>;
+    getInverse(): UserChange;
+}

package/dist/Changes/UserChange.js

@@ -0,0 +1,51 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.UserChange = void 0;
+/* eslint-disable @typescript-eslint/require-await */
+const common_1 = require("@apollo-annotation/common");
+class UserChange extends common_1.Change {
+    typeName = 'UserChange';
+    changes;
+    userId;
+    constructor(json, options) {
+        super(json, options);
+        this.changes = 'changes' in json ? json.changes : [json];
+        this.userId = json.userId;
+    }
+    toJSON() {
+        const { changes, typeName, userId } = this;
+        if (changes.length === 1) {
+            const [{ role }] = changes;
+            return { typeName, userId, role };
+        }
+        return { typeName, userId, changes };
+    }
+    async executeOnServer(backend) {
+        const { session, userModel } = backend;
+        const { changes, logger, userId } = this;
+        for (const change of changes) {
+            logger.debug?.(`change: ${JSON.stringify(changes)}`);
+            const { role } = change;
+            const user = await userModel
+                .findByIdAndUpdate(userId, { role })
+                .session(session)
+                .exec();
+            if (!user) {
+                const errMsg = `*** ERROR: User with id "${userId}" not found`;
+                logger.error(errMsg);
+                throw new Error(errMsg);
+            }
+        }
+    }
+    async executeOnLocalGFF3(_backend) {
+        throw new Error('executeOnLocalGFF3 not implemented');
+    }
+    // eslint-disable-next-line @typescript-eslint/no-empty-function
+    async executeOnClient(_dataStore) { }
+    getInverse() {
+        const { changes, logger, typeName, userId } = this;
+        return new UserChange({ typeName, changes, userId }, { logger });
+    }
+}
+exports.UserChange = UserChange;
+//# sourceMappingURL=UserChange.js.map

package/dist/Changes/UserChange.js.map

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

@@ -0,0 +1,50 @@
+import { AddAssemblyAndFeaturesFromFileChange } from './AddAssemblyAndFeaturesFromFileChange';
+import { AddAssemblyFromExternalChange } from './AddAssemblyFromExternalChange';
+import { AddAssemblyFromFileChange } from './AddAssemblyFromFileChange';
+import { AddFeatureChange } from './AddFeatureChange';
+import { AddFeaturesFromFileChange } from './AddFeaturesFromFileChange';
+import { AddRefSeqAliasesChange } from './AddRefSeqAliasesChange';
+import { DeleteAssemblyChange } from './DeleteAssemblyChange';
+import { DeleteFeatureChange } from './DeleteFeatureChange';
+import { DeleteUserChange } from './DeleteUserChange';
+import { FeatureAttributeChange } from './FeatureAttributeChange';
+import { ImportJBrowseConfigChange } from './ImportJBrowseConfigChange';
+import { LocationEndChange } from './LocationEndChange';
+import { LocationStartChange } from './LocationStartChange';
+import { StrandChange } from './StrandChange';
+import { TypeChange } from './TypeChange';
+import { UserChange } from './UserChange';
+export declare const changes: {
+    AddAssemblyAndFeaturesFromFileChange: typeof AddAssemblyAndFeaturesFromFileChange;
+    AddAssemblyFromFileChange: typeof AddAssemblyFromFileChange;
+    AddAssemblyFromExternalChange: typeof AddAssemblyFromExternalChange;
+    AddFeatureChange: typeof AddFeatureChange;
+    AddFeaturesFromFileChange: typeof AddFeaturesFromFileChange;
+    DeleteAssemblyChange: typeof DeleteAssemblyChange;
+    DeleteFeatureChange: typeof DeleteFeatureChange;
+    DeleteUserChange: typeof DeleteUserChange;
+    FeatureAttributeChange: typeof FeatureAttributeChange;
+    ImportJBrowseConfigChange: typeof ImportJBrowseConfigChange;
+    LocationEndChange: typeof LocationEndChange;
+    LocationStartChange: typeof LocationStartChange;
+    StrandChange: typeof StrandChange;
+    TypeChange: typeof TypeChange;
+    UserChange: typeof UserChange;
+    AddRefSeqAliasesChange: typeof AddRefSeqAliasesChange;
+};
+export * from './AddAssemblyAndFeaturesFromFileChange';
+export * from './AddAssemblyFromFileChange';
+export * from './AddAssemblyFromExternalChange';
+export * from './AddFeatureChange';
+export * from './AddFeaturesFromFileChange';
+export * from './DeleteAssemblyChange';
+export * from './DeleteFeatureChange';
+export * from './DeleteUserChange';
+export * from './FeatureAttributeChange';
+export * from './ImportJBrowseConfigChange';
+export * from './LocationEndChange';
+export * from './LocationStartChange';
+export * from './StrandChange';
+export * from './TypeChange';
+export * from './UserChange';
+export * from './AddRefSeqAliasesChange';

package/dist/Changes/index.js

@@ -0,0 +1,55 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.changes = void 0;
+const tslib_1 = require("tslib");
+const AddAssemblyAndFeaturesFromFileChange_1 = require("./AddAssemblyAndFeaturesFromFileChange");
+const AddAssemblyFromExternalChange_1 = require("./AddAssemblyFromExternalChange");
+const AddAssemblyFromFileChange_1 = require("./AddAssemblyFromFileChange");
+const AddFeatureChange_1 = require("./AddFeatureChange");
+const AddFeaturesFromFileChange_1 = require("./AddFeaturesFromFileChange");
+const AddRefSeqAliasesChange_1 = require("./AddRefSeqAliasesChange");
+const DeleteAssemblyChange_1 = require("./DeleteAssemblyChange");
+const DeleteFeatureChange_1 = require("./DeleteFeatureChange");
+const DeleteUserChange_1 = require("./DeleteUserChange");
+const FeatureAttributeChange_1 = require("./FeatureAttributeChange");
+const ImportJBrowseConfigChange_1 = require("./ImportJBrowseConfigChange");
+const LocationEndChange_1 = require("./LocationEndChange");
+const LocationStartChange_1 = require("./LocationStartChange");
+const StrandChange_1 = require("./StrandChange");
+const TypeChange_1 = require("./TypeChange");
+const UserChange_1 = require("./UserChange");
+exports.changes = {
+    AddAssemblyAndFeaturesFromFileChange: AddAssemblyAndFeaturesFromFileChange_1.AddAssemblyAndFeaturesFromFileChange,
+    AddAssemblyFromFileChange: AddAssemblyFromFileChange_1.AddAssemblyFromFileChange,
+    AddAssemblyFromExternalChange: AddAssemblyFromExternalChange_1.AddAssemblyFromExternalChange,
+    AddFeatureChange: AddFeatureChange_1.AddFeatureChange,
+    AddFeaturesFromFileChange: AddFeaturesFromFileChange_1.AddFeaturesFromFileChange,
+    DeleteAssemblyChange: DeleteAssemblyChange_1.DeleteAssemblyChange,
+    DeleteFeatureChange: DeleteFeatureChange_1.DeleteFeatureChange,
+    DeleteUserChange: DeleteUserChange_1.DeleteUserChange,
+    FeatureAttributeChange: FeatureAttributeChange_1.FeatureAttributeChange,
+    ImportJBrowseConfigChange: ImportJBrowseConfigChange_1.ImportJBrowseConfigChange,
+    LocationEndChange: LocationEndChange_1.LocationEndChange,
+    LocationStartChange: LocationStartChange_1.LocationStartChange,
+    StrandChange: StrandChange_1.StrandChange,
+    TypeChange: TypeChange_1.TypeChange,
+    UserChange: UserChange_1.UserChange,
+    AddRefSeqAliasesChange: AddRefSeqAliasesChange_1.AddRefSeqAliasesChange,
+};
+tslib_1.__exportStar(require("./AddAssemblyAndFeaturesFromFileChange"), exports);
+tslib_1.__exportStar(require("./AddAssemblyFromFileChange"), exports);
+tslib_1.__exportStar(require("./AddAssemblyFromExternalChange"), exports);
+tslib_1.__exportStar(require("./AddFeatureChange"), exports);
+tslib_1.__exportStar(require("./AddFeaturesFromFileChange"), exports);
+tslib_1.__exportStar(require("./DeleteAssemblyChange"), exports);
+tslib_1.__exportStar(require("./DeleteFeatureChange"), exports);
+tslib_1.__exportStar(require("./DeleteUserChange"), exports);
+tslib_1.__exportStar(require("./FeatureAttributeChange"), exports);
+tslib_1.__exportStar(require("./ImportJBrowseConfigChange"), exports);
+tslib_1.__exportStar(require("./LocationEndChange"), exports);
+tslib_1.__exportStar(require("./LocationStartChange"), exports);
+tslib_1.__exportStar(require("./StrandChange"), exports);
+tslib_1.__exportStar(require("./TypeChange"), exports);
+tslib_1.__exportStar(require("./UserChange"), exports);
+tslib_1.__exportStar(require("./AddRefSeqAliasesChange"), exports);
+//# sourceMappingURL=index.js.map

package/dist/Changes/index.js.map

@@ -0,0 +1 @@
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package/dist/Checks/CDSCheck.d.ts

@@ -0,0 +1,8 @@
+import { Check } from '@apollo-annotation/common';
+import { AnnotationFeatureSnapshot, CheckResultSnapshot } from '@apollo-annotation/mst';
+export declare class CDSCheck extends Check {
+    name: string;
+    version: number;
+    default: boolean;
+    checkFeature(feature: AnnotationFeatureSnapshot, getSequence: (start: number, end: number) => Promise<string>): Promise<CheckResultSnapshot[]>;
+}

package/dist/Checks/CDSCheck.js

@@ -0,0 +1,197 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.CDSCheck = void 0;
+const tslib_1 = require("tslib");
+const common_1 = require("@apollo-annotation/common");
+const util_1 = require("@jbrowse/core/util");
+const bson_objectid_1 = tslib_1.__importDefault(require("bson-objectid"));
+var STOP_CODONS;
+(function (STOP_CODONS) {
+    STOP_CODONS[STOP_CODONS["TAG"] = 0] = "TAG";
+    STOP_CODONS[STOP_CODONS["TAA"] = 1] = "TAA";
+    STOP_CODONS[STOP_CODONS["TGA"] = 2] = "TGA";
+})(STOP_CODONS || (STOP_CODONS = {}));
+const iupacComplements = {
+    G: 'C',
+    A: 'T',
+    T: 'A',
+    C: 'G',
+    R /* G or A */: 'Y',
+    Y /* T or C */: 'R',
+    M /* A or C */: 'K',
+    K /* G or T */: 'M',
+    S /* G or C */: 'S',
+    W /* A or T */: 'W',
+    H /* A or C or T */: 'D',
+    B /* G or T or C */: 'V',
+    V /* G or C or A */: 'B',
+    D /* G or A or T */: 'H',
+    N /* G or A or T or C */: 'N',
+};
+function reverseComplement(dna) {
+    const complement = [];
+    for (const nt of dna) {
+        const rc = iupacComplements[nt.toUpperCase()];
+        if (rc === undefined) {
+            throw new TypeError(`Cannot complement nucleotide: "${nt}"`);
+        }
+        if (nt === nt.toLowerCase()) {
+            complement.push(rc.toLowerCase());
+        }
+        else {
+            complement.push(rc);
+        }
+    }
+    return complement.reverse().join('');
+}
+async function getCDSSequence(cdsLocation, strand, getSequence) {
+    const sequences = await Promise.all(cdsLocation.map(({ max, min }) => getSequence(min, max)));
+    if (strand === -1) {
+        return sequences.map((seq) => reverseComplement(seq)).join('');
+    }
+    return sequences.join('');
+}
+function splitSequenceInCodons(cds) {
+    const codons = [];
+    for (let i = 0; i <= cds.length - 3; i += 3) {
+        codons.push(cds.slice(i, i + 3));
+    }
+    return codons;
+}
+function getOriginalCodonLocation(cdsLocation, strand, index) {
+    let lengthToStart = index * 3;
+    let lengthToEnd = lengthToStart + 3;
+    let startLocation = undefined, endLocation = undefined;
+    for (const loc of cdsLocation) {
+        const locLength = loc.max - loc.min;
+        if (startLocation === undefined && locLength > lengthToStart) {
+            startLocation = loc.min + lengthToStart;
+        }
+        else {
+            lengthToStart -= locLength;
+        }
+        if (endLocation === undefined && locLength > lengthToEnd) {
+            endLocation = loc.min + lengthToEnd;
+        }
+        else {
+            lengthToEnd -= locLength;
+        }
+        if (startLocation !== undefined && endLocation !== undefined) {
+            return [startLocation, endLocation];
+        }
+    }
+    return;
+}
+async function checkMRNA(feature, getSequence) {
+    const checkResults = [];
+    const { _id, max, min, refSeq, strand } = feature;
+    const cdsLocations = getCDSLocations(feature);
+    if (!cdsLocations) {
+        return checkResults;
+    }
+    const ids = [_id];
+    for (const cdsLocation of cdsLocations) {
+        const sequence = await getCDSSequence(cdsLocation, strand, getSequence);
+        const codons = splitSequenceInCodons(sequence);
+        if (sequence.length % 3 === 0) {
+            const lastCodon = codons.pop(); // Last codon is supposed to be a stop
+            if (lastCodon && !(lastCodon.toUpperCase() in STOP_CODONS)) {
+                checkResults.push({
+                    _id: new bson_objectid_1.default().toHexString(),
+                    name: 'MissingStopCodonCheck',
+                    ids,
+                    refSeq: refSeq.toString(),
+                    start: max,
+                    end: max,
+                    message: `Feature "${_id}" is missing a stop codon`,
+                });
+            }
+        }
+        else {
+            checkResults.push({
+                _id: new bson_objectid_1.default().toHexString(),
+                name: 'MultipleOfThreeCheck',
+                ids,
+                refSeq: refSeq.toString(),
+                start: min,
+                end: max,
+                message: `The coding sequence for feature "${_id}" is not a multiple of three`,
+            });
+        }
+        for (const [idx, codon] of codons.entries()) {
+            const location = getOriginalCodonLocation(cdsLocation, strand, idx);
+            if (location && codon.toUpperCase() in STOP_CODONS) {
+                const [codonStart, codonEnd] = location;
+                checkResults.push({
+                    _id: new bson_objectid_1.default().toHexString(),
+                    name: 'InternalStopCodonCheck',
+                    ids,
+                    refSeq: refSeq.toString(),
+                    start: codonStart,
+                    end: codonEnd,
+                    message: `The coding sequence for feature "${_id}" has an internal stop codon`,
+                });
+            }
+        }
+    }
+    return checkResults;
+}
+function getCDSLocations(feature) {
+    if (feature.type !== 'mRNA') {
+        return;
+    }
+    const { children, strand } = feature;
+    if (!children) {
+        return;
+    }
+    const cdsChildren = Object.values(children).filter((child) => child.type === 'CDS');
+    if (cdsChildren.length === 0) {
+        return;
+    }
+    const cdsLocations = [];
+    for (const cds of cdsChildren) {
+        const { max: cdsMax, min: cdsMin } = cds;
+        const locs = [];
+        for (const child of Object.values(children)) {
+            if (child.type !== 'exon') {
+                continue;
+            }
+            const [start, end] = (0, util_1.intersection2)(cdsMin, cdsMax, child.min, child.max);
+            if (start !== undefined && end !== undefined) {
+                locs.push({ min: start, max: end });
+            }
+        }
+        locs.sort(({ min: a }, { min: b }) => a - b);
+        if (strand === -1) {
+            locs.reverse();
+        }
+        let nextPhase = 0;
+        const phasedLocs = locs.map((loc) => {
+            const phase = nextPhase;
+            nextPhase = ((3 - ((loc.max - loc.min - phase + 3) % 3)) % 3);
+            return { ...loc, phase };
+        });
+        cdsLocations.push(phasedLocs);
+    }
+    return cdsLocations;
+}
+class CDSCheck extends common_1.Check {
+    name = 'CDSCheck';
+    version = 1;
+    default = true;
+    async checkFeature(feature, getSequence) {
+        if (feature.type === 'mRNA') {
+            return checkMRNA(feature, getSequence);
+        }
+        if (!feature.children) {
+            return [];
+        }
+        const checkResults = [];
+        for (const child of Object.values(feature.children)) {
+            checkResults.push(...(await this.checkFeature(child, getSequence)));
+        }
+        return checkResults;
+    }
+}
+exports.CDSCheck = CDSCheck;
+//# sourceMappingURL=CDSCheck.js.map

package/dist/Checks/CDSCheck.js.map

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package/dist/Checks/index.d.ts

@@ -0,0 +1 @@
+export * from './CDSCheck';

package/dist/Checks/index.js

@@ -0,0 +1,5 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+const tslib_1 = require("tslib");
+tslib_1.__exportStar(require("./CDSCheck"), exports);
+//# sourceMappingURL=index.js.map

package/dist/Checks/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/Checks/index.ts"],"names":[],"mappings":";;;AAAA,qDAA0B"}

package/dist/Common/index.d.ts

@@ -0,0 +1 @@
+export * from './jwtPayload';

package/dist/Common/index.js

@@ -0,0 +1,5 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+const tslib_1 = require("tslib");
+tslib_1.__exportStar(require("./jwtPayload"), exports);
+//# sourceMappingURL=index.js.map

package/dist/Common/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/Common/index.ts"],"names":[],"mappings":";;;AAAA,uDAA4B"}

package/dist/Common/jwtPayload.d.ts

@@ -0,0 +1,12 @@
+export interface JWTPayload {
+    username: string;
+    email: string;
+    role?: 'admin' | 'user' | 'readOnly' | 'none';
+    id: string;
+}
+export interface DecodedJWT extends JWTPayload {
+    iat: number;
+    exp: number;
+}
+export declare function makeUserSessionId(userOrToken: DecodedJWT | string): string;
+export declare function getDecodedToken(token: string): DecodedJWT;

package/dist/Common/jwtPayload.js

@@ -0,0 +1,16 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.makeUserSessionId = makeUserSessionId;
+exports.getDecodedToken = getDecodedToken;
+const tslib_1 = require("tslib");
+const jwt_decode_1 = tslib_1.__importDefault(require("jwt-decode"));
+function makeUserSessionId(userOrToken) {
+    const user = typeof userOrToken === 'string'
+        ? (0, jwt_decode_1.default)(userOrToken)
+        : userOrToken;
+    return `${user.id}-${user.iat}`;
+}
+function getDecodedToken(token) {
+    return (0, jwt_decode_1.default)(token);
+}
+//# sourceMappingURL=jwtPayload.js.map

package/dist/Common/jwtPayload.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"jwtPayload.js","sourceRoot":"","sources":["../../src/Common/jwtPayload.ts"],"names":[],"mappings":";;AAcA,8CAMC;AAED,0CAEC;;AAxBD,oEAAkC;AAclC,SAAgB,iBAAiB,CAAC,WAAgC;IAChE,MAAM,IAAI,GACR,OAAO,WAAW,KAAK,QAAQ;QAC7B,CAAC,CAAC,IAAA,oBAAS,EAAa,WAAW,CAAC;QACpC,CAAC,CAAC,WAAW,CAAA;IACjB,OAAO,GAAG,IAAI,CAAC,EAAE,IAAI,IAAI,CAAC,GAAG,EAAE,CAAA;AACjC,CAAC;AAED,SAAgB,eAAe,CAAC,KAAa;IAC3C,OAAO,IAAA,oBAAS,EAAa,KAAK,CAAC,CAAA;AACrC,CAAC"}

package/dist/GFF3/gff3ToAnnotationFeature.d.ts

@@ -0,0 +1,3 @@
+import { AnnotationFeatureSnapshot } from '@apollo-annotation/mst';
+import { GFF3Feature } from '@gmod/gff';
+export declare function gff3ToAnnotationFeature(gff3Feature: GFF3Feature, refSeq?: string, featureIds?: string[]): AnnotationFeatureSnapshot;