@apollo-annotation/cli 0.1.18 → 0.1.20

package/dist/commands/feature/add-child.js

@@ -1,19 +1,18 @@
-/* eslint-disable @typescript-eslint/restrict-template-expressions */
-/* eslint-disable @typescript-eslint/restrict-plus-operands */
 /* eslint-disable @typescript-eslint/no-unsafe-argument */
 /* eslint-disable @typescript-eslint/no-unsafe-assignment */
 import { Flags } from '@oclif/core';
 import { ObjectId } from 'bson';
 import { fetch } from 'undici';
 import { BaseCommand } from '../../baseCommand.js';
-import { createFetchErrorMessage, getFeatureById, idReader, localhostToAddress, queryApollo, wrapLines, } from '../../utils.js';
+import { createFetchErrorMessage, getFeatureById, idReader, localhostToAddress, queryApollo, } from '../../utils.js';
 export default class Get extends BaseCommand {
     static summary = 'Add a child feature (e.g. add an exon to an mRNA)';
-    static description = wrapLines('See the other commands under `apollo feature` to retrive the parent ID of interest and to populate the child feature with attributes.');
+    static description = 'See the other commands under `apollo feature` \
+to retrive the parent ID of interest and to populate the child feature with attributes.';
     static examples = [
         {
             description: 'Add an exon at genomic coordinates 10..20 to this feature ID:',
-            command: '<%= config.bin %> <%= command.id %> -i 6605826fbd0eee691f83e73f -t exon -s 10 -e 20',
+            command: '<%= config.bin %> <%= command.id %> -i 660...73f -t exon -s 10 -e 20',
         },
     ];
     static flags = {
@@ -46,12 +45,12 @@ export default class Get extends BaseCommand {
         if (flags.start <= 0) {
             this.error('Coordinates must be greater than 0');
         }
-        const ff = idReader([flags['feature-id']]);
+        const ff = await idReader([flags['feature-id']]);
         if (ff.length !== 1) {
             this.error(`Expected only one feature identifier. Got ${ff.length}`);
         }
         const [featureId] = ff;
-        const access = await this.getAccess(flags['config-file'], flags.profile);
+        const access = await this.getAccess();
         const res = await getFeatureById(access.address, access.accessToken, featureId);
         if (!res.ok) {
             const errorMessage = await createFetchErrorMessage(res, 'getFeatureById failed');
@@ -63,17 +62,16 @@ export default class Get extends BaseCommand {
             const errorMessage = await createFetchErrorMessage(childRes, 'Add child failed');
             throw new Error(errorMessage);
         }
-        this.exit(0);
     }
-    async addChild(address, accessToken, parentFeature, start, end, type) {
-        const pStart = parentFeature['start'];
-        const pEnd = parentFeature['end'];
-        if (start < pStart || end > pEnd) {
-            this.error(`Error: Child feature coordinates (${start + 1}-${end}) cannot extend beyond parent coordinates (${pStart + 1}-${pEnd})`);
+    async addChild(address, accessToken, parentFeature, min, max, type) {
+        const pMin = parentFeature.min;
+        const pMax = parentFeature.max;
+        if (min < pMin || max > pMax) {
+            this.error(`Error: Child feature coordinates (${min + 1}-${max}) cannot extend beyond parent coordinates (${pMin + 1}-${pMax})`);
         }
         const res = await queryApollo(address, accessToken, 'refSeqs');
         const refSeqs = (await res.json());
-        const refSeq = parentFeature['refSeq'];
+        const { refSeq } = parentFeature;
         let assembly = '';
         for (const x of refSeqs) {
             if (x['_id'] === refSeq) {
@@ -83,17 +81,18 @@ export default class Get extends BaseCommand {
         }
         const change = {
             typeName: 'AddFeatureChange',
-            changedIds: [parentFeature['_id']],
+            // eslint-disable-next-line unicorn/consistent-destructuring
+            changedIds: [parentFeature._id],
             assembly,
             addedFeature: {
                 _id: new ObjectId().toHexString(),
-                gffId: '',
                 refSeq,
-                start,
-                end,
+                min,
+                max,
                 type,
             },
-            parentFeatureId: parentFeature['_id'],
+            // eslint-disable-next-line unicorn/consistent-destructuring
+            parentFeatureId: parentFeature._id,
         };
         const url = new URL(localhostToAddress(`${address}/changes`));
         const auth = {

package/dist/commands/feature/check.js

@@ -1,11 +1,11 @@
 import { Flags } from '@oclif/core';
 import { fetch } from 'undici';
 import { BaseCommand } from '../../baseCommand.js';
-import { convertAssemblyNameToId, createFetchErrorMessage, idReader, localhostToAddress, queryApollo, wrapLines, } from '../../utils.js';
+import { convertAssemblyNameToId, createFetchErrorMessage, idReader, localhostToAddress, queryApollo, } from '../../utils.js';
 export default class Check extends BaseCommand {
     static summary = 'Get check results';
-    static description = wrapLines('Use this command to view which features fail checks along with the reason for failing.\
-    Use `apollo assembly check` for managing which checks should be applied to an assembly');
+    static description = 'Use this command to view which features fail checks along with the reason for failing.\
+Use `apollo assembly check` for managing which checks should be applied to an assembly';
     static examples = [
         {
             description: 'Get all check results in the database:',
@@ -29,10 +29,10 @@ export default class Check extends BaseCommand {
     };
     async run() {
         const { flags } = await this.parse(Check);
-        const access = await this.getAccess(flags['config-file'], flags.profile);
+        const access = await this.getAccess();
         let keepFeatures = new Set();
         if (flags['feature-id'] !== undefined) {
-            keepFeatures = new Set(idReader(flags['feature-id']));
+            keepFeatures = new Set(await idReader(flags['feature-id']));
         }
         const keepAsmId = await keepAssemblies(access.address, access.accessToken, flags.assembly);
         const res = await queryApollo(access.address, access.accessToken, 'refseqs');
@@ -50,15 +50,15 @@ export default class Check extends BaseCommand {
             if (flags['feature-id'] === undefined) {
                 keep = true;
             }
-            else {
-                for (const x of chk['ids']) {
-                    if (keepFeatures.has(x)) {
+            else if (chk.ids !== undefined) {
+                for (const x of chk.ids) {
+                    if (x !== undefined && keepFeatures.has(x.toString())) {
                         keep = true;
                         break;
                     }
                 }
             }
-            if (keep && refseqId.has(chk['refSeq'])) {
+            if (keep && refseqId.has(chk.refSeq)) {
                 results.push(chk);
             }
         }
@@ -71,11 +71,11 @@ async function keepAssemblies(address, accessToken, assembly) {
         const res = await queryApollo(address, accessToken, 'assemblies');
         const asm = (await res.json());
         for (const x of asm) {
-            keepAssembly.push(x['_id']);
+            keepAssembly.push(x._id);
         }
     }
     else {
-        const ids = idReader([assembly]);
+        const ids = await idReader([assembly]);
         keepAssembly = await convertAssemblyNameToId(address, accessToken, ids);
     }
     return keepAssembly;

package/dist/commands/feature/copy.js

@@ -2,11 +2,12 @@ import { Flags } from '@oclif/core';
 import { ObjectId } from 'bson';
 import { fetch } from 'undici';
 import { BaseCommand } from '../../baseCommand.js';
-import { createFetchErrorMessage, getAssemblyFromRefseq, getFeatureById, getRefseqId, localhostToAddress, wrapLines, } from '../../utils.js';
+import { createFetchErrorMessage, getAssemblyFromRefseq, getFeatureById, getRefseqId, localhostToAddress, } from '../../utils.js';
 export default class Copy extends BaseCommand {
     static summary = 'Copy a feature to another location';
-    static description = wrapLines('The feature may be copied to the same or to a different assembly. \
-    he destination reference sequence may be selected by name only if unique in the database or by name and assembly or by identifier.');
+    static description = 'The feature may be copied to the same or to a different assembly. \
+The destination reference sequence may be selected by name only if unique in \
+the database or by name and assembly or by identifier.';
     static examples = [
         {
             description: 'Copy this feature ID to chr1:100 in assembly hg38:',
@@ -40,7 +41,7 @@ export default class Copy extends BaseCommand {
         if (flags.start <= 0) {
             this.error('Start coordinate must be greater than 0');
         }
-        const access = await this.getAccess(flags['config-file'], flags.profile);
+        const access = await this.getAccess();
         const res = await getFeatureById(access.address, access.accessToken, flags['feature-id']);
         if (!res.ok) {
             const errorMessage = await createFetchErrorMessage(res, 'getFeatureById failed');
@@ -60,11 +61,9 @@ export default class Copy extends BaseCommand {
             const errorMessage = await createFetchErrorMessage(rescopy, 'Copy feature failed');
             throw new Error(errorMessage);
         }
-        this.exit(0);
     }
-    async copyFeature(address, accessToken, feature, refseq, start, assembly, newId) {
-        const featureLen = feature['end'] -
-            feature['start'];
+    async copyFeature(address, accessToken, feature, refseq, min, assembly, newId) {
+        const featureLen = feature.max - feature.min;
         const change = {
             typeName: 'AddFeatureChange',
             changedIds: [newId],
@@ -72,12 +71,11 @@ export default class Copy extends BaseCommand {
             addedFeature: {
                 _id: newId,
                 refSeq: refseq,
-                start: start - 1,
-                end: start + featureLen - 1,
-                type: feature['type'],
-                attributes: feature['attributes'],
-                discontinuousLocations: feature['discontinuousLocations'],
-                strand: feature['strand'],
+                min: min - 1,
+                max: min + featureLen - 1,
+                type: feature.type,
+                attributes: feature.attributes,
+                strand: feature.strand,
             },
             copyFeature: true,
             allIds: [newId],

package/dist/commands/feature/delete.js

@@ -1,24 +1,19 @@
-/* eslint-disable @typescript-eslint/no-unsafe-argument */
-/* eslint-disable @typescript-eslint/no-unsafe-assignment */
 import { Flags } from '@oclif/core';
 import { fetch } from 'undici';
 import { BaseCommand } from '../../baseCommand.js';
-import { createFetchErrorMessage, getFeatureById, idReader, localhostToAddress, wrapLines, } from '../../utils.js';
+import { createFetchErrorMessage, getFeatureById, idReader, localhostToAddress, } from '../../utils.js';
 async function deleteFeature(address, accessToken, feature) {
     const changeJson = {
         typeName: 'DeleteFeatureChange',
-        changedIds: [feature],
-        assembly: feature['assembly'],
+        changedIds: [feature._id],
+        assembly: '111222333444555666777888', // Use a placeholder objectId (i.e. some 24 chars)
         deletedFeature: {
-            _id: feature['_id'],
-            gffId: feature['gffId'],
-            refSeq: feature['refSeq'],
-            type: feature['type'],
-            start: feature['start'],
-            end: feature['end'],
-            discontinuousLocations: feature['discontinuousLocations'],
-            score: feature['score'],
-            attributes: feature['attributes'],
+            _id: feature._id,
+            refSeq: feature.refSeq,
+            type: feature.type,
+            min: feature.min,
+            max: feature.max,
+            attributes: feature.attributes,
         },
     };
     const url = new URL(localhostToAddress(`${address}/changes`));
@@ -39,7 +34,7 @@ async function deleteFeature(address, accessToken, feature) {
 }
 export default class Delete extends BaseCommand {
     static summary = 'Delete one or more features by ID';
-    static description = wrapLines('Note that deleting a child feature after deleting its parent will result in an error unless you set -f/--force.');
+    static description = 'Note that deleting a child feature after deleting its parent will result in an error unless you set -f/--force.';
     static flags = {
         'feature-id': Flags.string({
             char: 'i',
@@ -58,12 +53,12 @@ export default class Delete extends BaseCommand {
     };
     async run() {
         const { flags } = await this.parse(Delete);
-        const tmpIds = idReader(flags['feature-id']);
+        const tmpIds = await idReader(flags['feature-id']);
         const featureIds = new Set();
         for (const x of tmpIds) {
             featureIds.add(x);
         }
-        const access = await this.getAccess(flags['config-file'], flags.profile);
+        const access = await this.getAccess();
         for (const featureId of featureIds) {
             const res = await getFeatureById(access.address, access.accessToken, featureId);
             if (res.status === 404 && flags.force) {
@@ -75,7 +70,7 @@ export default class Delete extends BaseCommand {
             }
             const feature = JSON.parse(await res.text());
             if (flags['dry-run']) {
-                this.log(feature);
+                this.log(JSON.stringify(feature, null, 2));
             }
             else {
                 const delFet = await deleteFeature(access.address, access.accessToken, feature);
@@ -85,6 +80,5 @@ export default class Delete extends BaseCommand {
                 }
             }
         }
-        this.exit(0);
     }
 }

package/dist/commands/feature/edit-attribute.js

@@ -1,14 +1,12 @@
-/* eslint-disable @typescript-eslint/no-unsafe-argument */
-/* eslint-disable @typescript-eslint/no-unsafe-member-access */
-/* eslint-disable @typescript-eslint/no-unsafe-assignment */
 import { Flags } from '@oclif/core';
 import { fetch } from 'undici';
 import { BaseCommand } from '../../baseCommand.js';
-import { createFetchErrorMessage, getAssemblyFromRefseq, getFeatureById, idReader, localhostToAddress, wrapLines, } from '../../utils.js';
+import { createFetchErrorMessage, getAssemblyFromRefseq, getFeatureById, idReader, localhostToAddress, } from '../../utils.js';
 export default class EditAttibute extends BaseCommand {
     static summary = 'Add, edit, or view a feature attribute';
-    static description = wrapLines('Be aware that there is no checking whether attributes names and values are valid. \
-    For example, you can create non-unique ID attributes or you can set gene ontology terms to non-existing terms');
+    static description = 'Be aware that there is no checking whether attributes names and values are valid. \
+For example, you can create non-unique ID attributes or you can set gene ontology \
+terms to non-existing terms';
     static examples = [
         {
             description: 'Add attribute "domains" with a list of values:',
@@ -49,18 +47,21 @@ export default class EditAttibute extends BaseCommand {
         if (flags.delete && flags.value) {
             this.error('Error: Options --delete and --value are mutually exclusive');
         }
-        const ff = idReader([flags['feature-id']]);
+        const ff = await idReader([flags['feature-id']]);
         if (ff.length !== 1) {
             this.error(`Expected only one feature identifier. Got ${ff.length}`);
         }
         const [featureId] = ff;
-        const access = await this.getAccess(flags['config-file'], flags.profile);
+        const access = await this.getAccess();
         const response = await getFeatureById(access.address, access.accessToken, featureId);
         if (!response.ok) {
             const errorMessage = await createFetchErrorMessage(response, 'getFeatureById failed');
             throw new Error(errorMessage);
         }
         const featureJson = JSON.parse(await response.text());
+        if (featureJson.attributes === undefined) {
+            featureJson.attributes = {};
+        }
         if (flags.value === undefined && !flags.delete) {
             this.log(JSON.stringify(featureJson.attributes[flags.attribute]));
             return;
@@ -72,13 +73,20 @@ export default class EditAttibute extends BaseCommand {
         else {
             featureJson.attributes[flags.attribute] = flags.value;
         }
-        const assembly = await getAssemblyFromRefseq(access.address, access.accessToken, featureJson['refSeq']);
+        const assembly = await getAssemblyFromRefseq(access.address, access.accessToken, featureJson.refSeq);
+        const attrs = {};
+        for (const [key, val] of Object.entries(featureJson.attributes)) {
+            if (!val) {
+                continue;
+            }
+            attrs[key] = [...val];
+        }
         const changeJson = {
             typeName: 'FeatureAttributeChange',
             changedIds: [featureId],
             assembly,
             featureId,
-            attributes: featureJson.attributes,
+            attributes: attrs,
         };
         const url = new URL(localhostToAddress(`${access.address}/changes`));
         const auth = {
@@ -94,6 +102,5 @@ export default class EditAttibute extends BaseCommand {
             const errorMessage = await createFetchErrorMessage(res, 'edit-attribute failed');
             throw new Error(errorMessage);
         }
-        this.exit(0);
     }
 }

package/dist/commands/feature/edit-coords.js

@@ -1,14 +1,11 @@
-/* eslint-disable @typescript-eslint/no-unsafe-member-access */
-/* eslint-disable @typescript-eslint/no-unsafe-argument */
-/* eslint-disable @typescript-eslint/no-unsafe-assignment */
 import { Flags } from '@oclif/core';
 import { fetch } from 'undici';
 import { BaseCommand } from '../../baseCommand.js';
-import { createFetchErrorMessage, getAssemblyFromRefseq, getFeatureById, idReader, localhostToAddress, wrapLines, } from '../../utils.js';
+import { createFetchErrorMessage, getAssemblyFromRefseq, getFeatureById, idReader, localhostToAddress, } from '../../utils.js';
 export default class Get extends BaseCommand {
     static summary = 'Edit feature start and/or end coordinates';
-    static description = wrapLines("If editing a child feature that new coordinates must be within the parent's coordinates.\
-    To get the identifier of the feature to edit consider using `apollo feature get` or `apollo feature search`");
+    static description = "If editing a child feature that new coordinates must be within the parent's coordinates.\
+To get the identifier of the feature to edit consider using `apollo feature get` or `apollo feature search`";
     static examples = [
         {
             description: 'Edit start and end:',
@@ -50,27 +47,27 @@ export default class Get extends BaseCommand {
         if (flags.start !== undefined) {
             flags.start -= 1;
         }
-        const ff = idReader([flags['feature-id']]);
+        const ff = await idReader([flags['feature-id']]);
         if (ff.length !== 1) {
             this.error(`Expected only one feature identifier. Got ${ff.length}`);
         }
         const [featureId] = ff;
-        const access = await this.getAccess(flags['config-file'], flags.profile);
+        const access = await this.getAccess();
         const res = await getFeatureById(access.address, access.accessToken, featureId);
         if (!res.ok) {
             const errorMessage = await createFetchErrorMessage(res, 'getFeatureById failed');
             throw new Error(errorMessage);
         }
         const featureJson = JSON.parse(await res.text());
-        const assembly = await getAssemblyFromRefseq(access.address, access.accessToken, featureJson['refSeq']);
-        const currentEnd = featureJson['end'];
+        const assembly = await getAssemblyFromRefseq(access.address, access.accessToken, featureJson.refSeq);
+        const currentEnd = featureJson.max;
         let edit = ['Start', 'End'];
         if (flags.start !== undefined && flags.start > currentEnd) {
-            // Edit End first so you avoid an intermediate start > end
+            // Edit End (Max) first so you avoid an intermediate start > end
             edit = ['End', 'Start'];
         }
         for (const coord of edit) {
-            const currentStart = featureJson['start'];
+            const currentStart = featureJson.min;
             if (coord === 'Start' &&
                 (flags.start === undefined || flags.start === currentStart)) {
                 continue;
@@ -79,18 +76,36 @@ export default class Get extends BaseCommand {
                 (flags.end === undefined || flags.end === currentEnd)) {
                 continue;
             }
-            const changeJson = {
-                typeName: `Location${coord}Change`,
-                changedIds: [featureId],
-                assembly,
-                featureId,
-                [`old${coord}`]: featureJson[coord.toLowerCase()],
-                [`new${coord}`]: flags[coord.toLowerCase()],
-            };
+            let body;
+            if (coord === 'Start' && flags.start !== undefined) {
+                const oldCoord = featureJson.min;
+                body = {
+                    typeName: 'LocationStartChange',
+                    changedIds: [featureId],
+                    assembly,
+                    featureId,
+                    ['oldStart']: oldCoord,
+                    ['newStart']: flags.start,
+                };
+            }
+            else if (coord === 'End' && flags.end !== undefined) {
+                const oldCoord = featureJson.max;
+                body = {
+                    typeName: 'LocationEndChange',
+                    changedIds: [featureId],
+                    assembly,
+                    featureId,
+                    ['oldEnd']: oldCoord,
+                    ['newEnd']: flags.end,
+                };
+            }
+            else {
+                throw new Error(`Unexpected coordinate name: "${coord}"`);
+            }
             const url = new URL(localhostToAddress(`${access.address}/changes`));
             const auth = {
                 method: 'POST',
-                body: JSON.stringify(changeJson),
+                body: JSON.stringify(body),
                 headers: {
                     authorization: `Bearer ${access.accessToken}`,
                     'Content-Type': 'application/json',

package/dist/commands/feature/edit-type.js

@@ -1,14 +1,11 @@
-/* eslint-disable @typescript-eslint/no-unsafe-argument */
-/* eslint-disable @typescript-eslint/no-unsafe-member-access */
-/* eslint-disable @typescript-eslint/no-unsafe-assignment */
 import { Flags } from '@oclif/core';
 import { fetch } from 'undici';
 import { BaseCommand } from '../../baseCommand.js';
-import { createFetchErrorMessage, getAssemblyFromRefseq, getFeatureById, idReader, localhostToAddress, wrapLines, } from '../../utils.js';
+import { createFetchErrorMessage, getAssemblyFromRefseq, getFeatureById, idReader, localhostToAddress, } from '../../utils.js';
 export default class Get extends BaseCommand {
     static summary = 'Edit or view feature type';
-    static description = wrapLines('Feature type is column 3 in gff format.\
-    It must be a valid sequence ontology term although but the valifdity of the new term is not checked.');
+    static description = 'Feature type is column 3 in gff format.\
+It must be a valid sequence ontology term although but the valifdity of the new term is not checked.';
     static flags = {
         'feature-id': Flags.string({
             char: 'i',
@@ -22,19 +19,19 @@ export default class Get extends BaseCommand {
     };
     async run() {
         const { flags } = await this.parse(Get);
-        const ff = idReader([flags['feature-id']]);
+        const ff = await idReader([flags['feature-id']]);
         if (ff.length !== 1) {
             this.error(`Expected only one feature identifier. Got ${ff.length}`);
         }
         const [featureId] = ff;
-        const access = await this.getAccess(flags['config-file'], flags.profile);
+        const access = await this.getAccess();
         const response = await getFeatureById(access.address, access.accessToken, featureId);
         if (!response.ok) {
             const errorMessage = await createFetchErrorMessage(response, 'getFeatureById failed');
             throw new Error(errorMessage);
         }
         const featureJson = JSON.parse(await response.text());
-        const currentType = featureJson['type'];
+        const currentType = featureJson.type;
         if (flags.type === undefined) {
             this.log(currentType);
             return;
@@ -43,7 +40,7 @@ export default class Get extends BaseCommand {
             this.logToStderr(`NOTE: Feature ${featureId} is already of type "${flags.type}"`);
             return;
         }
-        const assembly = await getAssemblyFromRefseq(access.address, access.accessToken, featureJson['refSeq']);
+        const assembly = await getAssemblyFromRefseq(access.address, access.accessToken, featureJson.refSeq);
         const changeJson = {
             typeName: 'TypeChange',
             changedIds: [featureId],
@@ -66,6 +63,5 @@ export default class Get extends BaseCommand {
             const errorMessage = await createFetchErrorMessage(res, 'edit-type failed');
             throw new Error(errorMessage);
         }
-        this.exit(0);
     }
 }

package/dist/commands/feature/edit.js

@@ -3,10 +3,10 @@ import * as fs from 'node:fs';
 import { Flags } from '@oclif/core';
 import { fetch } from 'undici';
 import { BaseCommand } from '../../baseCommand.js';
-import { createFetchErrorMessage, localhostToAddress, wrapLines, } from '../../utils.js';
+import { createFetchErrorMessage, localhostToAddress, readStdin, } from '../../utils.js';
 export default class Get extends BaseCommand {
     static summary = 'Edit features using an appropiate json input';
-    static description = wrapLines(`Edit a feature by submitting a json input with all the required attributes for Apollo to process it. This is a very low level command which most users probably do not need.
+    static description = `Edit a feature by submitting a json input with all the required attributes for Apollo to process it. This is a very low level command which most users probably do not need.
 
     Input may be a json string or a json file and it may be an array of changes. This is an example input for editing feature type:
 
@@ -19,7 +19,7 @@ export default class Get extends BaseCommand {
       "featureId": "6613f7d22c957525d631b1cc",
       "oldType": "BAC",
       "newType": "G_quartet"
-    }`);
+    }`;
     static examples = [
         {
             description: 'Editing by passing a json to stdin:',
@@ -37,7 +37,7 @@ export default class Get extends BaseCommand {
         const { flags } = await this.parse(Get);
         let jsonStr = flags['json-input'];
         if (flags['json-input'] === '-') {
-            jsonStr = fs.readFileSync(process.stdin.fd).toString();
+            jsonStr = await readStdin();
         }
         else if (fs.existsSync(flags['json-input'])) {
             jsonStr = fs.readFileSync(flags['json-input']).toString();
@@ -46,7 +46,7 @@ export default class Get extends BaseCommand {
         if (!Array.isArray(json)) {
             json = [json];
         }
-        const access = await this.getAccess(flags['config-file'], flags.profile);
+        const access = await this.getAccess();
         for (const change of json) {
             const str = JSON.stringify(change);
             const url = new URL(localhostToAddress(`${access.address}/changes`));
@@ -64,6 +64,5 @@ export default class Get extends BaseCommand {
                 throw new Error(errorMessage);
             }
         }
-        this.exit(0);
     }
 }

package/dist/commands/feature/get-id.js

@@ -1,10 +1,10 @@
 import { Flags } from '@oclif/core';
 import { fetch } from 'undici';
 import { BaseCommand } from '../../baseCommand.js';
-import { createFetchErrorMessage, idReader, localhostToAddress, wrapLines, } from '../../utils.js';
+import { createFetchErrorMessage, idReader, localhostToAddress, } from '../../utils.js';
 export default class Get extends BaseCommand {
     static summary = 'Get features given their identifiers';
-    static description = wrapLines('Invalid identifiers or identifiers not found in the database will be silently ignored');
+    static description = 'Invalid identifiers or identifiers not found in the database will be silently ignored';
     static examples = [
         {
             description: 'Get features for these identifiers:',
@@ -14,15 +14,15 @@ export default class Get extends BaseCommand {
     static flags = {
         'feature-id': Flags.string({
             char: 'i',
-            description: wrapLines('Retrieves feature with these IDs. Use "-" to read IDs from stdin (one per line)', 40),
+            description: 'Retrieves feature with these IDs. Use "-" to read IDs from stdin (one per line)',
             multiple: true,
             default: ['-'],
         }),
     };
     async run() {
         const { flags } = await this.parse(Get);
-        const access = await this.getAccess(flags['config-file'], flags.profile);
-        let ids = idReader(flags['feature-id']);
+        const access = await this.getAccess();
+        let ids = await idReader(flags['feature-id']);
         ids = [...new Set(ids)];
         const results = [];
         for (const id of ids) {
@@ -33,7 +33,6 @@ export default class Get extends BaseCommand {
             results.push(res);
         }
         this.log(JSON.stringify(results, null, 2));
-        this.exit(0);
     }
     async getFeatureId(address, token, featureId) {
         const url = new URL(localhostToAddress(`${address}/features/${featureId}`));

package/dist/commands/feature/get.js

@@ -1,7 +1,7 @@
 import { Flags } from '@oclif/core';
 import { fetch } from 'undici';
 import { BaseCommand } from '../../baseCommand.js';
-import { createFetchErrorMessage, getRefseqId, localhostToAddress, wrapLines, } from '../../utils.js';
+import { createFetchErrorMessage, getRefseqId, localhostToAddress, } from '../../utils.js';
 export default class Get extends BaseCommand {
     static description = 'Get features in assembly, reference sequence or genomic window';
     static examples = [
@@ -10,7 +10,7 @@ export default class Get extends BaseCommand {
             command: '<%= config.bin %> <%= command.id %> -a myAssembly',
         },
         {
-            description: wrapLines('Get features intersecting chr1:1..1000. You can omit the assembly name if there are no other reference sequences named chr1:'),
+            description: 'Get features intersecting chr1:1..1000. You can omit the assembly name if there are no other reference sequences named chr1:',
             command: '<%= config.bin %> <%= command.id %> -a myAssembly -r chr1 -s 1 -e 1000',
         },
     ];
@@ -39,7 +39,7 @@ export default class Get extends BaseCommand {
         if (flags.start <= 0 || endCoord <= 0) {
             this.error('Start and end coordinates must be greater than 0.');
         }
-        const access = await this.getAccess(flags['config-file'], flags.profile);
+        const access = await this.getAccess();
         const refseqIds = await getRefseqId(access.address, access.accessToken, flags.refseq, flags.assembly);
         const results = [];
         for (const refseq of refseqIds) {
@@ -50,7 +50,6 @@ export default class Get extends BaseCommand {
             }
         }
         this.log(JSON.stringify(results, null, 2));
-        this.exit(0);
     }
     async getFeatures(address, token, refSeq, start, end) {
         const url = new URL(localhostToAddress(`${address}/features/getFeatures`));

package/dist/commands/feature/import.d.ts

@@ -1,5 +1,5 @@
-import { BaseCommand } from '../../baseCommand.js';
-export default class Import extends BaseCommand<typeof Import> {
+import { FileCommand } from '../../fileCommand.js';
+export default class Import extends FileCommand {
     static summary: string;
     static description: string;
     static examples: {