@apollo-annotation/cli 0.1.19 → 0.1.20

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

@@ -1,11 +1,12 @@
 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:',
@@ -46,12 +47,12 @@ 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');

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

@@ -1,11 +1,11 @@
 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:',
@@ -47,12 +47,12 @@ 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');

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

@@ -1,11 +1,11 @@
 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',
@@ -19,12 +19,12 @@ 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');

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`));

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) {

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) {

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: {

package/dist/commands/feature/import.js

@@ -1,9 +1,9 @@
 import * as fs from 'node:fs';
 import { Flags } from '@oclif/core';
 import { Agent, fetch } from 'undici';
-import { BaseCommand } from '../../baseCommand.js';
-import { convertAssemblyNameToId, createFetchErrorMessage, localhostToAddress, uploadFile, } from '../../utils.js';
-export default class Import extends BaseCommand {
+import { FileCommand } from '../../fileCommand.js';
+import { convertAssemblyNameToId, createFetchErrorMessage, localhostToAddress, } from '../../utils.js';
+export default class Import extends FileCommand {
     static summary = 'Import features from local gff file';
     static description = 'By default, features are added to the existing ones.';
     static examples = [
@@ -15,7 +15,7 @@ export default class Import extends BaseCommand {
     static flags = {
         'input-file': Flags.string({
             char: 'i',
-            description: 'Input gff or gtf file',
+            description: 'Input gff file',
             required: true,
         }),
         assembly: Flags.string({
@@ -33,12 +33,12 @@ export default class Import extends BaseCommand {
         if (!fs.existsSync(flags['input-file'])) {
             this.error(`File "${flags['input-file']}" does not exist`);
         }
-        const access = await this.getAccess(flags['config-file'], flags.profile);
+        const access = await this.getAccess();
         const assembly = await convertAssemblyNameToId(access.address, access.accessToken, [flags.assembly]);
         if (assembly.length === 0) {
             this.error(`Assembly "${flags.assembly}" does not exist. Perhaps you want to create this assembly first`);
         }
-        const uploadId = await uploadFile(access.address, access.accessToken, flags['input-file'], 'text/x-gff3');
+        const uploadId = await this.uploadFile(access.address, access.accessToken, flags['input-file'], 'text/x-gff3', false);
         const body = {
             typeName: 'AddFeaturesFromFileChange',
             assembly: assembly[0],

package/dist/commands/feature/search.js

@@ -2,7 +2,7 @@
 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';
 async function searchFeatures(address, accessToken, assemblies, term) {
     const url = new URL(localhostToAddress(`${address}/features/searchFeatures`));
     const searchParams = new URLSearchParams({
@@ -25,7 +25,7 @@ async function searchFeatures(address, accessToken, assemblies, term) {
 }
 export default class Search extends BaseCommand {
     static summary = 'Free text search for feature in one or more assemblies';
-    static description = wrapLines(`Return features matching a query string. This command searches only in:
+    static description = `Return features matching a query string. This command searches only in:
 
     - Attribute *values* (not attribute names)
     - Source field (which in fact is stored as an attribute)
@@ -47,7 +47,7 @@ export default class Search extends BaseCommand {
     - "with"
     - "Finger"
     - "chr1"
-    - "0.987"`);
+    - "0.987"`;
     static examples = [
         {
             description: 'Search "bac" in these assemblies:',
@@ -63,12 +63,12 @@ export default class Search extends BaseCommand {
         assembly: Flags.string({
             char: 'a',
             multiple: true,
-            description: wrapLines('Assembly names or IDs to search; use "-" to read it from stdin. If omitted search all assemblies'),
+            description: 'Assembly names or IDs to search; use "-" to read it from stdin. If omitted search all assemblies',
         }),
     };
     async run() {
         const { flags } = await this.parse(Search);
-        const access = await this.getAccess(flags['config-file'], flags.profile);
+        const access = await this.getAccess();
         let assemblyIds = [];
         if (flags.assembly === undefined) {
             const asm = await queryApollo(access.address, access.accessToken, 'assemblies');
@@ -77,7 +77,7 @@ export default class Search extends BaseCommand {
             }
         }
         else {
-            const assembly = idReader(flags.assembly);
+            const assembly = await idReader(flags.assembly);
             assemblyIds = await convertAssemblyNameToId(access.address, access.accessToken, assembly);
         }
         if (assemblyIds.length === 0) {

package/dist/commands/file/delete.d.ts

@@ -0,0 +1,13 @@
+import { BaseCommand } from '../../baseCommand.js';
+export default class Delete extends BaseCommand<typeof Delete> {
+    static summary: string;
+    static description: string;
+    static examples: {
+        description: string;
+        command: string;
+    }[];
+    static flags: {
+        'file-id': import("@oclif/core/lib/interfaces/parser.js").OptionFlag<string[], import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
+    };
+    run(): Promise<void>;
+}

package/dist/commands/file/delete.js

@@ -0,0 +1,58 @@
+import { Flags } from '@oclif/core';
+import { fetch } from 'undici';
+import { BaseCommand } from '../../baseCommand.js';
+import { createFetchErrorMessage, filterJsonList, idReader, localhostToAddress, queryApollo, } from '../../utils.js';
+export default class Delete extends BaseCommand {
+    static summary = 'Delete files from the Apollo server';
+    static description = 'Deleted files are printed to stdout. See also `apollo file get` to list the files on the server';
+    static examples = [
+        {
+            description: 'Delete file multiple files:',
+            command: '<%= config.bin %> <%= command.id %> -i 123...abc xyz...789',
+        },
+    ];
+    static flags = {
+        'file-id': Flags.string({
+            char: 'i',
+            description: 'IDs of the files to delete',
+            default: ['-'],
+            multiple: true,
+        }),
+    };
+    async run() {
+        const { flags } = await this.parse(Delete);
+        const access = await this.getAccess();
+        const files = await queryApollo(access.address, access.accessToken, 'files');
+        const json = (await files.json());
+        const ff = await idReader(flags['file-id']);
+        let deleted = [];
+        for (const id of ff) {
+            const res = await deleteFile(access.address, access.accessToken, id);
+            if (res.status === 404) {
+                this.logToStderr(`File id "${id}" not found`);
+            }
+            else {
+                const fid = filterJsonList(json, [id], '_id');
+                deleted = [...deleted, ...fid];
+            }
+        }
+        this.log(JSON.stringify(deleted, null, 2));
+        this.logToStderr(`${deleted.length.toString()} file(s) deleted.`);
+    }
+}
+async function deleteFile(address, accessToken, fileId) {
+    const auth = {
+        method: 'DELETE',
+        headers: {
+            Authorization: `Bearer ${accessToken}`,
+            'Content-Type': 'application/json',
+        },
+    };
+    const url = new URL(localhostToAddress(`${address}/files/${fileId}`));
+    const response = await fetch(url, auth);
+    if (!response.ok && response.status != 404) {
+        const errorMessage = await createFetchErrorMessage(response, 'deleteFile failed');
+        throw new Error(errorMessage);
+    }
+    return response;
+}

package/dist/commands/file/download.d.ts

@@ -0,0 +1,14 @@
+import { BaseCommand } from '../../baseCommand.js';
+export default class Download extends BaseCommand<typeof Download> {
+    static summary: string;
+    static description: string;
+    static examples: {
+        description: string;
+        command: string;
+    }[];
+    static flags: {
+        'file-id': import("@oclif/core/lib/interfaces/parser.js").OptionFlag<string, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
+        output: import("@oclif/core/lib/interfaces/parser.js").OptionFlag<string | undefined, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
+    };
+    run(): Promise<void>;
+}

package/dist/commands/file/download.js

@@ -0,0 +1,45 @@
+import { createWriteStream } from 'node:fs';
+import { Writable } from 'node:stream';
+import { Flags } from '@oclif/core';
+import { BaseCommand } from '../../baseCommand.js';
+import { filterJsonList, idReader, queryApollo } from '../../utils.js';
+export default class Download extends BaseCommand {
+    static summary = 'Download a file from the Apollo server';
+    static description = 'See also `apollo file get` to list the files on the server';
+    static examples = [
+        {
+            description: 'Download file with id xyz',
+            command: '<%= config.bin %> <%= command.id %> -i xyz -o genome.fa',
+        },
+    ];
+    static flags = {
+        'file-id': Flags.string({
+            char: 'i',
+            description: 'ID of the file to download',
+            default: '-',
+        }),
+        output: Flags.string({
+            char: 'o',
+            description: 'Write output to this file or "-" for stdout. Default to the name of the uploaded file.',
+        }),
+    };
+    async run() {
+        const { flags } = await this.parse(Download);
+        const access = await this.getAccess();
+        const ff = await idReader([flags['file-id']]);
+        let res = await queryApollo(access.address, access.accessToken, 'files');
+        // eslint-disable-next-line @typescript-eslint/no-unsafe-assignment
+        const json = JSON.parse(await res.text());
+        // eslint-disable-next-line @typescript-eslint/no-unsafe-argument
+        const [fileRec] = filterJsonList(json, ff, '_id');
+        const fileId = fileRec['_id'];
+        res = await queryApollo(access.address, access.accessToken, `files/${fileId}`);
+        let { output } = flags;
+        if (output === undefined) {
+            output = fileRec['basename'];
+        }
+        const fileWriteStream = createWriteStream(output);
+        await res.body?.pipeTo(Writable.toWeb(output === '-' ? process.stdout : fileWriteStream));
+        fileWriteStream.close();
+    }
+}

package/dist/commands/file/get.d.ts

@@ -0,0 +1,13 @@
+import { BaseCommand } from '../../baseCommand.js';
+export default class Get extends BaseCommand<typeof Get> {
+    static summary: string;
+    static description: string;
+    static examples: {
+        description: string;
+        command: string;
+    }[];
+    static flags: {
+        'file-id': import("@oclif/core/lib/interfaces/parser.js").OptionFlag<string[] | undefined, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
+    };
+    run(): Promise<void>;
+}

package/dist/commands/file/get.js

@@ -0,0 +1,38 @@
+import { Flags } from '@oclif/core';
+import { BaseCommand } from '../../baseCommand.js';
+import { idReader, queryApollo } from '../../utils.js';
+export default class Get extends BaseCommand {
+    static summary = 'Get list of files uploaded to the Apollo server';
+    static description = 'Print to stdout the list of files in json format';
+    static examples = [
+        {
+            description: 'Get files by id:',
+            command: '<%= config.bin %> <%= command.id %> -i xyz abc',
+        },
+    ];
+    static flags = {
+        'file-id': Flags.string({
+            char: 'i',
+            description: 'Get files matching this IDs',
+            multiple: true,
+        }),
+    };
+    async run() {
+        const { flags } = await this.parse(Get);
+        const access = await this.getAccess();
+        const files = await queryApollo(access.address, access.accessToken, 'files');
+        const json = (await files.json());
+        let fileIds = [];
+        if (flags['file-id'] !== undefined) {
+            fileIds = await idReader(flags['file-id']);
+        }
+        const keep = [];
+        for (const x of json) {
+            if (flags['file-id'] === undefined ||
+                fileIds.includes(x['_id'])) {
+                keep.push(x);
+            }
+        }
+        this.log(JSON.stringify(keep, null, 2));
+    }
+}

package/dist/commands/file/upload.d.ts

@@ -0,0 +1,16 @@
+import { FileCommand } from '../../fileCommand.js';
+export default class Upload extends FileCommand {
+    static summary: string;
+    static description: string;
+    static examples: {
+        description: string;
+        command: string;
+    }[];
+    static flags: {
+        'input-file': import("@oclif/core/lib/interfaces/parser.js").OptionFlag<string, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
+        type: import("@oclif/core/lib/interfaces/parser.js").OptionFlag<string | undefined, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
+        gzip: import("@oclif/core/lib/interfaces/parser.js").BooleanFlag<boolean>;
+        decompressed: import("@oclif/core/lib/interfaces/parser.js").BooleanFlag<boolean>;
+    };
+    run(): Promise<void>;
+}

package/dist/commands/file/upload.js

@@ -0,0 +1,88 @@
+import { Flags } from '@oclif/core';
+import { FileCommand } from '../../fileCommand.js';
+import { filterJsonList, queryApollo } from '../../utils.js';
+export default class Upload extends FileCommand {
+    static summary = 'Upload a local file to the Apollo server';
+    static description = `This command only uploads a file and returns the corresponding file id.
+  To add an assembly based on this file or to upload & add an assembly in a single pass \
+  see \`apollo assembly add-from-fasta\` and \`add-from-gff\``;
+    static examples = [
+        {
+            description: 'Upload local file, type auto-detected:',
+            command: '<%= config.bin %> <%= command.id %> -i genome.fa > file.json',
+        },
+    ];
+    static flags = {
+        'input-file': Flags.string({
+            char: 'i',
+            description: 'Local file to upload',
+            required: true,
+        }),
+        type: Flags.string({
+            char: 't',
+            description: 'Set file type or autodetected it if not set.\n\
+        NB: There is no check for whether the file complies to this type',
+            options: [
+                'text/x-fasta',
+                'text/x-gff3',
+                'application/x-bgzip-fasta',
+                'text/x-fai',
+                'application/x-gzi',
+            ],
+        }),
+        gzip: Flags.boolean({
+            char: 'z',
+            description: 'Override autodetection and instruct that input is gzip compressed',
+            exclusive: ['decompressed'],
+        }),
+        decompressed: Flags.boolean({
+            char: 'd',
+            description: 'Override autodetection and instruct that input is decompressed',
+            exclusive: ['gzip'],
+        }),
+    };
+    async run() {
+        const { flags } = await this.parse(Upload);
+        const access = await this.getAccess();
+        let { type } = flags;
+        if (type === undefined) {
+            const hasGzipExt = flags['input-file'].endsWith('.gz');
+            const infile = flags['input-file'].replace(/\.gz$/, '');
+            if (/\.fasta$|\.fas$|\.fa$|\.fna$/.test(infile) && hasGzipExt) {
+                this.error(`Unable to auto-detect file type for "${flags['input-file']}" since it may be gzip or bgzip compressed. Please set the -t/--type option`);
+            }
+            else if (/\.fasta$|\.fas$|\.fa$|\.fna$/.test(infile)) {
+                type = 'text/x-fasta';
+            }
+            else if (/\.gff$|\.gff3/.test(infile)) {
+                type = 'text/x-gff3';
+            }
+            else if (infile.endsWith('.fai')) {
+                type = 'text/x-fai';
+            }
+            else if (infile.endsWith('.gzi')) {
+                type = 'application/x-gzi';
+            }
+            else {
+                this.error(`Unable to auto-detect the type of file "${flags['input-file']}". Please set the --type/-t option.`);
+            }
+        }
+        let isGzip = flags['input-file'].endsWith('.gz');
+        // eslint-disable-next-line unicorn/consistent-destructuring
+        if (flags.gzip) {
+            isGzip = true;
+        }
+        // eslint-disable-next-line unicorn/consistent-destructuring
+        if (flags.decompressed) {
+            isGzip = false;
+        }
+        this.logToStderr(`Input is gzip'd: ${isGzip}`);
+        const fileId = await this.uploadFile(access.address, access.accessToken, flags['input-file'], type, isGzip);
+        const res = await queryApollo(access.address, access.accessToken, 'files');
+        // eslint-disable-next-line @typescript-eslint/no-unsafe-assignment
+        const json = JSON.parse(await res.text());
+        // eslint-disable-next-line @typescript-eslint/no-unsafe-argument
+        const [rec] = filterJsonList(json, [fileId], '_id');
+        this.log(JSON.stringify(rec, null, 2));
+    }
+}

package/dist/commands/jbrowse/get-config.d.ts

@@ -0,0 +1,10 @@
+import { BaseCommand } from '../../baseCommand.js';
+export default class GetConfig extends BaseCommand<typeof GetConfig> {
+    static summary: string;
+    static description: string;
+    static examples: {
+        description: string;
+        command: string;
+    }[];
+    run(): Promise<void>;
+}

package/dist/commands/jbrowse/get-config.js

@@ -0,0 +1,21 @@
+import { BaseCommand } from '../../baseCommand.js';
+import { queryApollo } from '../../utils.js';
+export default class GetConfig extends BaseCommand {
+    static summary = 'Get JBrowse configuration from Apollo';
+    static description = 'Print to stdout the JBrowse configuration from Apollo in JSON format';
+    static examples = [
+        {
+            description: 'Get JBrowse configuration:',
+            command: '<%= config.bin %> <%= command.id %> > config.json',
+        },
+    ];
+    async run() {
+        const access = await this.getAccess();
+        const response = await queryApollo(access.address, access.accessToken, 'jbrowse/config.json');
+        if (!response.ok) {
+            throw new Error('Failed to fetch JBrowse configuration');
+        }
+        const json = (await response.json());
+        this.log(JSON.stringify(json, null, 2));
+    }
+}

package/dist/commands/jbrowse/set-config.d.ts

@@ -0,0 +1,13 @@
+import { BaseCommand } from '../../baseCommand.js';
+export default class SetConfig extends BaseCommand<typeof SetConfig> {
+    static summary: string;
+    static description: string;
+    static examples: {
+        description: string;
+        command: string;
+    }[];
+    static args: {
+        inputFile: import("@oclif/core/lib/interfaces/parser.js").Arg<string, Record<string, unknown>>;
+    };
+    run(): Promise<void>;
+}