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@apollo-annotation/cli

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@apollo-annotation/cli - npm Package Compare versions

Comparing version 0.1.19 to 0.1.20

dist/commands/assembly/add-from-fasta.d.ts
dist/commands/assembly/add-from-fasta.js
dist/commands/assembly/add-from-gff.d.ts
dist/commands/assembly/add-from-gff.js
dist/commands/file/delete.d.ts
dist/commands/file/delete.js
dist/commands/file/download.d.ts
dist/commands/file/download.js
dist/commands/file/get.d.ts
dist/commands/file/get.js
dist/commands/file/upload.d.ts
dist/commands/file/upload.js
dist/commands/jbrowse/get-config.d.ts
dist/commands/jbrowse/get-config.js
dist/commands/jbrowse/set-config.d.ts
dist/commands/jbrowse/set-config.js
dist/fileCommand.d.ts
dist/fileCommand.js

2

dist/baseCommand.d.ts

@@ -13,3 +13,3 @@ import { Command, Interfaces } from '@oclif/core';

private getConfig;
getAccess(configFile: string | undefined, profileName: string | undefined): Promise<{
getAccess(): Promise<{
address: string;

@@ -16,0 +16,0 @@ accessToken: string;

7

dist/baseCommand.js

@@ -35,7 +35,6 @@ import path from 'node:path';

}
async getAccess(configFile, profileName) {
async getAccess() {
const { 'config-file': configFile, profile } = this.flags;
const config = this.getConfig(configFile);
if (profileName === undefined) {
profileName = process.env.APOLLO_PROFILE ?? 'default';
}
const profileName = process.env.APOLLO_PROFILE ?? profile ?? 'default';
return config.getAccess(profileName);

@@ -42,0 +41,0 @@ }

18

dist/commands/assembly/check.js
import { Flags } from '@oclif/core';
import { fetch } from 'undici';
import { BaseCommand } from '../../baseCommand.js';
import { convertCheckNameToId, createFetchErrorMessage, getAssembly, idReader, localhostToAddress, wrapLines, } from '../../utils.js';
import { convertCheckNameToId, createFetchErrorMessage, getAssembly, idReader, localhostToAddress, } from '../../utils.js';
async function setChecks(address, accessToken, assembly, checkId) {

@@ -57,4 +57,5 @@ const check = {

static summary = 'Add, view, or delete checks to assembly';
static description = wrapLines('Manage checks, i.e. the rules ensuring features in an assembly are plausible. \
This command only sets the checks to apply, to retrieve features flagged by these checks use `apollo feature check`.');
static description = 'Manage checks, i.e. the rules ensuring features in an assembly are plausible. \
This command only sets the checks to apply, to retrieve features flagged by \
these checks use `apollo feature check`.';
static examples = [

@@ -95,3 +96,3 @@ {

const { flags } = await this.parse(Check);
const access = await this.getAccess(flags['config-file'], flags.profile);
const access = await this.getAccess();
const checkTypes = await getCheckTypes(access.address, access.accessToken);

@@ -105,7 +106,4 @@ if (flags.check === undefined && flags.assembly === undefined) {

}
const asm = idReader([flags.assembly]);
const asm = await idReader([flags.assembly]);
const assembly = await getAssembly(access.address, access.accessToken, asm[0]);
if (Object.keys(assembly).length === 0) {
this.error(`Assembly ${flags.assembly} not found`);
}
const currentChecks = getCheckTypesForAssembly(checkTypes, assembly);

@@ -138,4 +136,6 @@ if (flags.check === undefined) {

}
await setChecks(access.address, access.accessToken, assembly['_id'], [...newChecks.values()]);
await setChecks(access.address, access.accessToken, assembly._id, [
...newChecks.values(),
]);
}
}

8

dist/commands/assembly/delete.js
import { Flags } from '@oclif/core';
import { BaseCommand } from '../../baseCommand.js';
import { convertAssemblyNameToId, deleteAssembly, getAssembly, idReader, wrapLines, } from '../../utils.js';
import { convertAssemblyNameToId, deleteAssembly, getAssembly, idReader, } from '../../utils.js';
export default class Delete extends BaseCommand {
static summary = 'Delete assemblies';
static description = wrapLines('Assemblies to delete may be names or IDs');
static description = 'Assemblies to delete may be names or IDs';
static examples = [

@@ -27,4 +27,4 @@ {

const { flags } = await this.parse(Delete);
const access = await this.getAccess(flags['config-file'], flags.profile);
const assembly = idReader(flags.assembly);
const access = await this.getAccess();
const assembly = await idReader(flags.assembly);
const deleteIds = await convertAssemblyNameToId(access.address, access.accessToken, assembly);

@@ -31,0 +31,0 @@ let i = 0;

8

dist/commands/assembly/get.js
import { Flags } from '@oclif/core';
import { BaseCommand } from '../../baseCommand.js';
import { convertAssemblyNameToId, idReader, queryApollo, wrapLines, } from '../../utils.js';
import { convertAssemblyNameToId, idReader, queryApollo } from '../../utils.js';
export default class Get extends BaseCommand {
static summary = 'Get available assemblies';
static description = wrapLines('Print to stdout the list of assemblies in json format');
static description = 'Print to stdout the list of assemblies in json format';
static flags = {

@@ -16,7 +16,7 @@ assembly: Flags.string({

const { flags } = await this.parse(Get);
const access = await this.getAccess(flags['config-file'], flags.profile);
const access = await this.getAccess();
const assemblies = await queryApollo(access.address, access.accessToken, 'assemblies');
let assemblyIds = [];
if (flags.assembly !== undefined) {
const assembly = idReader(flags.assembly);
const assembly = await idReader(flags.assembly);
assemblyIds = await convertAssemblyNameToId(access.address, access.accessToken, assembly);

@@ -23,0 +23,0 @@ }

8

dist/commands/assembly/sequence.js

@@ -5,3 +5,3 @@ /* eslint-disable @typescript-eslint/no-unsafe-argument */

import { BaseCommand } from '../../baseCommand.js';
import { createFetchErrorMessage, getRefseqId, idReader, localhostToAddress, queryApollo, wrapLines, } from '../../utils.js';
import { createFetchErrorMessage, getRefseqId, idReader, localhostToAddress, queryApollo, } from '../../utils.js';
async function getSequence(address, accessToken, refSeq, start, end) {

@@ -31,3 +31,3 @@ const url = new URL(localhostToAddress(`${address}/sequence`));

static summary = 'Get reference sequence in fasta format';
static description = wrapLines('Return the reference sequence for a given assembly and coordinates');
static description = 'Return the reference sequence for a given assembly and coordinates';
static examples = [

@@ -68,7 +68,7 @@ {

}
const access = await this.getAccess(flags['config-file'], flags.profile);
const access = await this.getAccess();
let assembly = undefined;
if (flags.assembly !== undefined) {
;
[assembly] = idReader([flags.assembly]);
[assembly] = await idReader([flags.assembly]);
}

@@ -75,0 +75,0 @@ let refseqIds = [];

14

dist/commands/change/get.js
import { Flags } from '@oclif/core';
import { BaseCommand } from '../../baseCommand.js';
import { convertAssemblyNameToId, idReader, queryApollo, wrapLines, } from '../../utils.js';
import { convertAssemblyNameToId, idReader, queryApollo } from '../../utils.js';
export default class Get extends BaseCommand {
static summary = 'Get list of changes';
static description = wrapLines('Return the change log in json format. Note \
that when an assembly is deleted the link between common name and ID is lost \
(it can still be recovered by inspecting the change log but at present this task is left to the user). \
In such cases you need to use the assembly ID.');
static description = 'Return the change log in json format. Note \
that when an assembly is deleted the link between common name and ID is lost \
(it can still be recovered by inspecting the change log but at present this task is left to the user). \
In such cases you need to use the assembly ID.';
static flags = {

@@ -19,3 +19,3 @@ assembly: Flags.string({

const { flags } = await this.parse(Get);
const access = await this.getAccess(flags['config-file'], flags.profile);
const access = await this.getAccess();
const changes = await queryApollo(access.address, access.accessToken, 'changes');

@@ -26,3 +26,3 @@ const json = (await changes.json());

keep = [];
const assembly = idReader(flags.assembly);
const assembly = await idReader(flags.assembly);
const assemblyIds = await convertAssemblyNameToId(access.address, access.accessToken, assembly);

@@ -29,0 +29,0 @@ for (const x of json) {

7

dist/commands/config.js

@@ -10,9 +10,8 @@ /* eslint-disable @typescript-eslint/no-unsafe-return */

import { BaseCommand } from '../baseCommand.js';
import { createFetchErrorMessage, localhostToAddress, wrapLines, } from '../utils.js';
import { createFetchErrorMessage, localhostToAddress } from '../utils.js';
export default class ApolloConfig extends BaseCommand {
static summary = 'Get or set apollo configuration options';
static description = wrapLines(`Use this command to create or edit a user profile with credentials to access Apollo. \
Configuration options are:
static description = `Use this command to create or edit a user profile with credentials to access Apollo. Configuration options are:
${optionDesc().join('\n\n')}`);
${optionDesc().join('\n\n')}`;
static args = {

@@ -19,0 +18,0 @@ key: Args.string({

11

dist/commands/feature/add-child.js

@@ -7,10 +7,11 @@ /* eslint-disable @typescript-eslint/no-unsafe-argument */

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',
},

@@ -48,3 +49,3 @@ ];

}
const ff = idReader([flags['feature-id']]);
const ff = await idReader([flags['feature-id']]);
if (ff.length !== 1) {

@@ -54,3 +55,3 @@ 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);

@@ -57,0 +58,0 @@ if (!res.ok) {

12

dist/commands/feature/check.js
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 = [

@@ -32,6 +32,6 @@ {

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']));
}

@@ -79,3 +79,3 @@ const keepAsmId = await keepAssemblies(access.address, access.accessToken, flags.assembly);

else {
const ids = idReader([assembly]);
const ids = await idReader([assembly]);
keepAssembly = await convertAssemblyNameToId(address, accessToken, ids);

@@ -82,0 +82,0 @@ }

9

dist/commands/feature/copy.js

@@ -5,7 +5,8 @@ import { Flags } from '@oclif/core';

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 = [

@@ -44,3 +45,3 @@ {

}
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']);

@@ -47,0 +48,0 @@ if (!res.ok) {

8

dist/commands/feature/delete.js
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) {

@@ -37,3 +37,3 @@ const changeJson = {

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 = {

@@ -57,3 +57,3 @@ 'feature-id': Flags.string({

const { flags } = await this.parse(Delete);
const tmpIds = idReader(flags['feature-id']);
const tmpIds = await idReader(flags['feature-id']);
const featureIds = new Set();

@@ -63,3 +63,3 @@ for (const x of tmpIds) {

}
const access = await this.getAccess(flags['config-file'], flags.profile);
const access = await this.getAccess();
for (const featureId of featureIds) {

@@ -66,0 +66,0 @@ const res = await getFeatureById(access.address, access.accessToken, featureId);

11

dist/commands/feature/edit-attribute.js
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 = [

@@ -49,3 +50,3 @@ {

}
const ff = idReader([flags['feature-id']]);
const ff = await idReader([flags['feature-id']]);
if (ff.length !== 1) {

@@ -55,3 +56,3 @@ 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);

@@ -58,0 +59,0 @@ if (!response.ok) {

10

dist/commands/feature/edit-coords.js
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 = [

@@ -50,3 +50,3 @@ {

}
const ff = idReader([flags['feature-id']]);
const ff = await idReader([flags['feature-id']]);
if (ff.length !== 1) {

@@ -56,3 +56,3 @@ 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);

@@ -59,0 +59,0 @@ if (!res.ok) {

10

dist/commands/feature/edit-type.js
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 = {

@@ -22,3 +22,3 @@ 'feature-id': Flags.string({

const { flags } = await this.parse(Get);
const ff = idReader([flags['feature-id']]);
const ff = await idReader([flags['feature-id']]);
if (ff.length !== 1) {

@@ -28,3 +28,3 @@ 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);

@@ -31,0 +31,0 @@ if (!response.ok) {

10

dist/commands/feature/edit.js

@@ -6,6 +6,6 @@ /* eslint-disable @typescript-eslint/no-unsafe-assignment */

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.

@@ -23,3 +23,3 @@ 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:

"newType": "G_quartet"
}`);
}`;
static examples = [

@@ -42,3 +42,3 @@ {

if (flags['json-input'] === '-') {
jsonStr = fs.readFileSync(process.stdin.fd).toString();
jsonStr = await readStdin();
}

@@ -52,3 +52,3 @@ else if (fs.existsSync(flags['json-input'])) {

}
const access = await this.getAccess(flags['config-file'], flags.profile);
const access = await this.getAccess();
for (const change of json) {

@@ -55,0 +55,0 @@ const str = JSON.stringify(change);

10

dist/commands/feature/get-id.js
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 = [

@@ -17,3 +17,3 @@ {

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,

@@ -25,4 +25,4 @@ default: ['-'],

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)];

@@ -29,0 +29,0 @@ const results = [];

6

dist/commands/feature/get.js
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 {

@@ -13,3 +13,3 @@ static description = 'Get features in assembly, reference sequence or genomic window';

{
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',

@@ -43,3 +43,3 @@ },

}
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);

@@ -46,0 +46,0 @@ const results = [];

4

dist/commands/feature/import.d.ts

@@ -1,3 +0,3 @@

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;

@@ -4,0 +4,0 @@ static description: string;

12

dist/commands/feature/import.js
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';

@@ -18,3 +18,3 @@ static description = 'By default, features are added to the existing ones.';

char: 'i',
description: 'Input gff or gtf file',
description: 'Input gff file',
required: true,

@@ -37,3 +37,3 @@ }),

}
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]);

@@ -43,3 +43,3 @@ if (assembly.length === 0) {

}
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 = {

@@ -46,0 +46,0 @@ typeName: 'AddFeaturesFromFileChange',

12

dist/commands/feature/search.js

@@ -5,3 +5,3 @@ /* eslint-disable @typescript-eslint/no-unsafe-assignment */

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) {

@@ -29,3 +29,3 @@ const url = new URL(localhostToAddress(`${address}/features/searchFeatures`));

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:

@@ -52,3 +52,3 @@ - Attribute *values* (not attribute names)

- "chr1"
- "0.987"`);
- "0.987"`;
static examples = [

@@ -69,3 +69,3 @@ {

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',
}),

@@ -75,3 +75,3 @@ };

const { flags } = await this.parse(Search);
const access = await this.getAccess(flags['config-file'], flags.profile);
const access = await this.getAccess();
let assemblyIds = [];

@@ -85,3 +85,3 @@ if (flags.assembly === undefined) {

else {
const assembly = idReader(flags.assembly);
const assembly = await idReader(flags.assembly);
assemblyIds = await convertAssemblyNameToId(access.address, access.accessToken, assembly);

@@ -88,0 +88,0 @@ }

26

dist/commands/login.js

@@ -11,17 +11,17 @@ /* eslint-disable @typescript-eslint/require-await */

import { fetch } from 'undici';
import { ApolloConf } from '../ApolloConf.js';
import { ApolloConf, KEYS } from '../ApolloConf.js';
import { BaseCommand } from '../baseCommand.js';
import { basicCheckConfig, createFetchErrorMessage, getUserCredentials, localhostToAddress, waitFor, wrapLines, } from '../utils.js';
import { basicCheckConfig, createFetchErrorMessage, localhostToAddress, waitFor, } from '../utils.js';
export default class Login extends BaseCommand {
static summary = 'Login to Apollo';
static description = wrapLines('Use the provided credentials to obtain and save the token to access Apollo. Once the token for \
the given profile has been saved in the configuration file, users do not normally need to execute \
this command again unless the token has expired. To setup a new profile use "apollo config"');
static description = 'Use the provided credentials to obtain and save the token to access Apollo. \
Once the token for the given profile has been saved in the configuration file, users do not normally \
need to execute this command again unless the token has expired. To setup a new profile use "apollo config"';
static examples = [
{
description: wrapLines('The most basic and probably most typical usage is to login using the default profile in configuration file:'),
description: 'The most basic and probably most typical usage is to login using the default profile in configuration file:',
command: '<%= config.bin %> <%= command.id %>',
},
{
description: wrapLines('Login with a different profile:'),
description: 'Login with a different profile:',
command: '<%= config.bin %> <%= command.id %> --profile my-profile',

@@ -75,3 +75,3 @@ },

if (!flags.force) {
await this.checkUserAlreadyLoggedIn();
await this.checkUserAlreadyLoggedIn(config, profileName);
}

@@ -109,11 +109,7 @@ if (accessType === 'root' || flags.username !== undefined) {

}
async checkUserAlreadyLoggedIn() {
const userCredentials = getUserCredentials();
if (!userCredentials) {
async checkUserAlreadyLoggedIn(userCredentials, profileName) {
const accessToken = userCredentials.get(`${profileName}.${KEYS.accessToken}`);
if (!accessToken) {
return;
}
const alreadyLoggedIn = Object.keys(userCredentials).every((key) => Boolean(userCredentials[key]));
if (!alreadyLoggedIn) {
return;
}
const reAuthenticate = await ux.confirm("You're already logged. Do you want to re-authenticate? (y/n)");

@@ -120,0 +116,0 @@ if (!reAuthenticate) {

4

dist/commands/logout.js
import path from 'node:path';
import { ApolloConf, KEYS } from '../ApolloConf.js';
import { BaseCommand } from '../baseCommand.js';
import { basicCheckConfig, wrapLines } from '../utils.js';
import { basicCheckConfig } from '../utils.js';
export default class Logout extends BaseCommand {
static summary = 'Logout of Apollo';
static description = wrapLines('Logout by removing the access token from the selected profile');
static description = 'Logout by removing the access token from the selected profile';
static examples = [

@@ -9,0 +9,0 @@ {

6

dist/commands/refseq/add-alias.js

@@ -5,7 +5,7 @@ import * as fs from 'node:fs';

import { BaseCommand } from '../../baseCommand.js';
import { createFetchErrorMessage, localhostToAddress, queryApollo, wrapLines, } from '../../utils.js';
import { createFetchErrorMessage, localhostToAddress, queryApollo, } from '../../utils.js';
import { ConfigError } from '../../ApolloConf.js';
export default class AddRefNameAlias extends BaseCommand {
static summary = 'Add reference name aliases from a file';
static description = wrapLines('Reference name aliasing is a process to make chromosomes that are named slightly differently but which refer to the same thing render properly. This command reads a file with reference name aliases and adds them to the database.');
static description = 'Reference name aliasing is a process to make chromosomes that are named slightly differently but which refer to the same thing render properly. This command reads a file with reference name aliases and adds them to the database.';
static examples = [

@@ -34,3 +34,3 @@ {

}
const access = await this.getAccess(flags['config-file'], flags.profile);
const access = await this.getAccess();
const filehandle = await fs.promises.open(flags['input-file']);

@@ -37,0 +37,0 @@ const fileContent = await filehandle.readFile({ encoding: 'utf8' });

16

dist/commands/refseq/get.js
import { Flags } from '@oclif/core';
import { BaseCommand } from '../../baseCommand.js';
import { convertAssemblyNameToId, idReader, queryApollo, wrapLines, } from '../../utils.js';
import { convertAssemblyNameToId, idReader, queryApollo } from '../../utils.js';
export default class Get extends BaseCommand {
static summary = 'Get reference sequences';
static description = wrapLines('Output the reference sequences in one or more assemblies in json format. \
This command returns the sequence characteristics (e.g., name, ID, etc), not the DNA sequences. \
Use `assembly sequence` for that.');
static description = 'Output the reference sequences in one or more assemblies in json format. \
This command returns the sequence characteristics (e.g., name, ID, etc), not the DNA sequences. \
Use `assembly sequence` for that.';
static examples = [
{
description: wrapLines('All sequences in the database:'),
description: 'All sequences in the database:',
command: '<%= config.bin %> <%= command.id %>',
},
{
description: wrapLines('Only sequences for these assemblies:'),
description: 'Only sequences for these assemblies:',
command: '<%= config.bin %> <%= command.id %> -a mm9 mm10',

@@ -28,3 +28,3 @@ },

const { flags } = await this.parse(Get);
const access = await this.getAccess(flags['config-file'], flags.profile);
const access = await this.getAccess();
const refSeqs = await queryApollo(access.address, access.accessToken, 'refSeqs');

@@ -35,3 +35,3 @@ const json = (await refSeqs.json());

keep = [];
const assembly = idReader(flags.assembly);
const assembly = await idReader(flags.assembly);
const assemblyIds = await convertAssemblyNameToId(access.address, access.accessToken, assembly);

@@ -38,0 +38,0 @@ for (const x of json) {

7

dist/commands/status.js

@@ -5,7 +5,8 @@ /* eslint-disable @typescript-eslint/no-unnecessary-condition */

import { BaseCommand } from '../baseCommand.js';
import { basicCheckConfig, wrapLines } from '../utils.js';
import { basicCheckConfig } from '../utils.js';
export default class Status extends BaseCommand {
static summary = 'View authentication status';
static description = wrapLines('This command returns "<profile>: Logged in" if the selected profile has an access token and "<profile>: Logged out" otherwise.\
Note that this command does not check the validity of the access token.');
static description = 'This command returns "<profile>: Logged in" if the selected profile \
has an access token and "<profile>: Logged out" otherwise.\
Note that this command does not check the validity of the access token.';
async run() {

@@ -12,0 +13,0 @@ const { flags } = await this.parse(Status);

6

dist/commands/user/get.js
import { Flags } from '@oclif/core';
import { BaseCommand } from '../../baseCommand.js';
import { queryApollo, wrapLines } from '../../utils.js';
import { queryApollo } from '../../utils.js';
export default class Get extends BaseCommand {
static summary = 'Get list of users';
static description = wrapLines('If set, filters username and role must be both satisfied to return an entry');
static description = 'If set, filters username and role must be both satisfied to return an entry';
static examples = [

@@ -33,3 +33,3 @@ {

const { flags } = await this.parse(Get);
const access = await this.getAccess(flags['config-file'], flags.profile);
const access = await this.getAccess();
const users = await queryApollo(access.address, access.accessToken, 'users');

@@ -36,0 +36,0 @@ const json = (await users.json());

29

dist/utils.d.ts
import EventEmitter from 'node:events';
import { Response } from 'undici';
import { ApolloConf } from './ApolloConf.js';
import { ApolloAssemblySnapshot } from '@apollo-annotation/mst';
export declare const CLI_SERVER_ADDRESS = "http://127.0.0.1:5657";

@@ -20,6 +21,6 @@ export declare const CLI_SERVER_ADDRESS_CALLBACK = "http://127.0.0.1:5657/auth/callback";

export declare function deleteAssembly(address: string, accessToken: string, assemblyId: string): Promise<void>;
export declare function getAssembly(address: string, accessToken: string, assemblyNameOrId: string): Promise<object>;
export declare function getAssembly(address: string, accessToken: string, assemblyNameOrId: string): Promise<ApolloAssemblySnapshot>;
export declare function getRefseqId(address: string, accessToken: string, refseqNameOrId?: string, inAssemblyNameOrId?: string): Promise<string[]>;
export declare function convertCheckNameToId(address: string, accessToken: string, namesOrIds: string[]): Promise<string[]>;
export declare function assemblyNameToIdDict(address: string, accessToken: string): Promise<Record<string, string>>;
export declare function assemblyNameToIdDict(address: string, accessToken: string): Promise<Record<string, string | undefined>>;
/** In input array namesOrIds, substitute common names with internal IDs */

@@ -31,3 +32,2 @@ export declare function convertAssemblyNameToId(address: string, accessToken: string, namesOrIds: string[], verbose?: boolean, removeDuplicates?: boolean): Promise<string[]>;

export declare function filterJsonList(json: object[], keep: string[], key: string): object[];
export declare const getUserCredentials: () => UserCredentials | null;
export declare const generatePkceChallenge: () => {

@@ -39,7 +39,19 @@ state: string;

export declare const waitFor: <T>(eventName: string, emitter: EventEmitter) => Promise<T>;
interface bodyLocalFile {
interface bodyFastaFile {
assemblyName: string;
typeName: string;
fileId: string;
fileIds: {
fa: string;
};
assembly: string;
}
interface bodyIndexedFiles {
assemblyName: string;
typeName: string;
fileIds: {
fa: string;
fai: string;
gzi: string;
};
}
interface bodyExternalFile {

@@ -53,6 +65,5 @@ assemblyName: string;

}
export declare function submitAssembly(address: string, accessToken: string, body: bodyLocalFile | bodyExternalFile, force: boolean): Promise<Response>;
export declare function uploadFile(address: string, accessToken: string, file: string, type: string): Promise<never>;
export declare function wrapLines(s: string, length?: number): string;
export declare function idReader(input: string[], removeDuplicates?: boolean): string[];
export declare function submitAssembly(address: string, accessToken: string, body: bodyFastaFile | bodyExternalFile | bodyIndexedFiles, force: boolean): Promise<object>;
export declare function readStdin(): Promise<string>;
export declare function idReader(input: string[], removeDuplicates?: boolean): Promise<string[]>;
export {};

128

dist/utils.js

@@ -1,15 +0,6 @@

/* eslint-disable @typescript-eslint/no-unnecessary-condition */
/* eslint-disable @typescript-eslint/no-unsafe-call */
/* eslint-disable @typescript-eslint/no-unsafe-member-access */
/* eslint-disable @typescript-eslint/no-unsafe-assignment */
/* eslint-disable @typescript-eslint/no-unsafe-return */
import * as crypto from 'node:crypto';
import * as fs from 'node:fs';
import * as os from 'node:os';
import * as path from 'node:path';
import { Transform, pipeline, } from 'node:stream';
import { SingleBar } from 'cli-progress';
import { stdin, stderr } from 'node:process';
import { Agent, fetch } from 'undici';
import { ApolloConf, ConfigError } from './ApolloConf.js';
const CONFIG_PATH = path.resolve(os.homedir(), '.clirc');
export const CLI_SERVER_ADDRESS = 'http://127.0.0.1:5657';

@@ -78,14 +69,12 @@ export const CLI_SERVER_ADDRESS_CALLBACK = `${CLI_SERVER_ADDRESS}/auth/callback`;

if (assemblyId.length === 0) {
return {};
throw new Error(`Assembly "${assemblyNameOrId}" not found`);
}
const res = await queryApollo(address, accessToken, 'assemblies');
const assemblies = (await res.json());
let assemblyObj = {};
for (const x of assemblies) {
if (x._id === assemblyId[0]) {
assemblyObj = JSON.parse(JSON.stringify(x));
break;
return JSON.parse(JSON.stringify(x));
}
}
return assemblyObj;
throw new Error(`Assembly "${assemblyNameOrId}" not found`);
}

@@ -180,3 +169,3 @@ export async function getRefseqId(address, accessToken, refseqNameOrId, inAssemblyNameOrId) {

else if (verbose) {
process.stderr.write(`Warning: Omitting unknown assembly: "${x}"\n`);
stderr.write(`Warning: Omitting unknown assembly: "${x}"\n`);
}

@@ -229,11 +218,2 @@ }

}
export const getUserCredentials = () => {
try {
const content = fs.readFileSync(CONFIG_PATH, { encoding: 'utf8' });
return JSON.parse(content);
}
catch {
return null;
}
};
export const generatePkceChallenge = () => {

@@ -265,3 +245,3 @@ const codeVerifier = crypto.randomBytes(64).toString('hex');

export async function submitAssembly(address, accessToken, body, force) {
const assemblies = await queryApollo(address, accessToken, 'assemblies');
let assemblies = await queryApollo(address, accessToken, 'assemblies');
for (const x of (await assemblies.json())) {

@@ -290,77 +270,20 @@ if (x['name'] === body.assemblyName) {

const errorMessage = await createFetchErrorMessage(response, 'submitAssembly failed');
throw new ConfigError(errorMessage);
throw new Error(errorMessage);
}
return response;
}
class ProgressTransform extends Transform {
size = 0;
progressBar;
constructor(opts) {
super(opts);
this.progressBar = opts.progressBar;
}
_transform(chunk, _encoding, callback) {
this.size += chunk.length;
this.progressBar.update(this.size);
callback(null, chunk);
}
}
export async function uploadFile(address, accessToken, file, type) {
const filehandle = await fs.promises.open(file);
const { size } = await filehandle.stat();
const stream = filehandle.createReadStream();
const progressBar = new SingleBar({ etaBuffer: 100_000_000 });
const progressTransform = new ProgressTransform({ progressBar });
const body = pipeline(stream, progressTransform, (error) => {
if (error) {
progressBar.stop();
console.error('Error processing file.', error);
throw error;
assemblies = await queryApollo(address, accessToken, 'assemblies');
for (const x of (await assemblies.json())) {
if (x['name'] === body.assemblyName) {
return x;
}
});
const init = {
method: 'POST',
body,
duplex: 'half',
headers: {
Authorization: `Bearer ${accessToken}`,
'Content-Type': type,
'Content-Length': String(size),
},
dispatcher: new Agent({ headersTimeout: 60 * 60 * 1000 }),
};
const fileName = path.basename(file);
const url = new URL(localhostToAddress(`${address}/files`));
url.searchParams.set('name', fileName);
url.searchParams.set('type', type);
progressBar.start(size, 0);
try {
const response = await fetch(url, init);
if (!response.ok) {
const errorMessage = await createFetchErrorMessage(response, 'uploadFile failed');
throw new ConfigError(errorMessage);
}
const json = (await response.json());
return json['_id'];
}
catch (error) {
console.error(error);
throw error;
}
finally {
progressBar.stop();
}
throw new Error(`Failed to retrieve assembly ${body.assemblyName}`);
}
/* Wrap text to max `length` per line */
export function wrapLines(s, length) {
if (length === undefined) {
length = 80;
export async function readStdin() {
const chunks = [];
for await (const chunk of stdin) {
chunks.push(Buffer.from(chunk));
}
// Credit: https://stackoverflow.com/questions/14484787/wrap-text-in-javascript
const re = new RegExp(`(?![^\\n]{1,${length}}$)([^\\n]{1,${length}})\\s`, 'g');
s = s.replaceAll(/ +/g, ' ');
const wr = s.replace(re, '$1\n');
return wr;
return Buffer.concat(chunks).toString('utf8');
}
export function idReader(input, removeDuplicates = true) {
export async function idReader(input, removeDuplicates = true) {
let ids = [];

@@ -370,3 +293,3 @@ for (const xin of input) {

if (xin == '-') {
data = fs.readFileSync('/dev/stdin').toString();
data = await readStdin();
}

@@ -380,10 +303,9 @@ else if (fs.existsSync(xin)) {

try {
data = JSON.parse(data);
if (data.length === undefined) {
data = [data];
let parsedData = JSON.parse(data);
if (!Array.isArray(parsedData)) {
parsedData = [parsedData];
}
for (const x of data) {
const id = x['_id'];
if (id !== undefined) {
ids.push(id);
for (const x of parsedData) {
if ('_id' in x && typeof x._id === 'string') {
ids.push(x._id);
}

@@ -390,0 +312,0 @@ }

93

package.json
{
"name": "@apollo-annotation/cli",
"version": "0.1.20",
"description": "Command line interface for the Apollo annotation server",
"version": "0.1.19",
"author": "Apollo Team",
"repository": {

@@ -11,11 +10,9 @@ "type": "git",

},
"bin": {
"apollo": "./bin/run.js"
},
"author": "Apollo Team",
"type": "module",
"exports": "./dist/index.js",
"main": "",
"types": "dist/index.d.ts",
"exports": "./dist/index.js",
"engines": {
"node": ">=18.0.0"
"bin": {
"apollo": "./bin/run.js"
},

@@ -30,10 +27,47 @@ "files": [

"dev": "tsx bin/dev.js",
"prepack": "yarn build && oclif manifest && oclif readme && prettier --write README.md",
"postpack": "shx rm -f oclif.manifest.json",
"posttest": "yarn lint",
"prepack": "yarn build && oclif manifest && oclif readme && prettier --write README.md",
"prepare": "yarn build",
"test": "mocha --require src/test/fixtures.ts 'src/**/*.test.ts'",
"posttest": "yarn lint",
"test:ci": "nyc mocha 'src/**/*.test.ts'",
"version": "oclif readme && git add README.md"
"version": "oclif readme --multi --dir ../website/docs/cli/ && oclif readme && git add README.md"
},
"oclif": {
"bin": "apollo",
"commands": "./dist/commands",
"dirname": "apollo-cli",
"helpOptions": {
"flagSortOrder": "none",
"maxWidth": 80
},
"plugins": [
"@oclif/plugin-help"
],
"repositoryPrefix": "<%- repo %>/blob/v<%- version %>/packages/apollo-cli/<%- commandPath %>",
"topicSeparator": " ",
"topics": {
"assembly": {
"description": "Commands to manage assemblies"
},
"change": {
"description": "Commands to manage the change log"
},
"feature": {
"description": "Commands to manage features"
},
"file": {
"description": "Commands to manage files"
},
"jbrowse": {
"description": "Commands to manage the JBrowse configuration"
},
"refseq": {
"description": "Commands to manage reference sequences"
},
"user": {
"description": "Commands to manage users"
}
}
},
"dependencies": {

@@ -55,8 +89,8 @@ "@inquirer/input": "^1.2.14",

"devDependencies": {
"@apollo-annotation/mst": "^0.1.19",
"@apollo-annotation/shared": "^0.1.19",
"@apollo-annotation/mst": "^0.1.20",
"@apollo-annotation/shared": "^0.1.20",
"@istanbuljs/esm-loader-hook": "^0.2.0",
"@istanbuljs/nyc-config-typescript": "^1.0.2",
"@oclif/test": "^3.1.3",
"@types/chai": "^4",
"@types/chai": "^4.3.19",
"@types/cli-progress": "^3",

@@ -78,31 +112,4 @@ "@types/inquirer": "^9.0.7",

},
"oclif": {
"helpOptions": {
"flagSortOrder": "none"
},
"bin": "apollo",
"dirname": "apollo-cli",
"commands": "./dist/commands",
"plugins": [
"@oclif/plugin-help"
],
"repositoryPrefix": "<%- repo %>/blob/v<%- version %>/packages/apollo-cli/<%- commandPath %>",
"topicSeparator": " ",
"topics": {
"assembly": {
"description": "Commands to handle assemblies"
},
"change": {
"description": "Commands to handle the log of changes made to the database"
},
"feature": {
"description": "Commands to handle features"
},
"refseq": {
"description": "Commands to handle reference sequences"
},
"user": {
"description": "Commands to handle users"
}
}
"engines": {
"node": ">=18.0.0"
},

@@ -109,0 +116,0 @@ "publishConfig": {

389

README.md

@@ -19,3 +19,3 @@ # Table of contents

$ apollo (--version)
@apollo-annotation/cli/0.1.19 linux-x64 node-v20.14.0
@apollo-annotation/cli/0.1.20 linux-x64 node-v18.20.4
$ apollo --help [COMMAND]

@@ -33,4 +33,4 @@ USAGE

- [`apollo assembly add-fasta`](#apollo-assembly-add-fasta)
- [`apollo assembly add-gff`](#apollo-assembly-add-gff)
- [`apollo assembly add-from-fasta INPUT`](#apollo-assembly-add-from-fasta-input)
- [`apollo assembly add-from-gff INPUT-FILE`](#apollo-assembly-add-from-gff-input-file)
- [`apollo assembly check`](#apollo-assembly-check)

@@ -54,3 +54,9 @@ - [`apollo assembly delete`](#apollo-assembly-delete)

- [`apollo feature search`](#apollo-feature-search)
- [`apollo file delete`](#apollo-file-delete)
- [`apollo file download`](#apollo-file-download)
- [`apollo file get`](#apollo-file-get)
- [`apollo file upload`](#apollo-file-upload)
- [`apollo help [COMMANDS]`](#apollo-help-commands)
- [`apollo jbrowse get-config`](#apollo-jbrowse-get-config)
- [`apollo jbrowse set-config INPUTFILE`](#apollo-jbrowse-set-config-inputfile)
- [`apollo login`](#apollo-login)

@@ -63,36 +69,51 @@ - [`apollo logout`](#apollo-logout)

## `apollo assembly add-fasta`
## `apollo assembly add-from-fasta INPUT`
Add new assembly from local or external fasta file
Add a new assembly from fasta input
```
USAGE
$ apollo assembly add-fasta -i <value> [--profile <value>] [--config-file <value>] [-a <value>] [-x <value>] [-f]
$ apollo assembly add-from-fasta INPUT [--profile <value>] [--config-file <value>] [-a <value>] [-x <value>] [-f] [-n]
[--fai <value>] [--gzi <value>] [-z | -d]
ARGUMENTS
INPUT Input fasta file, local or remote, or id of a previously uploaded file
FLAGS
-a, --assembly=<value> Name for this assembly. Use the file name if omitted
-d, --decompressed For local file input: Override autodetection and instruct that input is decompressed
-f, --force Delete existing assembly, if it exists
-i, --input-file=<value> (required) Input fasta file
-x, --index=<value> URL of the index. Required if input is an external source and ignored if input is a local
file
-n, --not-editable The fasta sequence is not editable. Apollo will not load it into the database and instead
use the provided indexes to query it. This option assumes the fasta file is bgzip'd with
`bgzip` and indexed with `samtools faidx`. Indexes should be named <my.fasta.gz>.gzi and
<my.fasta.gz>.fai unless options --fai and --gzi are set
-x, --index=<value> URL of the index. Required if input is an external source
-z, --gzip For local file input: Override autodetection and instruct that input is gzip compressed
--config-file=<value> Use this config file (mostly for testing)
--fai=<value> Fasta index of the (not-editable) fasta file
--gzi=<value> Gzi index of the (not-editable) fasta file
--profile=<value> Use credentials from this profile
DESCRIPTION
Add new assembly from local or external fasta file
Add a new assembly from fasta input
Add new assembly. The input fasta may be:
* A local file
* An external fasta file
* The id of a file previously uploaded to Apollo
EXAMPLES
From local file:
$ apollo assembly add-fasta -i genome.fa -a myAssembly
$ apollo assembly add-from-fasta genome.fa -a myAssembly
From external source we also need the URL of the index:
$ apollo assembly add-fasta -i https://.../genome.fa -x https://.../genome.fa.fai -a myAssembly
$ apollo assembly add-from-fasta https://.../genome.fa -x https://.../genome.fa.fai -a myAssembly
```
_See code:
[src/commands/assembly/add-fasta.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/assembly/add-fasta.ts)_
[src/commands/assembly/add-from-fasta.ts](https://github.com/GMOD/Apollo3/blob/v0.1.20/packages/apollo-cli/src/commands/assembly/add-from-fasta.ts)_
## `apollo assembly add-gff`
## `apollo assembly add-from-gff INPUT-FILE`

@@ -103,8 +124,10 @@ Add new assembly from gff or gft file

USAGE
$ apollo assembly add-gff -i <value> [--profile <value>] [--config-file <value>] [-a <value>] [-o] [-f]
$ apollo assembly add-from-gff INPUT-FILE [--profile <value>] [--config-file <value>] [-a <value>] [-o] [-f]
ARGUMENTS
INPUT-FILE Input gff file
FLAGS
-a, --assembly=<value> Name for this assembly. Use the file name if omitted
-f, --force Delete existing assembly, if it exists
-i, --input-file=<value> (required) Input gff or gtf file
-o, --omit-features Do not import features, only upload the sequences

@@ -117,4 +140,3 @@ --config-file=<value> Use this config file (mostly for testing)

The gff file is expected to contain sequences as per gff specifications.
Features are also imported by default.
The gff file is expected to contain sequences as per gff specifications. Features are also imported by default.

@@ -124,11 +146,11 @@ EXAMPLES

$ apollo assembly add-gff -i genome.gff -a myAssembly
$ apollo assembly add-from-gff -i genome.gff -a myAssembly
Import sequences only:
$ apollo assembly add-gff -i genome.gff -a myAssembly -o
$ apollo assembly add-from-gff genome.gff -a myAssembly -o
```
_See code:
[src/commands/assembly/add-gff.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/assembly/add-gff.ts)_
[src/commands/assembly/add-from-gff.ts](https://github.com/GMOD/Apollo3/blob/v0.1.20/packages/apollo-cli/src/commands/assembly/add-from-gff.ts)_

@@ -153,5 +175,4 @@ ## `apollo assembly check`

Manage checks, i.e. the rules ensuring features in an assembly are plausible.
This command only sets the checks to apply, to retrieve features flagged by
these checks use `apollo feature check`.
Manage checks, i.e. the rules ensuring features in an assembly are plausible. This command only sets the checks to
apply, to retrieve features flagged by these checks use `apollo feature check`.

@@ -177,3 +198,3 @@ EXAMPLES

_See code:
[src/commands/assembly/check.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/assembly/check.ts)_
[src/commands/assembly/check.ts](https://github.com/GMOD/Apollo3/blob/v0.1.20/packages/apollo-cli/src/commands/assembly/check.ts)_

@@ -206,3 +227,3 @@ ## `apollo assembly delete`

_See code:
[src/commands/assembly/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/assembly/delete.ts)_
[src/commands/assembly/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.1.20/packages/apollo-cli/src/commands/assembly/delete.ts)_

@@ -229,3 +250,3 @@ ## `apollo assembly get`

_See code:
[src/commands/assembly/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/assembly/get.ts)_
[src/commands/assembly/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.20/packages/apollo-cli/src/commands/assembly/get.ts)_

@@ -265,3 +286,3 @@ ## `apollo assembly sequence`

_See code:
[src/commands/assembly/sequence.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/assembly/sequence.ts)_
[src/commands/assembly/sequence.ts](https://github.com/GMOD/Apollo3/blob/v0.1.20/packages/apollo-cli/src/commands/assembly/sequence.ts)_

@@ -284,10 +305,9 @@ ## `apollo change get`

Return the change log in json format. Note that when an assembly is deleted the
link between common name and ID is lost (it can still be recovered by inspecting
the change log but at present this task is left to the user). In such cases you
need to use the assembly ID.
Return the change log in json format. Note that when an assembly is deleted the link between common name and ID is
lost (it can still be recovered by inspecting the change log but at present this task is left to the user). In such
cases you need to use the assembly ID.
```
_See code:
[src/commands/change/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/change/get.ts)_
[src/commands/change/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.20/packages/apollo-cli/src/commands/change/get.ts)_

@@ -314,4 +334,3 @@ ## `apollo config [KEY] [VALUE]`

Use this command to create or edit a user profile with credentials to access
Apollo. Configuration options are:
Use this command to create or edit a user profile with credentials to access Apollo. Configuration options are:

@@ -322,4 +341,4 @@ - address:

- accessType:
How to access Apollo. accessType is typically one of: google, microsoft, guest,
root. Allowed types depend on your Apollo setup
How to access Apollo. accessType is typically one of: google, microsoft, guest, root. Allowed types depend on your
Apollo setup

@@ -350,3 +369,3 @@ - accessToken:

_See code:
[src/commands/config.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/config.ts)_
[src/commands/config.ts](https://github.com/GMOD/Apollo3/blob/v0.1.20/packages/apollo-cli/src/commands/config.ts)_

@@ -372,4 +391,4 @@ ## `apollo feature add-child`

See the other commands under `apollo feature` to retrive the parent ID of
interest and to populate the child feature with attributes.
See the other commands under `apollo feature` to retrive the parent ID of interest and to populate the child feature
with attributes.

@@ -379,7 +398,7 @@ EXAMPLES

$ apollo feature add-child -i 6605826fbd0eee691f83e73f -t exon -s 10 -e 20
$ apollo feature add-child -i 660...73f -t exon -s 10 -e 20
```
_See code:
[src/commands/feature/add-child.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/feature/add-child.ts)_
[src/commands/feature/add-child.ts](https://github.com/GMOD/Apollo3/blob/v0.1.20/packages/apollo-cli/src/commands/feature/add-child.ts)_

@@ -403,5 +422,4 @@ ## `apollo feature check`

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
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

@@ -419,3 +437,3 @@ EXAMPLES

_See code:
[src/commands/feature/check.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/feature/check.ts)_
[src/commands/feature/check.ts](https://github.com/GMOD/Apollo3/blob/v0.1.20/packages/apollo-cli/src/commands/feature/check.ts)_

@@ -441,5 +459,4 @@ ## `apollo feature copy`

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.
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.

@@ -453,3 +470,3 @@ EXAMPLES

_See code:
[src/commands/feature/copy.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/feature/copy.ts)_
[src/commands/feature/copy.ts](https://github.com/GMOD/Apollo3/blob/v0.1.20/packages/apollo-cli/src/commands/feature/copy.ts)_

@@ -474,8 +491,7 @@ ## `apollo feature delete`

Note that deleting a child feature after deleting its parent will result in an
error unless you set -f/--force.
Note that deleting a child feature after deleting its parent will result in an error unless you set -f/--force.
```
_See code:
[src/commands/feature/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/feature/delete.ts)_
[src/commands/feature/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.1.20/packages/apollo-cli/src/commands/feature/delete.ts)_

@@ -498,8 +514,7 @@ ## `apollo feature edit`

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.
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:
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:

@@ -524,3 +539,3 @@ {

_See code:
[src/commands/feature/edit.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/feature/edit.ts)_
[src/commands/feature/edit.ts](https://github.com/GMOD/Apollo3/blob/v0.1.20/packages/apollo-cli/src/commands/feature/edit.ts)_

@@ -547,5 +562,4 @@ ## `apollo feature edit-attribute`

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
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

@@ -567,3 +581,3 @@ EXAMPLES

_See code:
[src/commands/feature/edit-attribute.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/feature/edit-attribute.ts)_
[src/commands/feature/edit-attribute.ts](https://github.com/GMOD/Apollo3/blob/v0.1.20/packages/apollo-cli/src/commands/feature/edit-attribute.ts)_

@@ -588,5 +602,4 @@ ## `apollo feature edit-coords`

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`
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`

@@ -604,3 +617,3 @@ EXAMPLES

_See code:
[src/commands/feature/edit-coords.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/feature/edit-coords.ts)_
[src/commands/feature/edit-coords.ts](https://github.com/GMOD/Apollo3/blob/v0.1.20/packages/apollo-cli/src/commands/feature/edit-coords.ts)_

@@ -624,8 +637,8 @@ ## `apollo feature edit-type`

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.
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.
```
_See code:
[src/commands/feature/edit-type.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/feature/edit-type.ts)_
[src/commands/feature/edit-type.ts](https://github.com/GMOD/Apollo3/blob/v0.1.20/packages/apollo-cli/src/commands/feature/edit-type.ts)_

@@ -657,4 +670,4 @@ ## `apollo feature get`

Get features intersecting chr1:1..1000. You can omit the assembly name if there
are no other reference sequences named chr1:
Get features intersecting chr1:1..1000. You can omit the assembly name if there are no other reference sequences
named chr1:

@@ -665,3 +678,3 @@ $ apollo feature get -a myAssembly -r chr1 -s 1 -e 1000

_See code:
[src/commands/feature/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/feature/get.ts)_
[src/commands/feature/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.20/packages/apollo-cli/src/commands/feature/get.ts)_

@@ -677,4 +690,3 @@ ## `apollo feature get-id`

FLAGS
-i, --feature-id=<value>... [default: -] Retrieves feature with these IDs. Use
"-" to read IDs from stdin (one per
-i, --feature-id=<value>... [default: -] Retrieves feature with these IDs. Use "-" to read IDs from stdin (one per
line)

@@ -687,4 +699,3 @@ --config-file=<value> Use this config file (mostly for testing)

Invalid identifiers or identifiers not found in the database will be silently
ignored
Invalid identifiers or identifiers not found in the database will be silently ignored

@@ -698,3 +709,3 @@ EXAMPLES

_See code:
[src/commands/feature/get-id.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/feature/get-id.ts)_
[src/commands/feature/get-id.ts](https://github.com/GMOD/Apollo3/blob/v0.1.20/packages/apollo-cli/src/commands/feature/get-id.ts)_

@@ -712,3 +723,3 @@ ## `apollo feature import`

-d, --delete-existing Delete existing features before importing
-i, --input-file=<value> (required) Input gff or gtf file
-i, --input-file=<value> (required) Input gff file
--config-file=<value> Use this config file (mostly for testing)

@@ -729,3 +740,3 @@ --profile=<value> Use credentials from this profile

_See code:
[src/commands/feature/import.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/feature/import.ts)_
[src/commands/feature/import.ts](https://github.com/GMOD/Apollo3/blob/v0.1.20/packages/apollo-cli/src/commands/feature/import.ts)_

@@ -741,4 +752,4 @@ ## `apollo feature search`

FLAGS
-a, --assembly=<value>... Assembly names or IDs to search; use "-" to read it from stdin. If omitted
search all assemblies
-a, --assembly=<value>... Assembly names or IDs to search; use "-" to read it from stdin. If omitted search all
assemblies
-t, --text=<value> (required) Search for this text query

@@ -767,4 +778,3 @@ --config-file=<value> Use this config file (mostly for testing)

Queries "bac" or "mRNA" return the feature. Instead these queries will NOT
match:
Queries "bac" or "mRNA" return the feature. Instead these queries will NOT match:

@@ -784,4 +794,121 @@ - "someKey"

_See code:
[src/commands/feature/search.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/feature/search.ts)_
[src/commands/feature/search.ts](https://github.com/GMOD/Apollo3/blob/v0.1.20/packages/apollo-cli/src/commands/feature/search.ts)_
## `apollo file delete`
Delete files from the Apollo server
```
USAGE
$ apollo file delete [--profile <value>] [--config-file <value>] [-i <value>]
FLAGS
-i, --file-id=<value>... [default: -] IDs of the files to delete
--config-file=<value> Use this config file (mostly for testing)
--profile=<value> Use credentials from this profile
DESCRIPTION
Delete files from the Apollo server
Deleted files are printed to stdout. See also `apollo file get` to list the files on the server
EXAMPLES
Delete file multiple files:
$ apollo file delete -i 123...abc xyz...789
```
_See code:
[src/commands/file/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.1.20/packages/apollo-cli/src/commands/file/delete.ts)_
## `apollo file download`
Download a file from the Apollo server
```
USAGE
$ apollo file download [--profile <value>] [--config-file <value>] [-i <value>] [-o <value>]
FLAGS
-i, --file-id=<value> [default: -] ID of the file to download
-o, --output=<value> Write output to this file or "-" for stdout. Default to the name of the uploaded file.
--config-file=<value> Use this config file (mostly for testing)
--profile=<value> Use credentials from this profile
DESCRIPTION
Download a file from the Apollo server
See also `apollo file get` to list the files on the server
EXAMPLES
Download file with id xyz
$ apollo file download -i xyz -o genome.fa
```
_See code:
[src/commands/file/download.ts](https://github.com/GMOD/Apollo3/blob/v0.1.20/packages/apollo-cli/src/commands/file/download.ts)_
## `apollo file get`
Get list of files uploaded to the Apollo server
```
USAGE
$ apollo file get [--profile <value>] [--config-file <value>] [-i <value>]
FLAGS
-i, --file-id=<value>... Get files matching this IDs
--config-file=<value> Use this config file (mostly for testing)
--profile=<value> Use credentials from this profile
DESCRIPTION
Get list of files uploaded to the Apollo server
Print to stdout the list of files in json format
EXAMPLES
Get files by id:
$ apollo file get -i xyz abc
```
_See code:
[src/commands/file/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.20/packages/apollo-cli/src/commands/file/get.ts)_
## `apollo file upload`
Upload a local file to the Apollo server
```
USAGE
$ apollo file upload -i <value> [--profile <value>] [--config-file <value>] [-t
text/x-fasta|text/x-gff3|application/x-bgzip-fasta|text/x-fai|application/x-gzi] [-z | -d]
FLAGS
-d, --decompressed Override autodetection and instruct that input is decompressed
-i, --input-file=<value> (required) Local file to upload
-t, --type=<option> Set file type or autodetected it if not set.
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>
-z, --gzip Override autodetection and instruct that input is gzip compressed
--config-file=<value> Use this config file (mostly for testing)
--profile=<value> Use credentials from this profile
DESCRIPTION
Upload a local file to the Apollo server
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`
EXAMPLES
Upload local file, type auto-detected:
$ apollo file upload -i genome.fa > file.json
```
_See code:
[src/commands/file/upload.ts](https://github.com/GMOD/Apollo3/blob/v0.1.20/packages/apollo-cli/src/commands/file/upload.ts)_
## `apollo help [COMMANDS]`

@@ -808,2 +935,57 @@

## `apollo jbrowse get-config`
Get JBrowse configuration from Apollo
```
USAGE
$ apollo jbrowse get-config [--profile <value>] [--config-file <value>]
FLAGS
--config-file=<value> Use this config file (mostly for testing)
--profile=<value> Use credentials from this profile
DESCRIPTION
Get JBrowse configuration from Apollo
Print to stdout the JBrowse configuration from Apollo in JSON format
EXAMPLES
Get JBrowse configuration:
$ apollo jbrowse get-config > config.json
```
_See code:
[src/commands/jbrowse/get-config.ts](https://github.com/GMOD/Apollo3/blob/v0.1.20/packages/apollo-cli/src/commands/jbrowse/get-config.ts)_
## `apollo jbrowse set-config INPUTFILE`
Set JBrowse configuration
```
USAGE
$ apollo jbrowse set-config INPUTFILE [--profile <value>] [--config-file <value>]
ARGUMENTS
INPUTFILE JBrowse configuration file
FLAGS
--config-file=<value> Use this config file (mostly for testing)
--profile=<value> Use credentials from this profile
DESCRIPTION
Set JBrowse configuration
Set JBrowse configuration in Apollo collaboration server
EXAMPLES
Add JBrowse configuration:
$ apollo jbrowse set-config config.json
```
_See code:
[src/commands/jbrowse/set-config.ts](https://github.com/GMOD/Apollo3/blob/v0.1.20/packages/apollo-cli/src/commands/jbrowse/set-config.ts)_
## `apollo login`

@@ -831,10 +1013,8 @@

Use the provided credentials to obtain and save the token to access Apollo. Once
the token for the given profile has been saved in the configuration file, users
do not normally need to execute this command again unless the token has expired.
To setup a new profile use "apollo config"
Use the provided credentials to obtain and save the token to access Apollo. Once the token for the given profile has
been saved in the configuration file, users do not normally need to execute this command again unless the token has
expired. To setup a new profile use "apollo config"
EXAMPLES
The most basic and probably most typical usage is to login using the default
profile in configuration file:
The most basic and probably most typical usage is to login using the default profile in configuration file:

@@ -849,3 +1029,3 @@ $ apollo login

_See code:
[src/commands/login.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/login.ts)_
[src/commands/login.ts](https://github.com/GMOD/Apollo3/blob/v0.1.20/packages/apollo-cli/src/commands/login.ts)_

@@ -880,3 +1060,3 @@ ## `apollo logout`

_See code:
[src/commands/logout.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/logout.ts)_
[src/commands/logout.ts](https://github.com/GMOD/Apollo3/blob/v0.1.20/packages/apollo-cli/src/commands/logout.ts)_

@@ -900,5 +1080,4 @@ ## `apollo refseq add-alias`

Reference name aliasing is a process to make chromosomes that are named slightly
differently but which refer to the same thing render properly. This command
reads a file with reference name aliases and adds them to the database.
Reference name aliasing is a process to make chromosomes that are named slightly differently but which refer to the
same thing render properly. This command reads a file with reference name aliases and adds them to the database.

@@ -912,3 +1091,3 @@ EXAMPLES

_See code:
[src/commands/refseq/add-alias.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/refseq/add-alias.ts)_
[src/commands/refseq/add-alias.ts](https://github.com/GMOD/Apollo3/blob/v0.1.20/packages/apollo-cli/src/commands/refseq/add-alias.ts)_

@@ -931,5 +1110,4 @@ ## `apollo refseq get`

Output the reference sequences in one or more assemblies in json format. This
command returns the sequence characteristics (e.g., name, ID, etc), not the DNA
sequences. Use `assembly sequence` for that.
Output the reference sequences in one or more assemblies in json format. This command returns the sequence
characteristics (e.g., name, ID, etc), not the DNA sequences. Use `assembly sequence` for that.

@@ -947,3 +1125,3 @@ EXAMPLES

_See code:
[src/commands/refseq/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/refseq/get.ts)_
[src/commands/refseq/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.20/packages/apollo-cli/src/commands/refseq/get.ts)_

@@ -965,9 +1143,8 @@ ## `apollo status`

This command returns "<profile>: Logged in" if the selected profile has an
access token and "<profile>: Logged out" otherwise. Note that this command does
not check the validity of the access token.
This command returns "<profile>: Logged in" if the selected profile has an access token and "<profile>: Logged out"
otherwise.Note that this command does not check the validity of the access token.
```
_See code:
[src/commands/status.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/status.ts)_
[src/commands/status.ts](https://github.com/GMOD/Apollo3/blob/v0.1.20/packages/apollo-cli/src/commands/status.ts)_

@@ -1008,4 +1185,4 @@ ## `apollo user get`

_See code:
[src/commands/user/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/user/get.ts)_
[src/commands/user/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.20/packages/apollo-cli/src/commands/user/get.ts)_
<!-- commandsstop -->
dist/commands/assembly/add-fasta.d.ts
dist/commands/assembly/add-fasta.js
dist/commands/assembly/add-gff.d.ts
dist/commands/assembly/add-gff.js
oclif.manifest.json

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