@apollo-annotation/cli 1.1.0 → 1.1.2

package/dist/utils.js

@@ -1,12 +1,8 @@
 import * as crypto from 'node:crypto';
 import * as fs from 'node:fs';
-import { stderr, stdin } from 'node:process';
-import { Agent, fetch } from 'undici';
-import { ApolloConf, ConfigError } from './ApolloConf.js';
+import { stdin } from 'node:process';
 export const CLI_SERVER_ADDRESS = 'http://127.0.0.1:5657';
 export const CLI_SERVER_ADDRESS_CALLBACK = `${CLI_SERVER_ADDRESS}/auth/callback`;
-export class CheckError extends Error {
-}
 export async function createFetchErrorMessage(response, additionalText) {
     let errorMessage;
     try {
@@ -18,21 +14,6 @@ export async function createFetchErrorMessage(response, additionalText) {
     const responseMessage = `${response.status} ${response.statusText}${errorMessage ? ` (${errorMessage})` : ''}`;
     return `${additionalText ? `${additionalText} — ` : ''}${responseMessage}`;
 }
-export function checkConfigfileExists(configFile) {
-    if (!fs.existsSync(configFile)) {
-        throw new ConfigError(`Configuration file "${configFile}" does not exist. Please run "apollo config" first`);
-    }
-}
-export function checkProfileExists(profileName, config) {
-    if (!config.getProfileNames().includes(profileName)) {
-        throw new ConfigError(`Profile "${profileName}" does not exist. Please run "apollo config" to set this profile up or choose a different profile`);
-    }
-}
-export function basicCheckConfig(configFile, profileName) {
-    checkConfigfileExists(configFile);
-    const config = new ApolloConf(configFile);
-    checkProfileExists(profileName, config);
-}
 /**
  * @deprecated Use this function while we wait to resolve the TypeError when using localhost in fetch.
  */
@@ -42,166 +23,6 @@ export function localhostToAddress(url) {
      * */
     return url.replace('//localhost', '127.0.0.1');
 }
-export async function deleteAssembly(address, accessToken, assemblyId) {
-    const body = {
-        typeName: 'DeleteAssemblyChange',
-        assembly: assemblyId,
-    };
-    const auth = {
-        method: 'POST',
-        body: JSON.stringify(body),
-        headers: {
-            Authorization: `Bearer ${accessToken}`,
-            'Content-Type': 'application/json',
-        },
-        dispatcher: new Agent({ headersTimeout: 60 * 60 * 1000 }),
-    };
-    const url = new URL(localhostToAddress(`${address}/changes`));
-    const response = await fetch(url, auth);
-    if (!response.ok) {
-        const errorMessage = await createFetchErrorMessage(response, 'deleteAssembly failed');
-        throw new Error(errorMessage);
-    }
-}
-export async function getAssembly(address, accessToken, assemblyNameOrId) {
-    const assemblyId = await convertAssemblyNameToId(address, accessToken, [assemblyNameOrId]);
-    if (assemblyId.length === 0) {
-        throw new Error(`Assembly "${assemblyNameOrId}" not found`);
-    }
-    const res = await queryApollo(address, accessToken, 'assemblies');
-    const assemblies = (await res.json());
-    for (const x of assemblies) {
-        if (x._id === assemblyId[0]) {
-            // eslint-disable-next-line unicorn/prefer-structured-clone
-            return JSON.parse(JSON.stringify(x));
-        }
-    }
-    throw new Error(`Assembly "${assemblyNameOrId}" not found`);
-}
-export async function getRefseqId(address, accessToken, refseqNameOrId, inAssemblyNameOrId) {
-    if (refseqNameOrId === undefined && inAssemblyNameOrId === undefined) {
-        throw new Error('Please provide refseq and/or assembly');
-    }
-    inAssemblyNameOrId ??= '';
-    let assemblyId = [];
-    if (inAssemblyNameOrId !== '') {
-        assemblyId = await convertAssemblyNameToId(address, accessToken, [
-            inAssemblyNameOrId,
-        ]);
-        if (assemblyId.length !== 1) {
-            throw new Error(`Assembly name or assembly id returned ${assemblyId.length} assemblies instead of just one`);
-        }
-    }
-    const res = await queryApollo(address, accessToken, 'refSeqs');
-    const refSeqs = (await res.json());
-    const refseqIds = [];
-    const nAssemblies = new Set();
-    for (const x of refSeqs) {
-        const aid = x['assembly'];
-        const rid = x['_id'];
-        const rname = x['name'];
-        if (refseqNameOrId === rid ||
-            refseqNameOrId === rname ||
-            refseqNameOrId === undefined) {
-            if (inAssemblyNameOrId === '' || assemblyId.includes(aid)) {
-                refseqIds.push(rid);
-                nAssemblies.add(aid);
-            }
-            else {
-                //
-            }
-        }
-        if (nAssemblies.size > 1) {
-            throw new Error(`Sequence name "${refseqNameOrId}" found in more than one assembly`);
-        }
-    }
-    return refseqIds;
-}
-async function checkNameToIdDict(address, accessToken) {
-    const asm = await queryApollo(address, accessToken, 'checks/types');
-    const ja = (await asm.json()); // Not sure if CheckResultSnapshot is the right interface
-    const nameToId = {};
-    for (const x of ja) {
-        const { _id, name } = x; // x['name' as keyof typeof x]
-        nameToId[name] = _id; // x['_id' as keyof typeof x]
-    }
-    return nameToId;
-}
-export async function convertCheckNameToId(address, accessToken, namesOrIds) {
-    const nameToId = await checkNameToIdDict(address, accessToken);
-    const ids = [];
-    for (const x of namesOrIds) {
-        if (nameToId[x] !== undefined) {
-            ids.push(nameToId[x]);
-        }
-        else if (Object.values(nameToId).includes(x)) {
-            ids.push(x);
-        }
-        else {
-            throw new CheckError(`Check name or id "${x}" not found`);
-        }
-    }
-    return ids;
-}
-export async function assemblyNameToIdDict(address, accessToken) {
-    const asm = await queryApollo(address, accessToken, 'assemblies');
-    const ja = (await asm.json());
-    const nameToId = {};
-    for (const x of ja) {
-        nameToId[x['name']] = x['_id'];
-    }
-    return nameToId;
-}
-/** In input array namesOrIds, substitute common names with internal IDs */
-export async function convertAssemblyNameToId(address, accessToken, namesOrIds, verbose = true, removeDuplicates = true) {
-    const nameToId = await assemblyNameToIdDict(address, accessToken);
-    let ids = [];
-    for (const x of namesOrIds) {
-        if (nameToId[x] !== undefined) {
-            ids.push(nameToId[x]);
-        }
-        else if (Object.values(nameToId).includes(x)) {
-            ids.push(x);
-        }
-        else if (verbose) {
-            stderr.write(`Warning: Omitting unknown assembly: "${x}"\n`);
-        }
-    }
-    if (removeDuplicates) {
-        ids = [...new Set(ids)];
-    }
-    return ids;
-}
-export async function getFeatureById(address, accessToken, id) {
-    const url = new URL(localhostToAddress(`${address}/features/${id}`));
-    const auth = {
-        headers: {
-            authorization: `Bearer ${accessToken}`,
-        },
-    };
-    const response = await fetch(url, auth);
-    return response;
-}
-export async function getAssemblyFromRefseq(address, accessToken, refSeq) {
-    const refSeqs = await queryApollo(address, accessToken, 'refSeqs');
-    const refJson = filterJsonList((await refSeqs.json()), [refSeq], '_id');
-    return refJson[0]['assembly'];
-}
-export async function queryApollo(address, accessToken, endpoint) {
-    const auth = {
-        headers: {
-            Authorization: `Bearer ${accessToken}`,
-            'Content-Type': 'application/json',
-        },
-    };
-    const url = new URL(localhostToAddress(`${address}/${endpoint}`));
-    const response = await fetch(url, auth);
-    if (!response.ok) {
-        const errorMessage = await createFetchErrorMessage(response, 'queryApollo failed');
-        throw new ConfigError(errorMessage);
-    }
-    return response;
-}
 export function filterJsonList(json, keep, key) {
     const unique = new Set(keep);
     const results = [];
@@ -242,47 +63,6 @@ export const waitFor = (eventName, emitter) => {
     });
     return promise;
 };
-export async function submitAssembly(address, accessToken, body, force) {
-    let assemblies = await queryApollo(address, accessToken, 'assemblies');
-    for (const x of (await assemblies.json())) {
-        const addedAssemblies = 'changes' in body ? body.changes : [body];
-        for (const addedAssembly of addedAssemblies) {
-            if (x.name === addedAssembly.assemblyName) {
-                if (force) {
-                    await deleteAssembly(address, accessToken, x._id);
-                }
-                else {
-                    throw new Error(`Error: Assembly "${addedAssembly.assemblyName}" already exists`);
-                }
-            }
-        }
-    }
-    const auth = {
-        method: 'POST',
-        body: JSON.stringify(body),
-        headers: {
-            Authorization: `Bearer ${accessToken}`,
-            'Content-Type': 'application/json',
-        },
-        dispatcher: new Agent({ headersTimeout: 60 * 60 * 1000 }),
-    };
-    const url = new URL(localhostToAddress(`${address}/changes`));
-    const response = await fetch(url, auth);
-    if (!response.ok) {
-        const errorMessage = await createFetchErrorMessage(response, 'submitAssembly failed');
-        throw new Error(errorMessage);
-    }
-    assemblies = await queryApollo(address, accessToken, 'assemblies');
-    for (const x of (await assemblies.json())) {
-        const addedAssemblies = 'changes' in body ? body.changes : [body];
-        for (const addedAssembly of addedAssemblies) {
-            if (x.name === addedAssembly.assemblyName) {
-                return x;
-            }
-        }
-    }
-    throw new Error(`Failed to retrieve assembly from ${body.assembly}`);
-}
 export async function readStdin() {
     const chunks = [];
     for await (const chunk of stdin) {
@@ -328,17 +108,4 @@ export async function idReader(input, removeDuplicates = true) {
     }
     return ids;
 }
-export async function isFileId(x, address, accessToken) {
-    if (x.length != 24) {
-        return false;
-    }
-    const files = await queryApollo(address, accessToken, 'files');
-    const json = (await files.json());
-    for (const fileDoc of json) {
-        if (fileDoc['_id'] === x) {
-            return true;
-        }
-    }
-    return false;
-}
 //# sourceMappingURL=utils.js.map

package/dist/utils.js.map

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