@jbrowse/cli 2.10.3 → 2.11.0

package/README.md

@@ -53,7 +53,7 @@ It is likely preferable in most cases to install the tools globally with
 - [`jbrowse add-track-json TRACK`](#jbrowse-add-track-json-track)
 - [`jbrowse admin-server`](#jbrowse-admin-server)
 - [`jbrowse create LOCALPATH`](#jbrowse-create-localpath)
-- [`jbrowse help [COMMANDS]`](#jbrowse-help-commands)
+- [`jbrowse help [COMMAND]`](#jbrowse-help-command)
 - [`jbrowse make-pif FILE`](#jbrowse-make-pif-file)
 - [`jbrowse remove-track TRACK`](#jbrowse-remove-track-track)
 - [`jbrowse set-default-session`](#jbrowse-set-default-session)
@@ -205,7 +205,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/add-assembly.ts](https://github.com/GMOD/jbrowse-components/blob/v2.10.3/products/jbrowse-cli/src/commands/add-assembly.ts)_
+[src/commands/add-assembly.ts](https://github.com/GMOD/jbrowse-components/blob/v2.11.0/products/jbrowse-cli/src/commands/add-assembly.ts)_
 
 ## `jbrowse add-connection CONNECTIONURLORPATH`
 
@@ -256,7 +256,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/add-connection.ts](https://github.com/GMOD/jbrowse-components/blob/v2.10.3/products/jbrowse-cli/src/commands/add-connection.ts)_
+[src/commands/add-connection.ts](https://github.com/GMOD/jbrowse-components/blob/v2.11.0/products/jbrowse-cli/src/commands/add-connection.ts)_
 
 ## `jbrowse add-track TRACK`
 
@@ -337,7 +337,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/add-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.10.3/products/jbrowse-cli/src/commands/add-track.ts)_
+[src/commands/add-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.11.0/products/jbrowse-cli/src/commands/add-track.ts)_
 
 ## `jbrowse add-track-json TRACK`
 
@@ -367,7 +367,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/add-track-json.ts](https://github.com/GMOD/jbrowse-components/blob/v2.10.3/products/jbrowse-cli/src/commands/add-track-json.ts)_
+[src/commands/add-track-json.ts](https://github.com/GMOD/jbrowse-components/blob/v2.11.0/products/jbrowse-cli/src/commands/add-track-json.ts)_
 
 ## `jbrowse admin-server`
 
@@ -399,7 +399,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/admin-server.ts](https://github.com/GMOD/jbrowse-components/blob/v2.10.3/products/jbrowse-cli/src/commands/admin-server.ts)_
+[src/commands/admin-server.ts](https://github.com/GMOD/jbrowse-components/blob/v2.11.0/products/jbrowse-cli/src/commands/admin-server.ts)_
 
 ## `jbrowse create LOCALPATH`
 
@@ -456,18 +456,18 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/create.ts](https://github.com/GMOD/jbrowse-components/blob/v2.10.3/products/jbrowse-cli/src/commands/create.ts)_
+[src/commands/create.ts](https://github.com/GMOD/jbrowse-components/blob/v2.11.0/products/jbrowse-cli/src/commands/create.ts)_
 
-## `jbrowse help [COMMANDS]`
+## `jbrowse help [COMMAND]`
 
 Display help for jbrowse.
 
 ```
 USAGE
-  $ jbrowse help [COMMANDS] [-n]
+  $ jbrowse help [COMMAND...] [-n]
 
 ARGUMENTS
-  COMMANDS  Command to show help for.
+  COMMAND...  Command to show help for.
 
 FLAGS
   -n, --nested-commands  Include all nested commands in the output.
@@ -477,7 +477,7 @@ DESCRIPTION
 ```
 
 _See code:
-[@oclif/plugin-help](https://github.com/oclif/plugin-help/blob/v6.0.15/src/commands/help.ts)_
+[@oclif/plugin-help](https://github.com/oclif/plugin-help/blob/v6.0.20/src/commands/help.ts)_
 
 ## `jbrowse make-pif FILE`
 
@@ -507,7 +507,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/make-pif.ts](https://github.com/GMOD/jbrowse-components/blob/v2.10.3/products/jbrowse-cli/src/commands/make-pif.ts)_
+[src/commands/make-pif.ts](https://github.com/GMOD/jbrowse-components/blob/v2.11.0/products/jbrowse-cli/src/commands/make-pif.ts)_
 
 ## `jbrowse remove-track TRACK`
 
@@ -535,7 +535,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/remove-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.10.3/products/jbrowse-cli/src/commands/remove-track.ts)_
+[src/commands/remove-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.11.0/products/jbrowse-cli/src/commands/remove-track.ts)_
 
 ## `jbrowse set-default-session`
 
@@ -568,7 +568,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/set-default-session.ts](https://github.com/GMOD/jbrowse-components/blob/v2.10.3/products/jbrowse-cli/src/commands/set-default-session.ts)_
+[src/commands/set-default-session.ts](https://github.com/GMOD/jbrowse-components/blob/v2.11.0/products/jbrowse-cli/src/commands/set-default-session.ts)_
 
 ## `jbrowse sort-gff FILE`
 
@@ -599,7 +599,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/sort-gff.ts](https://github.com/GMOD/jbrowse-components/blob/v2.10.3/products/jbrowse-cli/src/commands/sort-gff.ts)_
+[src/commands/sort-gff.ts](https://github.com/GMOD/jbrowse-components/blob/v2.11.0/products/jbrowse-cli/src/commands/sort-gff.ts)_
 
 ## `jbrowse text-index`
 
@@ -666,7 +666,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/text-index.ts](https://github.com/GMOD/jbrowse-components/blob/v2.10.3/products/jbrowse-cli/src/commands/text-index.ts)_
+[src/commands/text-index.ts](https://github.com/GMOD/jbrowse-components/blob/v2.11.0/products/jbrowse-cli/src/commands/text-index.ts)_
 
 ## `jbrowse upgrade [LOCALPATH]`
 
@@ -729,7 +729,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/upgrade.ts](https://github.com/GMOD/jbrowse-components/blob/v2.10.3/products/jbrowse-cli/src/commands/upgrade.ts)_
+[src/commands/upgrade.ts](https://github.com/GMOD/jbrowse-components/blob/v2.11.0/products/jbrowse-cli/src/commands/upgrade.ts)_
 
 <!-- commandsstop -->
 

package/lib/base.js

@@ -57,6 +57,7 @@ class JBrowseCommand extends core_1.Command {
         }
         if (locationUrl) {
             if (check) {
+                // @ts-expect-error
                 const response = await (0, fetchWithProxy_1.default)(locationUrl, { method: 'HEAD' });
                 if (!response.ok) {
                     throw new Error(`${locationUrl} result ${response.statusText}`);

package/lib/commands/add-connection.js

@@ -48,9 +48,11 @@ class AddConnection extends base_1.default {
                 }
                 : {}),
             connectionId: id,
-            assemblyNames: assemblyNames || type === 'JBrowse1Connection'
-                ? [configContents.assemblies[0]?.name]
-                : undefined,
+            assemblyNames: assemblyNames
+                ? assemblyNames.split(',')
+                : type === 'JBrowse1Connection'
+                    ? [configContents.assemblies[0]?.name]
+                    : undefined,
             ...(config ? (0, json_parse_better_errors_1.default)(config) : {}),
         };
         if (!configContents.connections) {
@@ -84,6 +86,7 @@ class AddConnection extends base_1.default {
             let response;
             try {
                 if (check) {
+                    // @ts-expect-error
                     response = await (0, fetchWithProxy_1.default)(locationUrl, { method: 'HEAD' });
                 }
                 if (!response || response.ok) {

package/lib/commands/add-track.js

@@ -241,7 +241,8 @@ class AddTrack extends base_1.default {
             /\.vcf$/i.test(location) ||
             /\.gtf?$/i.test(location) ||
             /\.gff3?$/i.test(location) ||
-            /\.chain(\.gz)?$/i.test(location)) {
+            /\.chain(\.gz)?$/i.test(location) ||
+            /\.hic$/i.test(location)) {
             return {
                 file: location,
             };

package/lib/fetchWithProxy.js

@@ -1,14 +1,12 @@
 "use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
 Object.defineProperty(exports, "__esModule", { value: true });
-const node_fetch_1 = __importDefault(require("node-fetch"));
-const proxy_agent_1 = require("proxy-agent");
+const node_1 = require("node-fetch-native/node");
+const proxy_1 = require("node-fetch-native/proxy");
+const proxy = (0, proxy_1.createProxy)();
 // The correct proxy `Agent` implementation to use will be determined
 // via the `http_proxy` / `https_proxy` / `no_proxy` / etc. env vars
+// https://github.com/unjs/node-fetch-native?tab=readme-ov-file#proxy-support
 function fetchWithProxy(url, options = {}) {
-    const agent = new proxy_agent_1.ProxyAgent();
-    return (0, node_fetch_1.default)(url, { agent, ...options });
+    return (0, node_1.fetch)(url, { ...options, ...proxy });
 }
 exports.default = fetchWithProxy;

package/lib/types/gff3Adapter.js

@@ -21,11 +21,13 @@ async function* indexGff3({ config, attributesToIndex, inLocation, outLocation,
     if (!quiet) {
         progressBar.start(totalBytes, 0);
     }
+    // @ts-expect-error
     stream.on('data', chunk => {
         receivedBytes += chunk.length;
         progressBar.update(receivedBytes);
     });
     const rl = readline_1.default.createInterface({
+        // @ts-expect-error
         input: inLocation.match(/.b?gz$/) ? stream.pipe((0, zlib_1.createGunzip)()) : stream,
     });
     for await (const line of rl) {
@@ -50,7 +52,7 @@ async function* indexGff3({ config, attributesToIndex, inLocation, outLocation,
                 .map(f => f.split('='))
                 .map(([key, val]) => [
                 key.trim(),
-                decodeURIComponent(val).trim().split(',').join(' '),
+                (0, util_1.decodeURIComponentNoThrow)(val).trim().split(',').join(' '),
             ]));
             const attrs = attributesToIndex
                 .map(attr => col9attrs[attr])

package/lib/types/vcfAdapter.js

@@ -21,12 +21,14 @@ async function* indexVcf({ config, attributesToIndex, inLocation, outLocation, q
     if (!quiet) {
         progressBar.start(totalBytes, 0);
     }
+    // @ts-expect-error
     stream.on('data', chunk => {
         receivedBytes += chunk.length;
         progressBar.update(receivedBytes);
     });
     const gzStream = inLocation.match(/.b?gz$/)
-        ? stream.pipe((0, zlib_1.createGunzip)())
+        ? // @ts-expect-error
+            stream.pipe((0, zlib_1.createGunzip)())
         : stream;
     const rl = readline_1.default.createInterface({
         input: gzStream,
@@ -46,7 +48,9 @@ async function* indexVcf({ config, attributesToIndex, inLocation, outLocation, q
             .map(f => f.split('='))
             .map(([key, val]) => [
             key.trim(),
-            val ? decodeURIComponent(val).trim().split(',').join(' ') : undefined,
+            val
+                ? (0, util_1.decodeURIComponentNoThrow)(val).trim().split(',').join(' ')
+                : undefined,
         ]));
         const end = fields.END;
         const locStr = `${ref}:${pos}..${end || +pos + 1}`;

package/lib/util.js

@@ -3,7 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getLocalOrRemoteStream = void 0;
+exports.decodeURIComponentNoThrow = exports.getLocalOrRemoteStream = void 0;
 const common_1 = require("./types/common");
 const fs_1 = __importDefault(require("fs"));
 const path_1 = __importDefault(require("path"));
@@ -23,3 +23,13 @@ async function getLocalOrRemoteStream(uri, out) {
     return { totalBytes, stream };
 }
 exports.getLocalOrRemoteStream = getLocalOrRemoteStream;
+function decodeURIComponentNoThrow(uri) {
+    try {
+        return decodeURIComponent(uri);
+    }
+    catch (e) {
+        // avoid throwing exception on a failure to decode URI component
+        return uri;
+    }
+}
+exports.decodeURIComponentNoThrow = decodeURIComponentNoThrow;

package/oclif.manifest.json

@@ -1123,5 +1123,5 @@
       ]
     }
   },
-  "version": "2.10.3"
+  "version": "2.11.0"
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/cli",
-  "version": "2.10.3",
+  "version": "2.11.0",
   "description": "A command line tool for working with JBrowse 2",
   "keywords": [
     "jbrowse",
@@ -56,8 +56,7 @@
     "express": "^4.17.1",
     "ixixx": "^2.0.1",
     "json-parse-better-errors": "^1.0.2",
-    "node-fetch": "^2.6.0",
-    "proxy-agent": "^6.2.1",
+    "node-fetch-native": "^1.6.4",
     "rimraf": "^5.0.0",
     "tslib": "^2.3.1"
   },
@@ -75,5 +74,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "c8fc800cd17decd72b2e971c7a6add3b95214e72"
+  "gitHead": "3d43a820b9274a6160aa4dc15616147f390d9094"
 }