@jbrowse/cli 2.10.1 → 2.10.2

package/README.md

@@ -205,7 +205,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/add-assembly.ts](https://github.com/GMOD/jbrowse-components/blob/v2.10.1/products/jbrowse-cli/src/commands/add-assembly.ts)_
+[src/commands/add-assembly.ts](https://github.com/GMOD/jbrowse-components/blob/v2.10.2/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/v2.10.1/products/jbrowse-cli/src/commands/add-connection.ts)_
+[src/commands/add-connection.ts](https://github.com/GMOD/jbrowse-components/blob/v2.10.2/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/v2.10.1/products/jbrowse-cli/src/commands/add-track.ts)_
+[src/commands/add-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.10.2/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/v2.10.1/products/jbrowse-cli/src/commands/add-track-json.ts)_
+[src/commands/add-track-json.ts](https://github.com/GMOD/jbrowse-components/blob/v2.10.2/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/v2.10.1/products/jbrowse-cli/src/commands/admin-server.ts)_
+[src/commands/admin-server.ts](https://github.com/GMOD/jbrowse-components/blob/v2.10.2/products/jbrowse-cli/src/commands/admin-server.ts)_
 
 ## `jbrowse create LOCALPATH`
 
@@ -456,7 +456,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/create.ts](https://github.com/GMOD/jbrowse-components/blob/v2.10.1/products/jbrowse-cli/src/commands/create.ts)_
+[src/commands/create.ts](https://github.com/GMOD/jbrowse-components/blob/v2.10.2/products/jbrowse-cli/src/commands/create.ts)_
 
 ## `jbrowse help [COMMANDS]`
 
@@ -507,7 +507,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/make-pif.ts](https://github.com/GMOD/jbrowse-components/blob/v2.10.1/products/jbrowse-cli/src/commands/make-pif.ts)_
+[src/commands/make-pif.ts](https://github.com/GMOD/jbrowse-components/blob/v2.10.2/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/v2.10.1/products/jbrowse-cli/src/commands/remove-track.ts)_
+[src/commands/remove-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.10.2/products/jbrowse-cli/src/commands/remove-track.ts)_
 
 ## `jbrowse set-default-session`
 
@@ -543,22 +543,16 @@ Set a default session with views and tracks
 
 ```
 USAGE
-  $ jbrowse set-default-session [-s <value>] [-n <value>] [-v <value>] [--viewId <value>] [-t <value>] [-c] [--target
-    <value>] [--out <value>] [--delete] [-h]
+  $ jbrowse set-default-session [-s <value>] [-n <value>] [-c] [--target <value>] [--out <value>] [--delete] [-h]
 
 FLAGS
   -c, --currentSession   List out the current default session
   -h, --help             Show CLI help.
   -n, --name=<value>     [default: New Default Session] Give a name for the default session
   -s, --session=<value>  set path to a file containing session in json format
-  -t, --tracks=<value>   Track id or track ids as comma separated string to put into default session
-  -v, --view=<value>     View type in config to be added as default session, i.e LinearGenomeView, CircularView,
-                         DotplotView.
-                         Must be provided if no default session file provided
       --delete           Delete any existing default session.
       --out=<value>      synonym for target
       --target=<value>   path to config file in JB2 installation directory to write out to
-      --viewId=<value>   Identifier for the view. Will be generated on default
 
 DESCRIPTION
   Set a default session with views and tracks
@@ -566,15 +560,15 @@ DESCRIPTION
 EXAMPLES
   $ jbrowse set-default-session --session /path/to/default/session.json
 
-  $ jbrowse set-default-session --target /path/to/jb2/installation/config.json --view LinearGenomeView --tracks track1, track2, track3
+  $ jbrowse set-default-session --target /path/to/jb2/installation/config.json
 
-  $ jbrowse set-default-session --view LinearGenomeView, --name newName --viewId view-no-tracks
+  $ jbrowse set-default-session --view LinearGenomeView, --name newName
 
   $ jbrowse set-default-session --currentSession # Prints out current default session
 ```
 
 _See code:
-[src/commands/set-default-session.ts](https://github.com/GMOD/jbrowse-components/blob/v2.10.1/products/jbrowse-cli/src/commands/set-default-session.ts)_
+[src/commands/set-default-session.ts](https://github.com/GMOD/jbrowse-components/blob/v2.10.2/products/jbrowse-cli/src/commands/set-default-session.ts)_
 
 ## `jbrowse sort-gff FILE`
 
@@ -605,7 +599,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/sort-gff.ts](https://github.com/GMOD/jbrowse-components/blob/v2.10.1/products/jbrowse-cli/src/commands/sort-gff.ts)_
+[src/commands/sort-gff.ts](https://github.com/GMOD/jbrowse-components/blob/v2.10.2/products/jbrowse-cli/src/commands/sort-gff.ts)_
 
 ## `jbrowse text-index`
 
@@ -672,7 +666,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/text-index.ts](https://github.com/GMOD/jbrowse-components/blob/v2.10.1/products/jbrowse-cli/src/commands/text-index.ts)_
+[src/commands/text-index.ts](https://github.com/GMOD/jbrowse-components/blob/v2.10.2/products/jbrowse-cli/src/commands/text-index.ts)_
 
 ## `jbrowse upgrade [LOCALPATH]`
 
@@ -735,7 +729,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/upgrade.ts](https://github.com/GMOD/jbrowse-components/blob/v2.10.1/products/jbrowse-cli/src/commands/upgrade.ts)_
+[src/commands/upgrade.ts](https://github.com/GMOD/jbrowse-components/blob/v2.10.2/products/jbrowse-cli/src/commands/upgrade.ts)_
 
 <!-- commandsstop -->
 

package/lib/base.js

@@ -139,8 +139,7 @@ class JBrowseCommand extends core_1.Command {
         const response = await (0, fetchWithProxy_1.default)(`https://api.github.com/repos/GMOD/jbrowse-components/releases/tags/${tag}`);
         if (response.ok) {
             const result = (await response.json());
-            const file = result?.assets?.find(f => f.name.includes('jbrowse-web'))
-                ?.browser_download_url;
+            const file = result?.assets?.find(f => f.name.includes('jbrowse-web'))?.browser_download_url;
             if (!file) {
                 this.error('Could not find version specified. Use --listVersions to see all available versions', { exit: 90 });
             }

package/lib/commands/set-default-session.js

@@ -11,70 +11,28 @@ const fsPromises = fs_1.default.promises;
 class SetDefaultSession extends base_1.default {
     async run() {
         const { flags: runFlags } = await this.parse(SetDefaultSession);
-        const { session, name, tracks, currentSession, view, viewId, delete: deleteDefaultSession, } = runFlags;
+        const { session, currentSession, delete: deleteDefaultSession } = runFlags;
         const output = runFlags.target || runFlags.out || '.';
         const isDir = (await fsPromises.lstat(output)).isDirectory();
         this.target = isDir ? `${output}/config.json` : output;
         const configContents = await this.readJsonFile(this.target);
         if (deleteDefaultSession) {
             delete configContents.defaultSession;
-            this.debug(`Writing configuration to file ${this.target}`);
             await this.writeJsonFile(this.target, configContents);
-            this.log(`Deleted defaultSession from ${this.target}`);
-            return;
         }
-        // if user passes current session flag, print out and exit
-        if (currentSession) {
+        else if (currentSession) {
             this.log(`The current default session is ${JSON.stringify(configContents.defaultSession)}`);
             this.exit();
         }
-        const foundTracks = [];
-        const existingDefaultSession = configContents.defaultSession?.length > 0;
-        // must provide default session, or view, or tracks + view
-        if (!session && !view && !tracks) {
-            this.error(`No default session information provided, Please either provide a default session file or enter information to build a default session`, { exit: 120 });
+        else if (!session) {
+            this.error(`Please either provide a default session file`, { exit: 120 });
         }
         else if (session) {
-            // if user provides a file, process and set as default session and exit
-            const defaultJson = await this.readDefaultSessionFile(session);
-            configContents.defaultSession = defaultJson;
-        }
-        else {
-            // use trackids if any to match to tracks in the config
-            let trackIds = [];
-            if (tracks && configContents.tracks) {
-                if (!view) {
-                    this.error('Tracks must have a view type specified. Please rerun using the --view flag', { exit: 130 });
-                }
-                trackIds = tracks.split(',').map(c => c.trim());
-                trackIds.forEach(trackId => {
-                    this.log(trackId);
-                    const matchingTrack = configContents.tracks?.find(track => trackId === track.trackId);
-                    if (!matchingTrack) {
-                        this.error(`Track ${trackId} has not been added to config yet.\nPlease add the track with the add-track command before adding to the default session`, { exit: 140 });
-                    }
-                    else {
-                        foundTracks.push({
-                            type: matchingTrack.type,
-                            configuration: matchingTrack.trackId,
-                        });
-                    }
-                });
-            }
-            configContents.defaultSession = {
-                name,
-                views: [
-                    {
-                        id: viewId || `${view}-${foundTracks.length}`,
-                        type: view,
-                        tracks: foundTracks,
-                    },
-                ],
-            };
+            await this.writeJsonFile(this.target, {
+                ...configContents,
+                defaultSession: await this.readDefaultSessionFile(session),
+            });
         }
-        this.debug(`Writing configuration to file ${this.target}`);
-        await this.writeJsonFile(this.target, configContents);
-        this.log(`${existingDefaultSession ? 'Overwrote' : 'Added'} defaultSession "${name}" ${existingDefaultSession ? 'in' : 'to'} ${this.target}`);
     }
     async readDefaultSessionFile(defaultSessionFile) {
         let defaultSessionJson;
@@ -102,8 +60,8 @@ class SetDefaultSession extends base_1.default {
 SetDefaultSession.description = 'Set a default session with views and tracks';
 SetDefaultSession.examples = [
     '$ jbrowse set-default-session --session /path/to/default/session.json',
-    '$ jbrowse set-default-session --target /path/to/jb2/installation/config.json --view LinearGenomeView --tracks track1, track2, track3',
-    '$ jbrowse set-default-session --view LinearGenomeView, --name newName --viewId view-no-tracks',
+    '$ jbrowse set-default-session --target /path/to/jb2/installation/config.json',
+    '$ jbrowse set-default-session --view LinearGenomeView, --name newName',
     '$ jbrowse set-default-session --currentSession # Prints out current default session',
 ];
 SetDefaultSession.flags = {
@@ -116,17 +74,6 @@ SetDefaultSession.flags = {
         description: 'Give a name for the default session',
         default: 'New Default Session',
     }),
-    view: core_1.Flags.string({
-        char: 'v',
-        description: 'View type in config to be added as default session, i.e LinearGenomeView, CircularView, DotplotView.\nMust be provided if no default session file provided',
-    }),
-    viewId: core_1.Flags.string({
-        description: 'Identifier for the view. Will be generated on default',
-    }),
-    tracks: core_1.Flags.string({
-        char: 't',
-        description: 'Track id or track ids as comma separated string to put into default session',
-    }),
     currentSession: core_1.Flags.boolean({
         char: 'c',
         description: 'List out the current default session',

package/oclif.manifest.json

@@ -784,8 +784,8 @@
       "description": "Set a default session with views and tracks",
       "examples": [
         "$ jbrowse set-default-session --session /path/to/default/session.json",
-        "$ jbrowse set-default-session --target /path/to/jb2/installation/config.json --view LinearGenomeView --tracks track1, track2, track3",
-        "$ jbrowse set-default-session --view LinearGenomeView, --name newName --viewId view-no-tracks",
+        "$ jbrowse set-default-session --target /path/to/jb2/installation/config.json",
+        "$ jbrowse set-default-session --view LinearGenomeView, --name newName",
         "$ jbrowse set-default-session --currentSession # Prints out current default session"
       ],
       "flags": {
@@ -806,29 +806,6 @@
           "multiple": false,
           "type": "option"
         },
-        "view": {
-          "char": "v",
-          "description": "View type in config to be added as default session, i.e LinearGenomeView, CircularView, DotplotView.\nMust be provided if no default session file provided",
-          "name": "view",
-          "hasDynamicHelp": false,
-          "multiple": false,
-          "type": "option"
-        },
-        "viewId": {
-          "description": "Identifier for the view. Will be generated on default",
-          "name": "viewId",
-          "hasDynamicHelp": false,
-          "multiple": false,
-          "type": "option"
-        },
-        "tracks": {
-          "char": "t",
-          "description": "Track id or track ids as comma separated string to put into default session",
-          "name": "tracks",
-          "hasDynamicHelp": false,
-          "multiple": false,
-          "type": "option"
-        },
         "currentSession": {
           "char": "c",
           "description": "List out the current default session",
@@ -1146,5 +1123,5 @@
       ]
     }
   },
-  "version": "2.10.1"
+  "version": "2.10.2"
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/cli",
-  "version": "2.10.1",
+  "version": "2.10.2",
   "description": "A command line tool for working with JBrowse 2",
   "keywords": [
     "jbrowse",
@@ -75,5 +75,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "442b5f87efddfdf4ccf520b4d9dd01ddd370cb07"
+  "gitHead": "7ca3b7db337ebd88853e2d96cdab940ed550c4fb"
 }