@apollo-annotation/cli 1.0.1 → 1.1.0

package/README.md

@@ -16,7 +16,7 @@ $ npm install -g @apollo-annotation/cli
 $ apollo COMMAND
 running command...
 $ apollo (--version)
-@apollo-annotation/cli/1.0.1 linux-x64 node-v24.14.1
+@apollo-annotation/cli/1.1.0 linux-x64 node-v24.14.1
 $ apollo --help [COMMAND]
 USAGE
   $ apollo COMMAND
@@ -117,7 +117,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/assembly/add-from-fasta.ts](https://github.com/GMOD/Apollo3/blob/v1.0.1/packages/apollo-cli/src/commands/assembly/add-from-fasta.ts)_
+[src/commands/assembly/add-from-fasta.ts](https://github.com/GMOD/Apollo3/blob/v1.1.0/packages/apollo-cli/src/commands/assembly/add-from-fasta.ts)_
 
 ## `apollo assembly add-from-gff INPUT-FILE`
 
@@ -156,7 +156,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/assembly/add-from-gff.ts](https://github.com/GMOD/Apollo3/blob/v1.0.1/packages/apollo-cli/src/commands/assembly/add-from-gff.ts)_
+[src/commands/assembly/add-from-gff.ts](https://github.com/GMOD/Apollo3/blob/v1.1.0/packages/apollo-cli/src/commands/assembly/add-from-gff.ts)_
 
 ## `apollo assembly check`
 
@@ -198,7 +198,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/assembly/check.ts](https://github.com/GMOD/Apollo3/blob/v1.0.1/packages/apollo-cli/src/commands/assembly/check.ts)_
+[src/commands/assembly/check.ts](https://github.com/GMOD/Apollo3/blob/v1.1.0/packages/apollo-cli/src/commands/assembly/check.ts)_
 
 ## `apollo assembly delete`
 
@@ -226,7 +226,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/assembly/delete.ts](https://github.com/GMOD/Apollo3/blob/v1.0.1/packages/apollo-cli/src/commands/assembly/delete.ts)_
+[src/commands/assembly/delete.ts](https://github.com/GMOD/Apollo3/blob/v1.1.0/packages/apollo-cli/src/commands/assembly/delete.ts)_
 
 ## `apollo assembly get`
 
@@ -248,7 +248,7 @@ DESCRIPTION
 ```
 
 _See code:
-[src/commands/assembly/get.ts](https://github.com/GMOD/Apollo3/blob/v1.0.1/packages/apollo-cli/src/commands/assembly/get.ts)_
+[src/commands/assembly/get.ts](https://github.com/GMOD/Apollo3/blob/v1.1.0/packages/apollo-cli/src/commands/assembly/get.ts)_
 
 ## `apollo assembly sequence`
 
@@ -283,7 +283,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/assembly/sequence.ts](https://github.com/GMOD/Apollo3/blob/v1.0.1/packages/apollo-cli/src/commands/assembly/sequence.ts)_
+[src/commands/assembly/sequence.ts](https://github.com/GMOD/Apollo3/blob/v1.1.0/packages/apollo-cli/src/commands/assembly/sequence.ts)_
 
 ## `apollo change get`
 
@@ -307,7 +307,7 @@ DESCRIPTION
 ```
 
 _See code:
-[src/commands/change/get.ts](https://github.com/GMOD/Apollo3/blob/v1.0.1/packages/apollo-cli/src/commands/change/get.ts)_
+[src/commands/change/get.ts](https://github.com/GMOD/Apollo3/blob/v1.1.0/packages/apollo-cli/src/commands/change/get.ts)_
 
 ## `apollo config [KEY] [VALUE]`
 
@@ -359,7 +359,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/config.ts](https://github.com/GMOD/Apollo3/blob/v1.0.1/packages/apollo-cli/src/commands/config.ts)_
+[src/commands/config.ts](https://github.com/GMOD/Apollo3/blob/v1.1.0/packages/apollo-cli/src/commands/config.ts)_
 
 ## `apollo export gff3 ASSEMBLY`
 
@@ -387,7 +387,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/export/gff3.ts](https://github.com/GMOD/Apollo3/blob/v1.0.1/packages/apollo-cli/src/commands/export/gff3.ts)_
+[src/commands/export/gff3.ts](https://github.com/GMOD/Apollo3/blob/v1.1.0/packages/apollo-cli/src/commands/export/gff3.ts)_
 
 ## `apollo feature add [FEATURE-JSON]`
 
@@ -443,7 +443,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/add.ts](https://github.com/GMOD/Apollo3/blob/v1.0.1/packages/apollo-cli/src/commands/feature/add.ts)_
+[src/commands/feature/add.ts](https://github.com/GMOD/Apollo3/blob/v1.1.0/packages/apollo-cli/src/commands/feature/add.ts)_
 
 ## `apollo feature add-child`
 
@@ -474,7 +474,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/add-child.ts](https://github.com/GMOD/Apollo3/blob/v1.0.1/packages/apollo-cli/src/commands/feature/add-child.ts)_
+[src/commands/feature/add-child.ts](https://github.com/GMOD/Apollo3/blob/v1.1.0/packages/apollo-cli/src/commands/feature/add-child.ts)_
 
 ## `apollo feature check`
 
@@ -507,7 +507,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/check.ts](https://github.com/GMOD/Apollo3/blob/v1.0.1/packages/apollo-cli/src/commands/feature/check.ts)_
+[src/commands/feature/check.ts](https://github.com/GMOD/Apollo3/blob/v1.1.0/packages/apollo-cli/src/commands/feature/check.ts)_
 
 ## `apollo feature copy`
 
@@ -538,7 +538,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/copy.ts](https://github.com/GMOD/Apollo3/blob/v1.0.1/packages/apollo-cli/src/commands/feature/copy.ts)_
+[src/commands/feature/copy.ts](https://github.com/GMOD/Apollo3/blob/v1.1.0/packages/apollo-cli/src/commands/feature/copy.ts)_
 
 ## `apollo feature delete`
 
@@ -562,7 +562,7 @@ DESCRIPTION
 ```
 
 _See code:
-[src/commands/feature/delete.ts](https://github.com/GMOD/Apollo3/blob/v1.0.1/packages/apollo-cli/src/commands/feature/delete.ts)_
+[src/commands/feature/delete.ts](https://github.com/GMOD/Apollo3/blob/v1.1.0/packages/apollo-cli/src/commands/feature/delete.ts)_
 
 ## `apollo feature edit`
 
@@ -604,7 +604,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/edit.ts](https://github.com/GMOD/Apollo3/blob/v1.0.1/packages/apollo-cli/src/commands/feature/edit.ts)_
+[src/commands/feature/edit.ts](https://github.com/GMOD/Apollo3/blob/v1.1.0/packages/apollo-cli/src/commands/feature/edit.ts)_
 
 ## `apollo feature edit-attribute`
 
@@ -644,7 +644,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/edit-attribute.ts](https://github.com/GMOD/Apollo3/blob/v1.0.1/packages/apollo-cli/src/commands/feature/edit-attribute.ts)_
+[src/commands/feature/edit-attribute.ts](https://github.com/GMOD/Apollo3/blob/v1.1.0/packages/apollo-cli/src/commands/feature/edit-attribute.ts)_
 
 ## `apollo feature edit-coords`
 
@@ -678,7 +678,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/edit-coords.ts](https://github.com/GMOD/Apollo3/blob/v1.0.1/packages/apollo-cli/src/commands/feature/edit-coords.ts)_
+[src/commands/feature/edit-coords.ts](https://github.com/GMOD/Apollo3/blob/v1.1.0/packages/apollo-cli/src/commands/feature/edit-coords.ts)_
 
 ## `apollo feature edit-type`
 
@@ -702,7 +702,7 @@ DESCRIPTION
 ```
 
 _See code:
-[src/commands/feature/edit-type.ts](https://github.com/GMOD/Apollo3/blob/v1.0.1/packages/apollo-cli/src/commands/feature/edit-type.ts)_
+[src/commands/feature/edit-type.ts](https://github.com/GMOD/Apollo3/blob/v1.1.0/packages/apollo-cli/src/commands/feature/edit-type.ts)_
 
 ## `apollo feature get`
 
@@ -736,7 +736,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/get.ts](https://github.com/GMOD/Apollo3/blob/v1.0.1/packages/apollo-cli/src/commands/feature/get.ts)_
+[src/commands/feature/get.ts](https://github.com/GMOD/Apollo3/blob/v1.1.0/packages/apollo-cli/src/commands/feature/get.ts)_
 
 ## `apollo feature get-id`
 
@@ -764,7 +764,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/get-id.ts](https://github.com/GMOD/Apollo3/blob/v1.0.1/packages/apollo-cli/src/commands/feature/get-id.ts)_
+[src/commands/feature/get-id.ts](https://github.com/GMOD/Apollo3/blob/v1.1.0/packages/apollo-cli/src/commands/feature/get-id.ts)_
 
 ## `apollo feature get-indexed-id ID`
 
@@ -796,7 +796,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/get-indexed-id.ts](https://github.com/GMOD/Apollo3/blob/v1.0.1/packages/apollo-cli/src/commands/feature/get-indexed-id.ts)_
+[src/commands/feature/get-indexed-id.ts](https://github.com/GMOD/Apollo3/blob/v1.1.0/packages/apollo-cli/src/commands/feature/get-indexed-id.ts)_
 
 ## `apollo feature import INPUT-FILE`
 
@@ -828,7 +828,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/import.ts](https://github.com/GMOD/Apollo3/blob/v1.0.1/packages/apollo-cli/src/commands/feature/import.ts)_
+[src/commands/feature/import.ts](https://github.com/GMOD/Apollo3/blob/v1.1.0/packages/apollo-cli/src/commands/feature/import.ts)_
 
 ## `apollo feature search`
 
@@ -879,7 +879,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/search.ts](https://github.com/GMOD/Apollo3/blob/v1.0.1/packages/apollo-cli/src/commands/feature/search.ts)_
+[src/commands/feature/search.ts](https://github.com/GMOD/Apollo3/blob/v1.1.0/packages/apollo-cli/src/commands/feature/search.ts)_
 
 ## `apollo file delete`
 
@@ -906,7 +906,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/file/delete.ts](https://github.com/GMOD/Apollo3/blob/v1.0.1/packages/apollo-cli/src/commands/file/delete.ts)_
+[src/commands/file/delete.ts](https://github.com/GMOD/Apollo3/blob/v1.1.0/packages/apollo-cli/src/commands/file/delete.ts)_
 
 ## `apollo file download`
 
@@ -934,7 +934,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/file/download.ts](https://github.com/GMOD/Apollo3/blob/v1.0.1/packages/apollo-cli/src/commands/file/download.ts)_
+[src/commands/file/download.ts](https://github.com/GMOD/Apollo3/blob/v1.1.0/packages/apollo-cli/src/commands/file/download.ts)_
 
 ## `apollo file get`
 
@@ -961,7 +961,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/file/get.ts](https://github.com/GMOD/Apollo3/blob/v1.0.1/packages/apollo-cli/src/commands/file/get.ts)_
+[src/commands/file/get.ts](https://github.com/GMOD/Apollo3/blob/v1.1.0/packages/apollo-cli/src/commands/file/get.ts)_
 
 ## `apollo file upload INPUT-FILE`
 
@@ -998,7 +998,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/file/upload.ts](https://github.com/GMOD/Apollo3/blob/v1.0.1/packages/apollo-cli/src/commands/file/upload.ts)_
+[src/commands/file/upload.ts](https://github.com/GMOD/Apollo3/blob/v1.1.0/packages/apollo-cli/src/commands/file/upload.ts)_
 
 ## `apollo help [COMMANDS]`
 
@@ -1064,7 +1064,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/jbrowse/desktop.ts](https://github.com/GMOD/Apollo3/blob/v1.0.1/packages/apollo-cli/src/commands/jbrowse/desktop.ts)_
+[src/commands/jbrowse/desktop.ts](https://github.com/GMOD/Apollo3/blob/v1.1.0/packages/apollo-cli/src/commands/jbrowse/desktop.ts)_
 
 ## `apollo jbrowse get-config`
 
@@ -1090,7 +1090,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/jbrowse/get-config.ts](https://github.com/GMOD/Apollo3/blob/v1.0.1/packages/apollo-cli/src/commands/jbrowse/get-config.ts)_
+[src/commands/jbrowse/get-config.ts](https://github.com/GMOD/Apollo3/blob/v1.1.0/packages/apollo-cli/src/commands/jbrowse/get-config.ts)_
 
 ## `apollo jbrowse set-config INPUTFILE`
 
@@ -1119,7 +1119,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/jbrowse/set-config.ts](https://github.com/GMOD/Apollo3/blob/v1.0.1/packages/apollo-cli/src/commands/jbrowse/set-config.ts)_
+[src/commands/jbrowse/set-config.ts](https://github.com/GMOD/Apollo3/blob/v1.1.0/packages/apollo-cli/src/commands/jbrowse/set-config.ts)_
 
 ## `apollo login`
 
@@ -1158,7 +1158,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/login.ts](https://github.com/GMOD/Apollo3/blob/v1.0.1/packages/apollo-cli/src/commands/login.ts)_
+[src/commands/login.ts](https://github.com/GMOD/Apollo3/blob/v1.1.0/packages/apollo-cli/src/commands/login.ts)_
 
 ## `apollo logout`
 
@@ -1188,7 +1188,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/logout.ts](https://github.com/GMOD/Apollo3/blob/v1.0.1/packages/apollo-cli/src/commands/logout.ts)_
+[src/commands/logout.ts](https://github.com/GMOD/Apollo3/blob/v1.1.0/packages/apollo-cli/src/commands/logout.ts)_
 
 ## `apollo refseq add-alias INPUT-FILE`
 
@@ -1219,7 +1219,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/refseq/add-alias.ts](https://github.com/GMOD/Apollo3/blob/v1.0.1/packages/apollo-cli/src/commands/refseq/add-alias.ts)_
+[src/commands/refseq/add-alias.ts](https://github.com/GMOD/Apollo3/blob/v1.1.0/packages/apollo-cli/src/commands/refseq/add-alias.ts)_
 
 ## `apollo refseq get`
 
@@ -1251,7 +1251,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/refseq/get.ts](https://github.com/GMOD/Apollo3/blob/v1.0.1/packages/apollo-cli/src/commands/refseq/get.ts)_
+[src/commands/refseq/get.ts](https://github.com/GMOD/Apollo3/blob/v1.1.0/packages/apollo-cli/src/commands/refseq/get.ts)_
 
 ## `apollo status`
 
@@ -1273,7 +1273,7 @@ DESCRIPTION
 ```
 
 _See code:
-[src/commands/status.ts](https://github.com/GMOD/Apollo3/blob/v1.0.1/packages/apollo-cli/src/commands/status.ts)_
+[src/commands/status.ts](https://github.com/GMOD/Apollo3/blob/v1.1.0/packages/apollo-cli/src/commands/status.ts)_
 
 ## `apollo user get`
 
@@ -1309,6 +1309,6 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/user/get.ts](https://github.com/GMOD/Apollo3/blob/v1.0.1/packages/apollo-cli/src/commands/user/get.ts)_
+[src/commands/user/get.ts](https://github.com/GMOD/Apollo3/blob/v1.1.0/packages/apollo-cli/src/commands/user/get.ts)_
 
 <!-- commandsstop -->

package/dist/baseCommand.d.ts.map

@@ -1 +1 @@
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package/dist/baseCommand.js

@@ -25,9 +25,7 @@ export class BaseCommand extends Command {
         this.args = args;
     }
     getConfig(configFile) {
-        if (configFile === undefined) {
-            configFile = path.join(this.config.configDir, 'config.yml');
-        }
+        configFile ??= path.join(this.config.configDir, 'config.yml');
         checkConfigfileExists(configFile);
         const config = new ApolloConf(configFile);
         return config;

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+{"version":3,"file":"baseCommand.js","sourceRoot":"","sources":["../src/baseCommand.ts"],"names":[],"mappings":"AAAA,OAAO,IAAI,MAAM,WAAW,CAAA;AAE5B,OAAO,EAAE,OAAO,EAAE,KAAK,EAAmB,MAAM,aAAa,CAAA;AAE7D,OAAO,EAAE,UAAU,EAAE,MAAM,iBAAiB,CAAA;AAC5C,OAAO,EAAE,qBAAqB,EAAE,MAAM,YAAY,CAAA;AAMlD,MAAM,OAAgB,WAAsC,SAAQ,OAAO;IACzE,MAAM,CAAC,SAAS,GAAG;QACjB,OAAO,EAAE,KAAK,CAAC,MAAM,CAAC;YACpB,WAAW,EAAE,mCAAmC;SACjD,CAAC;QACF,aAAa,EAAE,KAAK,CAAC,MAAM,CAAC;YAC1B,WAAW,EAAE,2CAA2C;SACzD,CAAC;KACH,CAAA;IAES,KAAK,CAAW;IAChB,IAAI,CAAU;IAEjB,KAAK,CAAC,IAAI;QACf,MAAM,KAAK,CAAC,IAAI,EAAE,CAAA;QAClB,MAAM,EAAE,IAAI,EAAE,KAAK,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC;YACvC,KAAK,EAAE,IAAI,CAAC,IAAI,CAAC,KAAK;YACtB,SAAS,EAAG,KAAK,CAAC,IAA2B,CAAC,SAAS;YACvD,IAAI,EAAE,IAAI,CAAC,IAAI,CAAC,IAAI;YACpB,MAAM,EAAE,IAAI,CAAC,IAAI,CAAC,MAAM;SACzB,CAAC,CAAA;QACF,IAAI,CAAC,KAAK,GAAG,KAAiB,CAAA;QAC9B,IAAI,CAAC,IAAI,GAAG,IAAe,CAAA;IAC7B,CAAC;IAEO,SAAS,CAAC,UAA8B;QAC9C,UAAU,KAAK,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,MAAM,CAAC,SAAS,EAAE,YAAY,CAAC,CAAA;QAC7D,qBAAqB,CAAC,UAAU,CAAC,CAAA;QACjC,MAAM,MAAM,GAAe,IAAI,UAAU,CAAC,UAAU,CAAC,CAAA;QACrD,OAAO,MAAM,CAAA;IACf,CAAC;IAEM,KAAK,CAAC,SAAS;QACpB,MAAM,EAAE,aAAa,EAAE,UAAU,EAAE,OAAO,EAAE,GAAG,IAAI,CAAC,KAAK,CAAA;QACzD,MAAM,MAAM,GAAe,IAAI,CAAC,SAAS,CAAC,UAAU,CAAC,CAAA;QAErD,MAAM,WAAW,GAAG,OAAO,CAAC,GAAG,CAAC,cAAc,IAAI,OAAO,IAAI,SAAS,CAAA;QAEtE,OAAO,MAAM,CAAC,SAAS,CAAC,WAAW,CAAC,CAAA;IACtC,CAAC;IAES,KAAK,CAAC,KAAK,CAAC,GAAkC;QACtD,IAAI,GAAG,CAAC,KAAK,YAAY,KAAK,EAAE,CAAC;YAC/B,OAAO,CAAC,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;QAC1B,CAAC;QACD,OAAO,KAAK,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;IACzB,CAAC;IAES,KAAK,CAAC,OAAO,CAAC,CAAoB;QAC1C,8EAA8E;QAC9E,OAAO,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,CAAA;IACzB,CAAC"}

package/dist/commands/assembly/check.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"check.d.ts","sourceRoot":"","sources":["../../../src/commands/assembly/check.ts"],"names":[],"mappings":"AAGA,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAA;AAgFlD,MAAM,CAAC,OAAO,OAAO,KAAM,SAAQ,WAAW,CAAC,OAAO,KAAK,CAAC;IAC1D,MAAM,CAAC,OAAO,SAA4C;IAC1D,MAAM,CAAC,WAAW,SAGqB;IAEvC,MAAM,CAAC,QAAQ;;;QAkBd;IAED,MAAM,CAAC,KAAK;;;;MAeX;IAEY,GAAG,IAAI,OAAO,CAAC,IAAI,CAAC;CA8DlC"}
+{"version":3,"file":"check.d.ts","sourceRoot":"","sources":["../../../src/commands/assembly/check.ts"],"names":[],"mappings":"AAGA,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAA;AAgFlD,MAAM,CAAC,OAAO,OAAO,KAAM,SAAQ,WAAW,CAAC,OAAO,KAAK,CAAC;IAC1D,MAAM,CAAC,OAAO,SAA4C;IAC1D,MAAM,CAAC,WAAW,SAGqB;IAEvC,MAAM,CAAC,QAAQ;;;QAkBd;IAED,MAAM,CAAC,KAAK;;;;MAeX;IAEY,GAAG,IAAI,OAAO,CAAC,IAAI,CAAC;CA6DlC"}

package/dist/commands/assembly/check.js

@@ -108,8 +108,7 @@ these checks use `apollo feature check`.';
             this.log(JSON.stringify(currentChecks, null, 2));
             return;
         }
-        let inputCheckIds = [];
-        inputCheckIds = await convertCheckNameToId(access.address, access.accessToken, flags.check);
+        const inputCheckIds = await convertCheckNameToId(access.address, access.accessToken, flags.check);
         const newChecks = new Set();
         if (flags.delete) {
             for (const chk of currentChecks) {

package/dist/commands/assembly/check.js.map

@@ -1 +1 @@
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package/dist/commands/assembly/sequence.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"sequence.d.ts","sourceRoot":"","sources":["../../../src/commands/assembly/sequence.ts"],"names":[],"mappings":"AAMA,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAA;AA0ClD,MAAM,CAAC,OAAO,OAAO,SAAU,SAAQ,WAAW,CAAC,OAAO,SAAS,CAAC;IAClE,MAAM,CAAC,OAAO,SAA2C;IACzD,MAAM,CAAC,WAAW,SACoD;IAEtE,MAAM,CAAC,QAAQ;;;QAUd;IAED,MAAM,CAAC,KAAK;;;;;MAkBX;IAEY,GAAG,IAAI,OAAO,CAAC,IAAI,CAAC;CAuDlC"}
+{"version":3,"file":"sequence.d.ts","sourceRoot":"","sources":["../../../src/commands/assembly/sequence.ts"],"names":[],"mappings":"AAMA,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAA;AA0ClD,MAAM,CAAC,OAAO,OAAO,SAAU,SAAQ,WAAW,CAAC,OAAO,SAAS,CAAC;IAClE,MAAM,CAAC,OAAO,SAA2C;IACzD,MAAM,CAAC,WAAW,SACoD;IAEtE,MAAM,CAAC,QAAQ;;;QAUd;IAED,MAAM,CAAC,KAAK;;;;;MAkBX;IAEY,GAAG,IAAI,OAAO,CAAC,IAAI,CAAC;CAsDlC"}

package/dist/commands/assembly/sequence.js

@@ -69,8 +69,7 @@ export default class ApolloCmd extends BaseCommand {
             ;
             [assembly] = await idReader([flags.assembly]);
         }
-        let refseqIds = [];
-        refseqIds = await getRefseqId(access.address, access.accessToken, flags.refseq, assembly);
+        const refseqIds = await getRefseqId(access.address, access.accessToken, flags.refseq, assembly);
         if (refseqIds.length === 0) {
             this.error('No reference sequence found');
         }

package/dist/commands/assembly/sequence.js.map

@@ -1 +1 @@
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package/dist/commands/config.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"config.d.ts","sourceRoot":"","sources":["../../src/commands/config.ts"],"names":[],"mappings":"AAUA,OAAO,EAAE,WAAW,EAAE,MAAM,mBAAmB,CAAA;AAG/C,MAAM,CAAC,OAAO,OAAO,YAAa,SAAQ,WAAW,CAAC,OAAO,YAAY,CAAC;IACxE,MAAM,CAAC,OAAO,SAA4C;IAC1D,MAAM,CAAC,WAAW,SAEc;IAEhC,MAAM,CAAC,IAAI;;;MASV;IAED,MAAM,CAAC,KAAK;;;MASX;IAED,MAAM,CAAC,QAAQ;;;QAcd;IAEY,GAAG,IAAI,OAAO,CAAC,IAAI,CAAC;YAwCnB,gBAAgB;YA6BhB,cAAc;YAuBd,WAAW;YAYX,WAAW;YAaX,UAAU;YAaV,gBAAgB;YAahB,aAAa;CAe5B"}
+{"version":3,"file":"config.d.ts","sourceRoot":"","sources":["../../src/commands/config.ts"],"names":[],"mappings":"AAUA,OAAO,EAAE,WAAW,EAAE,MAAM,mBAAmB,CAAA;AAG/C,MAAM,CAAC,OAAO,OAAO,YAAa,SAAQ,WAAW,CAAC,OAAO,YAAY,CAAC;IACxE,MAAM,CAAC,OAAO,SAA4C;IAC1D,MAAM,CAAC,WAAW,SAEc;IAEhC,MAAM,CAAC,IAAI;;;MASV;IAED,MAAM,CAAC,KAAK;;;MASX;IAED,MAAM,CAAC,QAAQ;;;QAcd;IAEY,GAAG,IAAI,OAAO,CAAC,IAAI,CAAC;YAqCnB,gBAAgB;YA0BhB,cAAc;YAuBd,WAAW;YAYX,WAAW;YAaX,UAAU;YAaV,gBAAgB;YAahB,aAAa;CAe5B"}

package/dist/commands/config.js

@@ -62,10 +62,7 @@ export default class ApolloConfig extends BaseCommand {
             await this.interactiveSetup(config, flags.profile);
         }
         else {
-            let profileName = flags.profile;
-            if (profileName === undefined) {
-                profileName = process.env.APOLLO_PROFILE ?? 'default';
-            }
+            let profileName = flags.profile ?? process.env.APOLLO_PROFILE ?? 'default';
             if (flags.profile !== undefined) {
                 profileName = flags.profile;
             }
@@ -83,9 +80,7 @@ export default class ApolloConfig extends BaseCommand {
         }
     }
     async interactiveSetup(config, profileName) {
-        if (profileName === undefined) {
-            profileName = await this.askProfileName(config.getProfileNames());
-        }
+        profileName ??= await this.askProfileName(config.getProfileNames());
         let setMe = true;
         while (setMe) {
             const address = await this.askAddress(config.get(`${profileName}.${KEYS[KEYS.address]}`));
@@ -93,8 +88,7 @@ export default class ApolloConfig extends BaseCommand {
             setMe = false;
         }
         const address = config.get(`${profileName}.${KEYS[KEYS.address]}`);
-        let accessType = '';
-        accessType = await this.selectAccessType(address);
+        const accessType = await this.selectAccessType(address);
         config.setAccessType(profileName, accessType);
         if (accessType === 'root') {
             const password = await this.askPassword();

package/dist/commands/config.js.map

@@ -1 +1 @@
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package/dist/commands/feature/copy.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"copy.d.ts","sourceRoot":"","sources":["../../../src/commands/feature/copy.ts"],"names":[],"mappings":"AAMA,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAA;AASlD,MAAM,CAAC,OAAO,OAAO,IAAK,SAAQ,WAAW,CAAC,OAAO,IAAI,CAAC;IACxD,MAAM,CAAC,OAAO,SAAuC;IACrD,MAAM,CAAC,WAAW,SAGmC;IAErD,MAAM,CAAC,QAAQ;;;QAMd;IAED,MAAM,CAAC,KAAK;;;;;MAsBX;IAEY,GAAG,IAAI,OAAO,CAAC,IAAI,CAAC;YA2DnB,WAAW;CA8C1B"}
+{"version":3,"file":"copy.d.ts","sourceRoot":"","sources":["../../../src/commands/feature/copy.ts"],"names":[],"mappings":"AAMA,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAA;AASlD,MAAM,CAAC,OAAO,OAAO,IAAK,SAAQ,WAAW,CAAC,OAAO,IAAI,CAAC;IACxD,MAAM,CAAC,OAAO,SAAuC;IACrD,MAAM,CAAC,WAAW,SAGmC;IAErD,MAAM,CAAC,QAAQ;;;QAMd;IAED,MAAM,CAAC,KAAK;;;;;MAsBX;IAEY,GAAG,IAAI,OAAO,CAAC,IAAI,CAAC;YA0DnB,WAAW;CA8C1B"}

package/dist/commands/feature/copy.js

@@ -48,8 +48,7 @@ the database or by name and assembly or by identifier.';
             throw new Error(errorMessage);
         }
         const feature = (await res.json());
-        let refseqIds = [];
-        refseqIds = await getRefseqId(access.address, access.accessToken, flags.refseq, flags.assembly);
+        const refseqIds = await getRefseqId(access.address, access.accessToken, flags.refseq, flags.assembly);
         if (refseqIds.length === 0) {
             this.error('No reference sequence found');
         }

package/dist/commands/feature/copy.js.map

@@ -1 +1 @@
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package/dist/commands/feature/edit-attribute.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"edit-attribute.d.ts","sourceRoot":"","sources":["../../../src/commands/feature/edit-attribute.ts"],"names":[],"mappings":"AAKA,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAA;AASlD,MAAM,CAAC,OAAO,OAAO,YAAa,SAAQ,WAAW,CAAC,OAAO,YAAY,CAAC;IACxE,MAAM,CAAC,OAAO,SAA2C;IACzD,MAAM,CAAC,WAAW,SAGQ;IAE1B,MAAM,CAAC,QAAQ;;;QAcd;IAED,MAAM,CAAC,KAAK;;;;;MAqBX;IAEY,GAAG,IAAI,OAAO,CAAC,IAAI,CAAC;CA8FlC"}
+{"version":3,"file":"edit-attribute.d.ts","sourceRoot":"","sources":["../../../src/commands/feature/edit-attribute.ts"],"names":[],"mappings":"AAKA,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAA;AASlD,MAAM,CAAC,OAAO,OAAO,YAAa,SAAQ,WAAW,CAAC,OAAO,YAAY,CAAC;IACxE,MAAM,CAAC,OAAO,SAA2C;IACzD,MAAM,CAAC,WAAW,SAGQ;IAE1B,MAAM,CAAC,QAAQ;;;QAcd;IAED,MAAM,CAAC,KAAK;;;;;MAqBX;IAEY,GAAG,IAAI,OAAO,CAAC,IAAI,CAAC;CA4FlC"}

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

@@ -59,9 +59,7 @@ terms to non-existing terms';
             throw new Error(errorMessage);
         }
         const featureJson = JSON.parse(await response.text());
-        if (featureJson.attributes === undefined) {
-            featureJson.attributes = {};
-        }
+        featureJson.attributes ??= {};
         const oldAttributes = {};
         for (const [key, val] of Object.entries(featureJson.attributes)) {
             if (!val) {

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

@@ -1 +1 @@
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package/dist/commands/file/download.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"download.d.ts","sourceRoot":"","sources":["../../../src/commands/file/download.ts"],"names":[],"mappings":"AAMA,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAA;AAGlD,MAAM,CAAC,OAAO,OAAO,QAAS,SAAQ,WAAW,CAAC,OAAO,QAAQ,CAAC;IAChE,MAAM,CAAC,OAAO,SAA2C;IACzD,MAAM,CAAC,WAAW,SAC4C;IAE9D,MAAM,CAAC,QAAQ;;;QAKd;IAED,MAAM,CAAC,KAAK;;;MAWX;IAEY,GAAG,IAAI,OAAO,CAAC,IAAI,CAAC;CAgClC"}
+{"version":3,"file":"download.d.ts","sourceRoot":"","sources":["../../../src/commands/file/download.ts"],"names":[],"mappings":"AAMA,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAA;AAGlD,MAAM,CAAC,OAAO,OAAO,QAAS,SAAQ,WAAW,CAAC,OAAO,QAAQ,CAAC;IAChE,MAAM,CAAC,OAAO,SAA2C;IACzD,MAAM,CAAC,WAAW,SAC4C;IAE9D,MAAM,CAAC,QAAQ;;;QAKd;IAED,MAAM,CAAC,KAAK;;;MAWX;IAEY,GAAG,IAAI,OAAO,CAAC,IAAI,CAAC;CA6BlC"}

package/dist/commands/file/download.js

@@ -34,10 +34,7 @@ export default class Download extends BaseCommand {
         const [fileRec] = filterJsonList(json, ff, '_id');
         const fileId = fileRec['_id'];
         res = await queryApollo(access.address, access.accessToken, `files/${fileId}`);
-        let { output } = flags;
-        if (output === undefined) {
-            output = fileRec['basename'];
-        }
+        const { output = fileRec['basename'] } = flags;
         const fileWriteStream = createWriteStream(output);
         await res.body?.pipeTo(Writable.toWeb(output === '-' ? process.stdout : fileWriteStream));
         fileWriteStream.close();

package/dist/commands/file/download.js.map

@@ -1 +1 @@
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+{"version":3,"file":"download.js","sourceRoot":"","sources":["../../../src/commands/file/download.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,iBAAiB,EAAE,MAAM,SAAS,CAAA;AAC3C,OAAO,EAAE,QAAQ,EAAE,MAAM,aAAa,CAAA;AAEtC,OAAO,EAAE,KAAK,EAAE,MAAM,aAAa,CAAA;AAGnC,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAA;AAClD,OAAO,EAAE,cAAc,EAAE,QAAQ,EAAE,WAAW,EAAE,MAAM,gBAAgB,CAAA;AAEtE,MAAM,CAAC,OAAO,OAAO,QAAS,SAAQ,WAA4B;IAChE,MAAM,CAAC,OAAO,GAAG,wCAAwC,CAAA;IACzD,MAAM,CAAC,WAAW,GAChB,4DAA4D,CAAA;IAE9D,MAAM,CAAC,QAAQ,GAAG;QAChB;YACE,WAAW,EAAE,2BAA2B;YACxC,OAAO,EAAE,yDAAyD;SACnE;KACF,CAAA;IAED,MAAM,CAAC,KAAK,GAAG;QACb,SAAS,EAAE,KAAK,CAAC,MAAM,CAAC;YACtB,IAAI,EAAE,GAAG;YACT,WAAW,EAAE,4BAA4B;YACzC,OAAO,EAAE,GAAG;SACb,CAAC;QACF,MAAM,EAAE,KAAK,CAAC,MAAM,CAAC;YACnB,IAAI,EAAE,GAAG;YACT,WAAW,EACT,wFAAwF;SAC3F,CAAC;KACH,CAAA;IAEM,KAAK,CAAC,GAAG;QACd,MAAM,EAAE,KAAK,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,QAAQ,CAAC,CAAA;QAE5C,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QAErC,MAAM,EAAE,GAAG,MAAM,QAAQ,CAAC,CAAC,KAAK,CAAC,SAAS,CAAC,CAAC,CAAC,CAAA;QAC7C,IAAI,GAAG,GAAa,MAAM,WAAW,CACnC,MAAM,CAAC,OAAO,EACd,MAAM,CAAC,WAAW,EAClB,OAAO,CACR,CAAA;QACD,mEAAmE;QACnE,MAAM,IAAI,GAAG,IAAI,CAAC,KAAK,CAAC,MAAM,GAAG,CAAC,IAAI,EAAE,CAAC,CAAA;QACzC,iEAAiE;QACjE,MAAM,CAAC,OAAO,CAAC,GAAG,cAAc,CAAC,IAAI,EAAE,EAAE,EAAE,KAAK,CAAC,CAAA;QACjD,MAAM,MAAM,GAAG,OAAO,CAAC,KAA6B,CAAW,CAAA;QAE/D,GAAG,GAAG,MAAM,WAAW,CACrB,MAAM,CAAC,OAAO,EACd,MAAM,CAAC,WAAW,EAClB,SAAS,MAAM,EAAE,CAClB,CAAA;QACD,MAAM,EAAE,MAAM,GAAG,OAAO,CAAC,UAAkC,CAAC,EAAE,GAAG,KAAK,CAAA;QACtE,MAAM,eAAe,GAAG,iBAAiB,CAAC,MAAM,CAAC,CAAA;QACjD,MAAM,GAAG,CAAC,IAAI,EAAE,MAAM,CACpB,QAAQ,CAAC,KAAK,CAAC,MAAM,KAAK,GAAG,CAAC,CAAC,CAAC,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,eAAe,CAAC,CAClE,CAAA;QACD,eAAe,CAAC,KAAK,EAAE,CAAA;IACzB,CAAC"}

package/dist/commands/login.d.ts.map

@@ -1 +1 @@
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