@apollo-annotation/cli 0.3.11 → 0.3.12

package/README.md

@@ -16,7 +16,7 @@ $ npm install -g @apollo-annotation/cli
 $ apollo COMMAND
 running command...
 $ apollo (--version)
-@apollo-annotation/cli/0.3.11 linux-x64 node-v24.11.1
+@apollo-annotation/cli/0.3.12 linux-x64 node-v24.14.0
 $ 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/v0.3.11/packages/apollo-cli/src/commands/assembly/add-from-fasta.ts)_
+[src/commands/assembly/add-from-fasta.ts](https://github.com/GMOD/Apollo3/blob/v0.3.12/packages/apollo-cli/src/commands/assembly/add-from-fasta.ts)_
 
 ## `apollo assembly add-from-gff INPUT-FILE`
 
@@ -126,6 +126,7 @@ Add new assembly from gff or gft file
 ```
 USAGE
   $ apollo assembly add-from-gff INPUT-FILE [--profile <value>] [--config-file <value>] [-a <value>] [-o] [-f]
+  [--no-strict]
 
 ARGUMENTS
   INPUT-FILE  Input gff file
@@ -135,6 +136,8 @@ FLAGS
   -f, --force                Delete existing assembly, if it exists
   -o, --omit-features        Do not import features, only upload the sequences
       --config-file=<value>  Use this config file (mostly for testing)
+      --no-strict            If any feature lines in the GFF3 can't be processed, skip them instead of aborting the
+                             import
       --profile=<value>      Use credentials from this profile
 
 DESCRIPTION
@@ -153,7 +156,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/assembly/add-from-gff.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/assembly/add-from-gff.ts)_
+[src/commands/assembly/add-from-gff.ts](https://github.com/GMOD/Apollo3/blob/v0.3.12/packages/apollo-cli/src/commands/assembly/add-from-gff.ts)_
 
 ## `apollo assembly check`
 
@@ -195,7 +198,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/assembly/check.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/assembly/check.ts)_
+[src/commands/assembly/check.ts](https://github.com/GMOD/Apollo3/blob/v0.3.12/packages/apollo-cli/src/commands/assembly/check.ts)_
 
 ## `apollo assembly delete`
 
@@ -223,7 +226,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/assembly/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/assembly/delete.ts)_
+[src/commands/assembly/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.3.12/packages/apollo-cli/src/commands/assembly/delete.ts)_
 
 ## `apollo assembly get`
 
@@ -245,7 +248,7 @@ DESCRIPTION
 ```
 
 _See code:
-[src/commands/assembly/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/assembly/get.ts)_
+[src/commands/assembly/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.12/packages/apollo-cli/src/commands/assembly/get.ts)_
 
 ## `apollo assembly sequence`
 
@@ -280,7 +283,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/assembly/sequence.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/assembly/sequence.ts)_
+[src/commands/assembly/sequence.ts](https://github.com/GMOD/Apollo3/blob/v0.3.12/packages/apollo-cli/src/commands/assembly/sequence.ts)_
 
 ## `apollo change get`
 
@@ -304,7 +307,7 @@ DESCRIPTION
 ```
 
 _See code:
-[src/commands/change/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/change/get.ts)_
+[src/commands/change/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.12/packages/apollo-cli/src/commands/change/get.ts)_
 
 ## `apollo config [KEY] [VALUE]`
 
@@ -356,7 +359,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/config.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/config.ts)_
+[src/commands/config.ts](https://github.com/GMOD/Apollo3/blob/v0.3.12/packages/apollo-cli/src/commands/config.ts)_
 
 ## `apollo export gff3 ASSEMBLY`
 
@@ -384,7 +387,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/export/gff3.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/export/gff3.ts)_
+[src/commands/export/gff3.ts](https://github.com/GMOD/Apollo3/blob/v0.3.12/packages/apollo-cli/src/commands/export/gff3.ts)_
 
 ## `apollo feature add [FEATURE-JSON]`
 
@@ -440,7 +443,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/add.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/feature/add.ts)_
+[src/commands/feature/add.ts](https://github.com/GMOD/Apollo3/blob/v0.3.12/packages/apollo-cli/src/commands/feature/add.ts)_
 
 ## `apollo feature add-child`
 
@@ -471,7 +474,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/add-child.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/feature/add-child.ts)_
+[src/commands/feature/add-child.ts](https://github.com/GMOD/Apollo3/blob/v0.3.12/packages/apollo-cli/src/commands/feature/add-child.ts)_
 
 ## `apollo feature check`
 
@@ -504,7 +507,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/check.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/feature/check.ts)_
+[src/commands/feature/check.ts](https://github.com/GMOD/Apollo3/blob/v0.3.12/packages/apollo-cli/src/commands/feature/check.ts)_
 
 ## `apollo feature copy`
 
@@ -535,7 +538,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/copy.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/feature/copy.ts)_
+[src/commands/feature/copy.ts](https://github.com/GMOD/Apollo3/blob/v0.3.12/packages/apollo-cli/src/commands/feature/copy.ts)_
 
 ## `apollo feature delete`
 
@@ -559,7 +562,7 @@ DESCRIPTION
 ```
 
 _See code:
-[src/commands/feature/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/feature/delete.ts)_
+[src/commands/feature/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.3.12/packages/apollo-cli/src/commands/feature/delete.ts)_
 
 ## `apollo feature edit`
 
@@ -601,7 +604,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/edit.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/feature/edit.ts)_
+[src/commands/feature/edit.ts](https://github.com/GMOD/Apollo3/blob/v0.3.12/packages/apollo-cli/src/commands/feature/edit.ts)_
 
 ## `apollo feature edit-attribute`
 
@@ -641,7 +644,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/edit-attribute.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/feature/edit-attribute.ts)_
+[src/commands/feature/edit-attribute.ts](https://github.com/GMOD/Apollo3/blob/v0.3.12/packages/apollo-cli/src/commands/feature/edit-attribute.ts)_
 
 ## `apollo feature edit-coords`
 
@@ -675,7 +678,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/edit-coords.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/feature/edit-coords.ts)_
+[src/commands/feature/edit-coords.ts](https://github.com/GMOD/Apollo3/blob/v0.3.12/packages/apollo-cli/src/commands/feature/edit-coords.ts)_
 
 ## `apollo feature edit-type`
 
@@ -699,7 +702,7 @@ DESCRIPTION
 ```
 
 _See code:
-[src/commands/feature/edit-type.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/feature/edit-type.ts)_
+[src/commands/feature/edit-type.ts](https://github.com/GMOD/Apollo3/blob/v0.3.12/packages/apollo-cli/src/commands/feature/edit-type.ts)_
 
 ## `apollo feature get`
 
@@ -733,7 +736,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/feature/get.ts)_
+[src/commands/feature/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.12/packages/apollo-cli/src/commands/feature/get.ts)_
 
 ## `apollo feature get-id`
 
@@ -761,7 +764,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/get-id.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/feature/get-id.ts)_
+[src/commands/feature/get-id.ts](https://github.com/GMOD/Apollo3/blob/v0.3.12/packages/apollo-cli/src/commands/feature/get-id.ts)_
 
 ## `apollo feature get-indexed-id ID`
 
@@ -793,7 +796,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/get-indexed-id.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/feature/get-indexed-id.ts)_
+[src/commands/feature/get-indexed-id.ts](https://github.com/GMOD/Apollo3/blob/v0.3.12/packages/apollo-cli/src/commands/feature/get-indexed-id.ts)_
 
 ## `apollo feature import INPUT-FILE`
 
@@ -801,7 +804,7 @@ Import features from local gff file
 
 ```
 USAGE
-  $ apollo feature import INPUT-FILE -a <value> [--profile <value>] [--config-file <value>] [-d]
+  $ apollo feature import INPUT-FILE -a <value> [--profile <value>] [--config-file <value>] [-d] [--no-strict]
 
 ARGUMENTS
   INPUT-FILE  Input gff file
@@ -810,6 +813,7 @@ FLAGS
   -a, --assembly=<value>     (required) Import into this assembly name or assembly ID
   -d, --delete-existing      Delete existing features before importing
       --config-file=<value>  Use this config file (mostly for testing)
+      --no-strict            If any lines in the GFF3 can't be processed, skip them instead of aborting the import
       --profile=<value>      Use credentials from this profile
 
 DESCRIPTION
@@ -824,7 +828,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/import.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/feature/import.ts)_
+[src/commands/feature/import.ts](https://github.com/GMOD/Apollo3/blob/v0.3.12/packages/apollo-cli/src/commands/feature/import.ts)_
 
 ## `apollo feature search`
 
@@ -875,7 +879,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/search.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/feature/search.ts)_
+[src/commands/feature/search.ts](https://github.com/GMOD/Apollo3/blob/v0.3.12/packages/apollo-cli/src/commands/feature/search.ts)_
 
 ## `apollo file delete`
 
@@ -902,7 +906,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/file/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/file/delete.ts)_
+[src/commands/file/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.3.12/packages/apollo-cli/src/commands/file/delete.ts)_
 
 ## `apollo file download`
 
@@ -930,7 +934,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/file/download.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/file/download.ts)_
+[src/commands/file/download.ts](https://github.com/GMOD/Apollo3/blob/v0.3.12/packages/apollo-cli/src/commands/file/download.ts)_
 
 ## `apollo file get`
 
@@ -957,7 +961,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/file/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/file/get.ts)_
+[src/commands/file/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.12/packages/apollo-cli/src/commands/file/get.ts)_
 
 ## `apollo file upload INPUT-FILE`
 
@@ -994,7 +998,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/file/upload.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/file/upload.ts)_
+[src/commands/file/upload.ts](https://github.com/GMOD/Apollo3/blob/v0.3.12/packages/apollo-cli/src/commands/file/upload.ts)_
 
 ## `apollo help [COMMANDS]`
 
@@ -1060,7 +1064,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/jbrowse/desktop.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/jbrowse/desktop.ts)_
+[src/commands/jbrowse/desktop.ts](https://github.com/GMOD/Apollo3/blob/v0.3.12/packages/apollo-cli/src/commands/jbrowse/desktop.ts)_
 
 ## `apollo jbrowse get-config`
 
@@ -1086,7 +1090,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/jbrowse/get-config.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/jbrowse/get-config.ts)_
+[src/commands/jbrowse/get-config.ts](https://github.com/GMOD/Apollo3/blob/v0.3.12/packages/apollo-cli/src/commands/jbrowse/get-config.ts)_
 
 ## `apollo jbrowse set-config INPUTFILE`
 
@@ -1115,7 +1119,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/jbrowse/set-config.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/jbrowse/set-config.ts)_
+[src/commands/jbrowse/set-config.ts](https://github.com/GMOD/Apollo3/blob/v0.3.12/packages/apollo-cli/src/commands/jbrowse/set-config.ts)_
 
 ## `apollo login`
 
@@ -1154,7 +1158,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/login.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/login.ts)_
+[src/commands/login.ts](https://github.com/GMOD/Apollo3/blob/v0.3.12/packages/apollo-cli/src/commands/login.ts)_
 
 ## `apollo logout`
 
@@ -1184,7 +1188,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/logout.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/logout.ts)_
+[src/commands/logout.ts](https://github.com/GMOD/Apollo3/blob/v0.3.12/packages/apollo-cli/src/commands/logout.ts)_
 
 ## `apollo refseq add-alias INPUT-FILE`
 
@@ -1215,7 +1219,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/refseq/add-alias.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/refseq/add-alias.ts)_
+[src/commands/refseq/add-alias.ts](https://github.com/GMOD/Apollo3/blob/v0.3.12/packages/apollo-cli/src/commands/refseq/add-alias.ts)_
 
 ## `apollo refseq get`
 
@@ -1247,7 +1251,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/refseq/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/refseq/get.ts)_
+[src/commands/refseq/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.12/packages/apollo-cli/src/commands/refseq/get.ts)_
 
 ## `apollo status`
 
@@ -1269,7 +1273,7 @@ DESCRIPTION
 ```
 
 _See code:
-[src/commands/status.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/status.ts)_
+[src/commands/status.ts](https://github.com/GMOD/Apollo3/blob/v0.3.12/packages/apollo-cli/src/commands/status.ts)_
 
 ## `apollo user get`
 
@@ -1305,6 +1309,6 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/user/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/user/get.ts)_
+[src/commands/user/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.12/packages/apollo-cli/src/commands/user/get.ts)_
 
 <!-- commandsstop -->

package/dist/ApolloConf.d.ts

@@ -19,3 +19,4 @@ export declare class ApolloConf extends Conf {
         accessToken: string;
     }>;
 }
+//# sourceMappingURL=ApolloConf.d.ts.map

package/dist/ApolloConf.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"ApolloConf.d.ts","sourceRoot":"","sources":["../src/ApolloConf.ts"],"names":[],"mappings":"AAIA,OAAO,IAAI,MAAM,MAAM,CAAA;AAMvB,qBAAa,WAAY,SAAQ,KAAK;CAAG;AAEzC,oBAAY,IAAI;IACd,OAAO,YAAY;IACnB,UAAU,eAAe;IACzB,WAAW,gBAAgB;IAC3B,YAAY,iBAAiB;CAC9B;AA4CD,wBAAgB,UAAU,IAAI,MAAM,EAAE,CAMrC;AAED,qBAAa,UAAW,SAAQ,IAAI;gBACtB,UAAU,EAAE,MAAM;IA2B9B,IAAI,KAAK,4BAOR;IAED,IAAI,KAAK,CAAC,QAAQ,yBAAA,EAMjB;IAEM,eAAe,IAAI,MAAM,EAAE;IAI3B,aAAa,CAAC,WAAW,EAAE,MAAM,EAAE,UAAU,EAAE,MAAM;IAO/C,SAAS,CAAC,WAAW,EAAE,MAAM;;;;CAoB3C"}

package/dist/ApolloConf.js

@@ -131,3 +131,4 @@ const profileSchema = Joi.object({
     }),
 });
 const configSchema = Joi.object().pattern(Joi.string(), profileSchema);
+//# sourceMappingURL=ApolloConf.js.map

package/dist/ApolloConf.js.map

@@ -0,0 +1 @@
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package/dist/baseCommand.d.ts

@@ -19,3 +19,4 @@ export declare abstract class BaseCommand<T extends typeof Command> extends Comm
     }): Promise<unknown>;
     protected finally(_: Error | undefined): Promise<unknown>;
 }
+//# sourceMappingURL=baseCommand.d.ts.map

package/dist/baseCommand.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"baseCommand.d.ts","sourceRoot":"","sources":["../src/baseCommand.ts"],"names":[],"mappings":"AAEA,OAAO,EAAE,OAAO,EAAS,KAAK,UAAU,EAAE,MAAM,aAAa,CAAA;AAK7D,MAAM,MAAM,KAAK,CAAC,CAAC,SAAS,OAAO,OAAO,IAAI,UAAU,CAAC,aAAa,CACpE,CAAC,OAAO,WAAW,CAAC,CAAC,WAAW,CAAC,GAAG,CAAC,CAAC,OAAO,CAAC,CAC/C,CAAA;AACD,MAAM,MAAM,IAAI,CAAC,CAAC,SAAS,OAAO,OAAO,IAAI,UAAU,CAAC,YAAY,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAA;AAC/E,8BAAsB,WAAW,CAAC,CAAC,SAAS,OAAO,OAAO,CAAE,SAAQ,OAAO;IACzE,MAAM,CAAC,SAAS;;;MAOf;IAED,SAAS,CAAC,KAAK,EAAG,KAAK,CAAC,CAAC,CAAC,CAAA;IAC1B,SAAS,CAAC,IAAI,EAAG,IAAI,CAAC,CAAC,CAAC,CAAA;IAEX,IAAI,IAAI,OAAO,CAAC,IAAI,CAAC;IAYlC,OAAO,CAAC,SAAS;IASJ,SAAS,IAAI,OAAO,CAAC;QAAE,OAAO,EAAE,MAAM,CAAC;QAAC,WAAW,EAAE,MAAM,CAAA;KAAE,CAAC;cAS3D,KAAK,CAAC,GAAG,EAAE,KAAK,GAAG;QAAE,QAAQ,CAAC,EAAE,MAAM,CAAA;KAAE,GAAG,OAAO,CAAC,OAAO,CAAC;cAO3D,OAAO,CAAC,CAAC,EAAE,KAAK,GAAG,SAAS,GAAG,OAAO,CAAC,OAAO,CAAC;CAIhE"}

package/dist/baseCommand.js

@@ -49,3 +49,4 @@ export class BaseCommand extends Command {
         return super.finally(_);
     }
 }
+//# sourceMappingURL=baseCommand.js.map

package/dist/baseCommand.js.map

@@ -0,0 +1 @@
+{"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,IAAI,UAAU,KAAK,SAAS,EAAE,CAAC;YAC7B,UAAU,GAAG,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,MAAM,CAAC,SAAS,EAAE,YAAY,CAAC,CAAA;QAC7D,CAAC;QACD,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/add-from-fasta.d.ts

@@ -20,3 +20,4 @@ export default class AddFasta extends FileCommand {
     };
     run(): Promise<void>;
 }
+//# sourceMappingURL=add-from-fasta.d.ts.map

package/dist/commands/assembly/add-from-fasta.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"add-from-fasta.d.ts","sourceRoot":"","sources":["../../../src/commands/assembly/add-from-fasta.ts"],"names":[],"mappings":"AAWA,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAA;AAGlD,MAAM,CAAC,OAAO,OAAO,QAAS,SAAQ,WAAW;IAC/C,MAAM,CAAC,OAAO,SAAwC;IACtD,MAAM,CAAC,WAAW,SAGiC;IAEnD,MAAM,CAAC,QAAQ;;;QAiBd;IAED,MAAM,CAAC,IAAI;;MAUV;IAED,MAAM,CAAC,KAAK;;;;;;;;MAkCX;IAEY,GAAG,IAAI,OAAO,CAAC,IAAI,CAAC;CAyIlC"}

package/dist/commands/assembly/add-from-fasta.js

@@ -4,7 +4,7 @@ import path from 'node:path';
 import { Args, Flags } from '@oclif/core';
 import { ObjectId } from 'bson';
 import { FileCommand } from '../../fileCommand.js';
-import { queryApollo, submitAssembly } from '../../utils.js';
+import { isFileId, submitAssembly } from '../../utils.js';
 export default class AddFasta extends FileCommand {
     static summary = 'Add a new assembly from fasta input';
     static description = `Add new assembly. The input fasta may be:
@@ -157,16 +157,4 @@ function isValidHttpUrl(x) {
     }
     return url.protocol === 'http:' || url.protocol === 'https:';
 }
-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=add-from-fasta.js.map

package/dist/commands/assembly/add-from-fasta.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"add-from-fasta.js","sourceRoot":"","sources":["../../../src/commands/assembly/add-from-fasta.ts"],"names":[],"mappings":"AAAA,gEAAgE;AAChE,OAAO,KAAK,EAAE,MAAM,SAAS,CAAA;AAC7B,OAAO,IAAI,MAAM,WAAW,CAAA;AAM5B,OAAO,EAAE,IAAI,EAAE,KAAK,EAAE,MAAM,aAAa,CAAA;AACzC,OAAO,EAAE,QAAQ,EAAE,MAAM,MAAM,CAAA;AAE/B,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAA;AAClD,OAAO,EAAE,QAAQ,EAAE,cAAc,EAAE,MAAM,gBAAgB,CAAA;AAEzD,MAAM,CAAC,OAAO,OAAO,QAAS,SAAQ,WAAW;IAC/C,MAAM,CAAC,OAAO,GAAG,qCAAqC,CAAA;IACtD,MAAM,CAAC,WAAW,GAAG;;;qDAG8B,CAAA;IAEnD,MAAM,CAAC,QAAQ,GAAG;QAChB;YACE,WAAW,EACT,+EAA+E;YACjF,OAAO,EAAE,gEAAgE;SAC1E;QACD;YACE,WAAW,EACT,8EAA8E;YAChF,OAAO,EAAE,6DAA6D;SACvE;QACD;YACE,WAAW,EACT,qHAAqH;YACvH,OAAO,EACL,4EAA4E;SAC/E;KACF,CAAA;IAED,MAAM,CAAC,IAAI,GAAG;QACZ,KAAK,EAAE,IAAI,CAAC,MAAM,CAAC;YACjB,WAAW,EACT;;;;2GAImG;YACrG,QAAQ,EAAE,IAAI;SACf,CAAC;KACH,CAAA;IAED,MAAM,CAAC,KAAK,GAAG;QACb,QAAQ,EAAE,KAAK,CAAC,MAAM,CAAC;YACrB,IAAI,EAAE,GAAG;YACT,WAAW,EAAE,sDAAsD;SACpE,CAAC;QACF,KAAK,EAAE,KAAK,CAAC,OAAO,CAAC;YACnB,IAAI,EAAE,GAAG;YACT,WAAW,EAAE,wCAAwC;SACtD,CAAC;QACF,QAAQ,EAAE,KAAK,CAAC,OAAO,CAAC;YACtB,IAAI,EAAE,GAAG;YACT,WAAW,EACT;;mCAE2B;SAC9B,CAAC;QACF,GAAG,EAAE,KAAK,CAAC,MAAM,CAAC;YAChB,WAAW,EAAE,8CAA8C;SAC5D,CAAC;QACF,GAAG,EAAE,KAAK,CAAC,MAAM,CAAC;YAChB,WAAW,EAAE,4CAA4C;SAC1D,CAAC;QACF,IAAI,EAAE,KAAK,CAAC,OAAO,CAAC;YAClB,IAAI,EAAE,GAAG;YACT,WAAW,EACT,yFAAyF;YAC3F,SAAS,EAAE,CAAC,cAAc,CAAC;SAC5B,CAAC;QACF,YAAY,EAAE,KAAK,CAAC,OAAO,CAAC;YAC1B,IAAI,EAAE,GAAG;YACT,WAAW,EACT,sFAAsF;YACxF,SAAS,EAAE,CAAC,MAAM,CAAC;SACpB,CAAC;KACH,CAAA;IAEM,KAAK,CAAC,GAAG;QACd,MAAM,EAAE,IAAI,EAAE,KAAK,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,QAAQ,CAAC,CAAA;QAElD,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QAErC,MAAM,YAAY,GAAG,KAAK,CAAC,QAAQ,IAAI,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;QAEhE,MAAM,aAAa,GAAG,MAAM,QAAQ,CAClC,IAAI,CAAC,KAAK,EACV,MAAM,CAAC,OAAO,EACd,MAAM,CAAC,WAAW,CACnB,CAAA;QACD,MAAM,UAAU,GAAG,cAAc,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;QAE7C,IAAI,IAEuC,CAAA;QAC3C,IAAI,UAAU,EAAE,CAAC;YACf,IAAI,KAAK,CAAC,QAAQ,EAAE,CAAC;gBACnB,IAAI,CAAC,KAAK,CACR,oGAAoG,CACrG,CAAA;YACH,CAAC;YACD,MAAM,GAAG,GAAG,KAAK,CAAC,GAAG,IAAI,GAAG,IAAI,CAAC,KAAK,MAAM,CAAA;YAC5C,MAAM,SAAS,GAAG,MAAM,KAAK,CAAC,GAAG,CAAC,CAAA;YAClC,IAAI,CAAC,SAAS,CAAC,EAAE,EAAE,CAAC;gBAClB,IAAI,CAAC,KAAK,CAAC,cAAc,GAAG,iBAAiB,CAAC,CAAA;YAChD,CAAC;YACD,MAAM,GAAG,GAAG,KAAK,CAAC,GAAG,IAAI,GAAG,IAAI,CAAC,KAAK,MAAM,CAAA;YAC5C,MAAM,SAAS,GAAG,MAAM,KAAK,CAAC,GAAG,CAAC,CAAA;YAClC,IAAI,CAAC,SAAS,CAAC,EAAE,EAAE,CAAC;gBAClB,IAAI,CAAC,KAAK,CAAC,cAAc,GAAG,iBAAiB,CAAC,CAAA;YAChD,CAAC;YACD,IAAI,GAAG;gBACL,YAAY;gBACZ,QAAQ,EAAE,+BAA+B;gBACzC,gBAAgB,EAAE,EAAE,EAAE,EAAE,IAAI,CAAC,KAAK,EAAE,GAAG,EAAE,GAAG,EAAE;gBAC9C,QAAQ,EAAE,IAAI,QAAQ,EAAE,CAAC,WAAW,EAAE;aACvC,CAAA;QACH,CAAC;aAAM,IAAI,KAAK,CAAC,QAAQ,EAAE,CAAC;YAC1B,IAAI,CAAC,UAAU,IAAI,CAAC,EAAE,CAAC,UAAU,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,aAAa,EAAE,CAAC;gBAChE,IAAI,CAAC,KAAK,CAAC,UAAU,IAAI,CAAC,KAAK,gBAAgB,CAAC,CAAA;YAClD,CAAC;YACD,IAAI,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAA;YACvC,IAAI,KAAK,CAAC,IAAI,EAAE,CAAC;gBACf,MAAM,GAAG,IAAI,CAAA;YACf,CAAC;YACD,IAAI,KAAK,CAAC,YAAY,EAAE,CAAC;gBACvB,MAAM,GAAG,KAAK,CAAA;YAChB,CAAC;YAED,MAAM,MAAM,GAAG,aAAa;gBAC1B,CAAC,CAAC,IAAI,CAAC,KAAK;gBACZ,CAAC,CAAC,MAAM,IAAI,CAAC,UAAU,CACnB,MAAM,CAAC,OAAO,EACd,MAAM,CAAC,WAAW,EAClB,IAAI,CAAC,KAAK,EACV,cAAc,EACd,MAAM,CACP,CAAA;YACL,IAAI,GAAG;gBACL,YAAY;gBACZ,OAAO,EAAE,EAAE,EAAE,EAAE,MAAM,EAAE;gBACvB,QAAQ,EAAE,2BAA2B;gBACrC,QAAQ,EAAE,IAAI,QAAQ,EAAE,CAAC,WAAW,EAAE;aACvC,CAAA;QACH,CAAC;aAAM,CAAC;YACN,MAAM,GAAG,GAAG,KAAK,CAAC,GAAG,IAAI,GAAG,IAAI,CAAC,KAAK,MAAM,CAAA;YAC5C,MAAM,GAAG,GAAG,KAAK,CAAC,GAAG,IAAI,GAAG,IAAI,CAAC,KAAK,MAAM,CAAA;YAE5C,MAAM,WAAW,GAAG,MAAM,QAAQ,CAChC,GAAG,EACH,MAAM,CAAC,OAAO,EACd,MAAM,CAAC,WAAW,CACnB,CAAA;YACD,MAAM,WAAW,GAAG,MAAM,QAAQ,CAChC,GAAG,EACH,MAAM,CAAC,OAAO,EACd,MAAM,CAAC,WAAW,CACnB,CAAA;YAED,IAAI,CAAC,EAAE,CAAC,UAAU,CAAC,GAAG,CAAC,IAAI,CAAC,WAAW,IAAI,CAAC,KAAK,CAAC,QAAQ,EAAE,CAAC;gBAC3D,IAAI,CAAC,KAAK,CACR,2FAA2F,GAAG,kCAAkC,CACjI,CAAA;YACH,CAAC;YACD,IAAI,CAAC,EAAE,CAAC,UAAU,CAAC,GAAG,CAAC,IAAI,CAAC,WAAW,EAAE,CAAC;gBACxC,IAAI,CAAC,KAAK,CACR,sEAAsE,GAAG,kCAAkC,CAC5G,CAAA;YACH,CAAC;YAED,MAAM,IAAI,GAAG,aAAa;gBACxB,CAAC,CAAC,IAAI,CAAC,KAAK;gBACZ,CAAC,CAAC,MAAM,IAAI,CAAC,UAAU,CACnB,MAAM,CAAC,OAAO,EACd,MAAM,CAAC,WAAW,EAClB,IAAI,CAAC,KAAK,EACV,2BAA2B,EAC3B,IAAI,CACL,CAAA;YAEL,MAAM,KAAK,GAAG,WAAW;gBACvB,CAAC,CAAC,GAAG;gBACL,CAAC,CAAC,MAAM,IAAI,CAAC,UAAU,CACnB,MAAM,CAAC,OAAO,EACd,MAAM,CAAC,WAAW,EAClB,GAAG,EACH,YAAY,EACZ,KAAK,CACN,CAAA;YAEL,MAAM,KAAK,GAAG,WAAW;gBACvB,CAAC,CAAC,GAAG;gBACL,CAAC,CAAC,MAAM,IAAI,CAAC,UAAU,CACnB,MAAM,CAAC,OAAO,EACd,MAAM,CAAC,WAAW,EAClB,GAAG,EACH,mBAAmB,EACnB,KAAK,CACN,CAAA;YAEL,IAAI,GAAG;gBACL,YAAY;gBACZ,QAAQ,EAAE,2BAA2B;gBACrC,OAAO,EAAE,EAAE,EAAE,EAAE,IAAI,EAAE,GAAG,EAAE,KAAK,EAAE,GAAG,EAAE,KAAK,EAAE;gBAC7C,QAAQ,EAAE,IAAI,QAAQ,EAAE,CAAC,WAAW,EAAE;aACvC,CAAA;QACH,CAAC;QACD,MAAM,GAAG,GAAG,MAAM,cAAc,CAC9B,MAAM,CAAC,OAAO,EACd,MAAM,CAAC,WAAW,EAClB,IAAI,EACJ,KAAK,CAAC,KAAK,CACZ,CAAA;QACD,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,SAAS,CAAC,GAAG,EAA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package/dist/commands/assembly/add-from-gff.d.ts

@@ -13,6 +13,8 @@ export default class AddGff extends FileCommand {
         assembly: import("@oclif/core/lib/interfaces/parser.js").OptionFlag<string | undefined, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
         'omit-features': import("@oclif/core/lib/interfaces/parser.js").BooleanFlag<boolean>;
         force: import("@oclif/core/lib/interfaces/parser.js").BooleanFlag<boolean>;
+        'no-strict': import("@oclif/core/lib/interfaces/parser.js").BooleanFlag<boolean>;
     };
     run(): Promise<void>;
 }
+//# sourceMappingURL=add-from-gff.d.ts.map

package/dist/commands/assembly/add-from-gff.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"add-from-gff.d.ts","sourceRoot":"","sources":["../../../src/commands/assembly/add-from-gff.ts"],"names":[],"mappings":"AAWA,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAA;AAGlD,MAAM,CAAC,OAAO,OAAO,MAAO,SAAQ,WAAW;IAC7C,MAAM,CAAC,OAAO,SAA0C;IACxD,MAAM,CAAC,WAAW,SACiG;IAEnH,MAAM,CAAC,QAAQ;;;QAUd;IAED,MAAM,CAAC,IAAI;;MAKV;IAED,MAAM,CAAC,KAAK;;;;;MAiBX;IAEY,GAAG,IAAI,OAAO,CAAC,IAAI,CAAC;CA4ClC"}

package/dist/commands/assembly/add-from-gff.js

@@ -36,6 +36,9 @@ export default class AddGff extends FileCommand {
             char: 'f',
             description: 'Delete existing assembly, if it exists',
         }),
+        'no-strict': Flags.boolean({
+            description: "If any feature lines in the GFF3 can't be processed, skip them instead of aborting the import",
+        }),
     };
     async run() {
         const { args, flags } = await this.parse(AddGff);
@@ -57,8 +60,10 @@ export default class AddGff extends FileCommand {
                 fileIds: { fa: fileId },
                 typeName: 'AddAssemblyAndFeaturesFromFileChange',
                 assembly: new ObjectId().toHexString(),
+                parseOptions: { strict: !flags['no-strict'] },
             };
         const rec = await submitAssembly(access.address, access.accessToken, body, flags.force);
         this.log(JSON.stringify(rec, null, 2));
     }
 }
+//# sourceMappingURL=add-from-gff.js.map

package/dist/commands/assembly/add-from-gff.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"add-from-gff.js","sourceRoot":"","sources":["../../../src/commands/assembly/add-from-gff.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,MAAM,SAAS,CAAA;AAC7B,OAAO,IAAI,MAAM,WAAW,CAAA;AAO5B,OAAO,EAAE,IAAI,EAAE,KAAK,EAAE,MAAM,aAAa,CAAA;AACzC,OAAO,EAAE,QAAQ,EAAE,MAAM,MAAM,CAAA;AAE/B,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAA;AAClD,OAAO,EAAE,cAAc,EAAE,MAAM,gBAAgB,CAAA;AAE/C,MAAM,CAAC,OAAO,OAAO,MAAO,SAAQ,WAAW;IAC7C,MAAM,CAAC,OAAO,GAAG,uCAAuC,CAAA;IACxD,MAAM,CAAC,WAAW,GAChB,iHAAiH,CAAA;IAEnH,MAAM,CAAC,QAAQ,GAAG;QAChB;YACE,WAAW,EAAE,gCAAgC;YAC7C,OAAO,EAAE,8DAA8D;SACxE;QACD;YACE,WAAW,EAAE,wBAAwB;YACrC,OAAO,EACL,iEAAiE;SACpE;KACF,CAAA;IAED,MAAM,CAAC,IAAI,GAAG;QACZ,YAAY,EAAE,IAAI,CAAC,MAAM,CAAC;YACxB,WAAW,EAAE,gBAAgB;YAC7B,QAAQ,EAAE,IAAI;SACf,CAAC;KACH,CAAA;IAED,MAAM,CAAC,KAAK,GAAG;QACb,QAAQ,EAAE,KAAK,CAAC,MAAM,CAAC;YACrB,IAAI,EAAE,GAAG;YACT,WAAW,EAAE,sDAAsD;SACpE,CAAC;QACF,eAAe,EAAE,KAAK,CAAC,OAAO,CAAC;YAC7B,IAAI,EAAE,GAAG;YACT,WAAW,EAAE,mDAAmD;SACjE,CAAC;QACF,KAAK,EAAE,KAAK,CAAC,OAAO,CAAC;YACnB,IAAI,EAAE,GAAG;YACT,WAAW,EAAE,wCAAwC;SACtD,CAAC;QACF,WAAW,EAAE,KAAK,CAAC,OAAO,CAAC;YACzB,WAAW,EACT,+FAA+F;SAClG,CAAC;KACH,CAAA;IAEM,KAAK,CAAC,GAAG;QACd,MAAM,EAAE,IAAI,EAAE,KAAK,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;QAEhD,IAAI,CAAC,EAAE,CAAC,UAAU,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC,EAAE,CAAC;YACvC,IAAI,CAAC,KAAK,CAAC,QAAQ,IAAI,CAAC,YAAY,CAAC,iBAAiB,CAAC,CAAA;QACzD,CAAC;QAED,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QAErC,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,UAAU,CAClC,MAAM,CAAC,OAAO,EACd,MAAM,CAAC,WAAW,EAClB,IAAI,CAAC,YAAY,CAAC,EAClB,aAAa,EACb,IAAI,CAAC,YAAY,CAAC,CAAC,QAAQ,CAAC,KAAK,CAAC,CACnC,CAAA;QAED,MAAM,YAAY,GAAG,KAAK,CAAC,QAAQ,IAAI,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC,CAAA;QAExE,MAAM,IAAI,GAG2C,KAAK,CAAC,eAAe,CAAC;YACzE,CAAC,CAAC;gBACE,YAAY;gBACZ,OAAO,EAAE,EAAE,EAAE,EAAE,MAAM,EAAE;gBACvB,QAAQ,EAAE,2BAA2B;gBACrC,QAAQ,EAAE,IAAI,QAAQ,EAAE,CAAC,WAAW,EAAE;aACvC;YACH,CAAC,CAAC;gBACE,YAAY;gBACZ,OAAO,EAAE,EAAE,EAAE,EAAE,MAAM,EAAE;gBACvB,QAAQ,EAAE,sCAAsC;gBAChD,QAAQ,EAAE,IAAI,QAAQ,EAAE,CAAC,WAAW,EAAE;gBACtC,YAAY,EAAE,EAAE,MAAM,EAAE,CAAC,KAAK,CAAC,WAAW,CAAC,EAAE;aAC9C,CAAA;QACL,MAAM,GAAG,GAAG,MAAM,cAAc,CAC9B,MAAM,CAAC,OAAO,EACd,MAAM,CAAC,WAAW,EAClB,IAAI,EACJ,KAAK,CAAC,KAAK,CACZ,CAAA;QACD,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,SAAS,CAAC,GAAG,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,CAAA;IACxC,CAAC"}

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

@@ -13,3 +13,4 @@ export default class Check extends BaseCommand<typeof Check> {
     };
     run(): Promise<void>;
 }
+//# sourceMappingURL=check.d.ts.map

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

@@ -0,0 +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"}

package/dist/commands/assembly/check.js

@@ -132,3 +132,4 @@ these checks use `apollo feature check`.';
         ]);
     }
 }
+//# sourceMappingURL=check.js.map

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

@@ -0,0 +1 @@
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package/dist/commands/assembly/delete.d.ts

@@ -12,3 +12,4 @@ export default class Delete extends BaseCommand<typeof Delete> {
     };
     run(): Promise<void>;
 }
+//# sourceMappingURL=delete.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"delete.d.ts","sourceRoot":"","sources":["../../../src/commands/assembly/delete.ts"],"names":[],"mappings":"AAEA,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAA;AAQlD,MAAM,CAAC,OAAO,OAAO,MAAO,SAAQ,WAAW,CAAC,OAAO,MAAM,CAAC;IAC5D,MAAM,CAAC,OAAO,SAAsB;IACpC,MAAM,CAAC,WAAW,SAA6C;IAC/D,MAAM,CAAC,QAAQ;;;QAMd;IAED,MAAM,CAAC,KAAK;;;MAWX;IAEY,GAAG,IAAI,OAAO,CAAC,IAAI,CAAC;CAwBlC"}

package/dist/commands/assembly/delete.js

@@ -41,3 +41,4 @@ export default class Delete extends BaseCommand {
         this.logToStderr(`${i} assemblies deleted`); // Keep as logToStderr
     }
 }
+//# sourceMappingURL=delete.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"delete.js","sourceRoot":"","sources":["../../../src/commands/assembly/delete.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,aAAa,CAAA;AAEnC,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAA;AAClD,OAAO,EACL,uBAAuB,EACvB,cAAc,EACd,WAAW,EACX,QAAQ,GACT,MAAM,gBAAgB,CAAA;AAEvB,MAAM,CAAC,OAAO,OAAO,MAAO,SAAQ,WAA0B;IAC5D,MAAM,CAAC,OAAO,GAAG,mBAAmB,CAAA;IACpC,MAAM,CAAC,WAAW,GAAG,0CAA0C,CAAA;IAC/D,MAAM,CAAC,QAAQ,GAAG;QAChB;YACE,WAAW,EAAE,8CAA8C;YAC3D,OAAO,EACL,uEAAuE;SAC1E;KACF,CAAA;IAED,MAAM,CAAC,KAAK,GAAG;QACb,QAAQ,EAAE,KAAK,CAAC,MAAM,CAAC;YACrB,IAAI,EAAE,GAAG;YACT,WAAW,EAAE,iCAAiC;YAC9C,QAAQ,EAAE,IAAI;YACd,QAAQ,EAAE,IAAI;SACf,CAAC;QACF,OAAO,EAAE,KAAK,CAAC,OAAO,CAAC;YACrB,IAAI,EAAE,GAAG;YACT,WAAW,EAAE,iDAAiD;SAC/D,CAAC;KACH,CAAA;IAEM,KAAK,CAAC,GAAG;QACd,MAAM,EAAE,KAAK,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;QAE1C,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QAErC,MAAM,QAAQ,GAAa,MAAM,QAAQ,CAAC,KAAK,CAAC,QAAQ,CAAC,CAAA;QACzD,MAAM,SAAS,GAAG,MAAM,uBAAuB,CAC7C,MAAM,CAAC,OAAO,EACd,MAAM,CAAC,WAAW,EAClB,QAAQ,CACT,CAAA;QACD,IAAI,CAAC,GAAG,CAAC,CAAA;QACT,MAAM,OAAO,GAAa,EAAE,CAAA;QAC5B,KAAK,MAAM,CAAC,IAAI,SAAS,EAAE,CAAC;YAC1B,MAAM,GAAG,GAAG,MAAM,WAAW,CAAC,MAAM,CAAC,OAAO,EAAE,MAAM,CAAC,WAAW,EAAE,CAAC,CAAC,CAAA;YACpE,MAAM,cAAc,CAAC,MAAM,CAAC,OAAO,EAAE,MAAM,CAAC,WAAW,EAAE,CAAC,CAAC,CAAA;YAC3D,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;YACjB,CAAC,IAAI,CAAC,CAAA;QACR,CAAC;QACD,IAAI,KAAK,CAAC,OAAO,EAAE,CAAC;YAClB,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,SAAS,CAAC,OAAO,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,CAAA;QAC5C,CAAC;QACD,IAAI,CAAC,WAAW,CAAC,GAAG,CAAC,qBAAqB,CAAC,CAAA,CAAC,sBAAsB;IACpE,CAAC"}

package/dist/commands/assembly/get.d.ts

@@ -7,3 +7,4 @@ export default class Get extends BaseCommand<typeof Get> {
     };
     run(): Promise<void>;
 }
+//# sourceMappingURL=get.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"get.d.ts","sourceRoot":"","sources":["../../../src/commands/assembly/get.ts"],"names":[],"mappings":"AAGA,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAA;AAGlD,MAAM,CAAC,OAAO,OAAO,GAAI,SAAQ,WAAW,CAAC,OAAO,GAAG,CAAC;IACtD,MAAM,CAAC,OAAO,SAA6B;IAC3C,MAAM,CAAC,WAAW,SAA0D;IAE5E,MAAM,CAAC,KAAK;;MAMX;IAEY,GAAG,IAAI,OAAO,CAAC,IAAI,CAAC;CAiClC"}

package/dist/commands/assembly/get.js

@@ -31,3 +31,4 @@ export default class Get extends BaseCommand {
         this.log(JSON.stringify(keep, null, 2));
     }
 }
+//# sourceMappingURL=get.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"get.js","sourceRoot":"","sources":["../../../src/commands/assembly/get.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,aAAa,CAAA;AAGnC,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAA;AAClD,OAAO,EAAE,uBAAuB,EAAE,QAAQ,EAAE,WAAW,EAAE,MAAM,gBAAgB,CAAA;AAE/E,MAAM,CAAC,OAAO,OAAO,GAAI,SAAQ,WAAuB;IACtD,MAAM,CAAC,OAAO,GAAG,0BAA0B,CAAA;IAC3C,MAAM,CAAC,WAAW,GAAG,uDAAuD,CAAA;IAE5E,MAAM,CAAC,KAAK,GAAG;QACb,QAAQ,EAAE,KAAK,CAAC,MAAM,CAAC;YACrB,IAAI,EAAE,GAAG;YACT,WAAW,EAAE,6CAA6C;YAC1D,QAAQ,EAAE,IAAI;SACf,CAAC;KACH,CAAA;IAEM,KAAK,CAAC,GAAG;QACd,MAAM,EAAE,KAAK,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;QAEvC,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QAErC,MAAM,UAAU,GAAa,MAAM,WAAW,CAC5C,MAAM,CAAC,OAAO,EACd,MAAM,CAAC,WAAW,EAClB,YAAY,CACb,CAAA;QAED,IAAI,WAAW,GAAa,EAAE,CAAA;QAC9B,IAAI,KAAK,CAAC,QAAQ,KAAK,SAAS,EAAE,CAAC;YACjC,MAAM,QAAQ,GAAG,MAAM,QAAQ,CAAC,KAAK,CAAC,QAAQ,CAAC,CAAA;YAC/C,WAAW,GAAG,MAAM,uBAAuB,CACzC,MAAM,CAAC,OAAO,EACd,MAAM,CAAC,WAAW,EAClB,QAAQ,CACT,CAAA;QACH,CAAC;QAED,MAAM,IAAI,GAAG,CAAC,MAAM,UAAU,CAAC,IAAI,EAAE,CAAa,CAAA;QAClD,MAAM,IAAI,GAAG,EAAE,CAAA;QACf,KAAK,MAAM,CAAC,IAAI,IAAI,EAAE,CAAC;YACrB,IACE,KAAK,CAAC,QAAQ,KAAK,SAAS;gBAC5B,WAAW,CAAC,QAAQ,CAAC,CAAC,CAAC,KAAuB,CAAC,CAAC,EAChD,CAAC;gBACD,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;YACd,CAAC;QACH,CAAC;QACD,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,SAAS,CAAC,IAAI,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,CAAA;IACzC,CAAC"}

package/dist/commands/assembly/sequence.d.ts

@@ -14,3 +14,4 @@ export default class ApolloCmd extends BaseCommand<typeof ApolloCmd> {
     };
     run(): Promise<void>;
 }
+//# sourceMappingURL=sequence.d.ts.map

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

@@ -0,0 +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"}

package/dist/commands/assembly/sequence.js

@@ -101,3 +101,4 @@ function splitStringIntoChunks(input, chunkSize) {
     }
     return chunks;
 }
+//# sourceMappingURL=sequence.js.map

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

@@ -0,0 +1 @@
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package/dist/commands/change/get.d.ts

@@ -7,3 +7,4 @@ export default class Get extends BaseCommand<typeof Get> {
     };
     run(): Promise<void>;
 }
+//# sourceMappingURL=get.d.ts.map

package/dist/commands/change/get.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"get.d.ts","sourceRoot":"","sources":["../../../src/commands/change/get.ts"],"names":[],"mappings":"AAGA,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAA;AAGlD,MAAM,CAAC,OAAO,OAAO,GAAI,SAAQ,WAAW,CAAC,OAAO,GAAG,CAAC;IACtD,MAAM,CAAC,OAAO,SAAwB;IACtC,MAAM,CAAC,WAAW,SAI2B;IAE7C,MAAM,CAAC,KAAK;;MAOX;IAEY,GAAG,IAAI,OAAO,CAAC,IAAI,CAAC;CA6BlC"}

package/dist/commands/change/get.js

@@ -33,3 +33,4 @@ In such cases you need to use the assembly ID.';
         this.log(JSON.stringify(keep, null, 2));
     }
 }
+//# sourceMappingURL=get.js.map

package/dist/commands/change/get.js.map

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