@jbrowse/plugin-legacy-jbrowse 2.1.4 → 2.1.5

package/dist/JBrowse1Connection/model.d.ts

@@ -1,14 +1,27 @@
-export default function _default(pluginManager: any): import("mobx-state-tree").IModelType<{
+import PluginManager from '@jbrowse/core/PluginManager';
+export default function (pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
     name: import("mobx-state-tree").ISimpleType<string>;
-    tracks: import("mobx-state-tree").IArrayType<any>;
+    tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
 } & {
     configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
     type: import("mobx-state-tree").ISimpleType<"JBrowse1Connection">;
 }, {
     afterAttach(): void;
-    addTrackConf(trackConf: any): any;
-    addTrackConfs(trackConfs: any): any[];
-    setTrackConfs(trackConfs: any): import("mobx-state-tree").IMSTArray<any> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<any>>;
+    addTrackConf(trackConf: {
+        [x: string]: any;
+    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+        setSubschema(slotName: string, data: unknown): any;
+    } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>): any;
+    addTrackConfs(trackConfs: ({
+        [x: string]: any;
+    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+        setSubschema(slotName: string, data: unknown): any;
+    } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[]): any[];
+    setTrackConfs(trackConfs: ({
+        [x: string]: any;
+    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+        setSubschema(slotName: string, data: unknown): any;
+    } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[]): import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IAnyModelType> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>>;
     clear(): void;
 } & {
     connect(): void;

package/dist/JBrowse1Connection/model.js

@@ -11,28 +11,34 @@ const configSchema_1 = __importDefault(require("./configSchema"));
 const jb1ConfigLoad_1 = require("./jb1ConfigLoad");
 const jb1ToJb2_1 = require("./jb1ToJb2");
 function default_1(pluginManager) {
-    return mobx_state_tree_1.types.compose('JBrowse1Connection', (0, models_1.BaseConnectionModelFactory)(pluginManager), mobx_state_tree_1.types
-        .model({
+    return mobx_state_tree_1.types
+        .compose('JBrowse1Connection', (0, models_1.BaseConnectionModelFactory)(pluginManager), mobx_state_tree_1.types.model({
         configuration: (0, configuration_1.ConfigurationReference)(configSchema_1.default),
         type: mobx_state_tree_1.types.literal('JBrowse1Connection'),
-    })
+    }))
         .actions(self => ({
         connect() {
             const dataDirLocation = (0, configuration_1.readConfObject)(self.configuration, 'dataDirLocation');
             const session = (0, util_1.getSession)(self);
             (0, jb1ConfigLoad_1.fetchJb1)(dataDirLocation)
                 .then(config => {
+                var _a;
                 const assemblyName = (0, configuration_1.readConfObject)(self.configuration, 'assemblyNames')[0];
                 if (!assemblyName) {
                     throw new Error('assembly name required for JBrowse 1 connection');
                 }
                 const assemblyConf = session.assemblies.find(assembly => (0, configuration_1.readConfObject)(assembly, 'name') === assemblyName);
+                if (!assemblyConf) {
+                    throw new Error(`Assembly "${assemblyName}" not found`);
+                }
                 const sequenceAdapter = (0, configuration_1.readConfObject)(assemblyConf, [
                     'sequence',
                     'adapter',
                 ]);
-                const jb2Tracks = config.tracks.map(jb1Track => {
-                    const jb2Track = (0, jb1ToJb2_1.convertTrackConfig)(jb1Track, config.dataRoot, sequenceAdapter);
+                // @ts-ignore
+                const jb2Tracks = (_a = config.tracks) === null || _a === void 0 ? void 0 : _a.map(jb1Track => {
+                    const jb2Track = (0, jb1ToJb2_1.convertTrackConfig)(jb1Track, config.dataRoot || '', sequenceAdapter);
+                    // @ts-ignore
                     jb2Track.assemblyNames = [assemblyName];
                     return jb2Track;
                 });
@@ -44,7 +50,7 @@ function default_1(pluginManager) {
                 session.breakConnection(self.configuration);
             });
         },
-    })));
+    }));
 }
 exports.default = default_1;
 //# sourceMappingURL=model.js.map

package/dist/JBrowse1Connection/model.js.map

@@ -1 +1 @@
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+{"version":3,"file":"model.js","sourceRoot":"","sources":["../../src/JBrowse1Connection/model.tsx"],"names":[],"mappings":";;;;;AAAA,+DAGoC;AACpC,6CAA+C;AAC/C,uEAAuF;AACvF,qDAAuC;AACvC,kEAAyC;AAEzC,mDAA0C;AAC1C,yCAA+C;AAG/C,mBAAyB,aAA4B;IACnD,OAAO,uBAAK;SACT,OAAO,CACN,oBAAoB,EACpB,IAAA,mCAA0B,EAAC,aAAa,CAAC,EACzC,uBAAK,CAAC,KAAK,CAAC;QACV,aAAa,EAAE,IAAA,sCAAsB,EAAC,sBAAY,CAAC;QACnD,IAAI,EAAE,uBAAK,CAAC,OAAO,CAAC,oBAAoB,CAAC;KAC1C,CAAC,CACH;SAEA,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB,OAAO;YACL,MAAM,eAAe,GAAG,IAAA,8BAAc,EACpC,IAAI,CAAC,aAAa,EAClB,iBAAiB,CAClB,CAAA;YACD,MAAM,OAAO,GAAG,IAAA,iBAAU,EAAC,IAAI,CAAC,CAAA;YAChC,IAAA,wBAAQ,EAAC,eAAe,CAAC;iBACtB,IAAI,CAAC,MAAM,CAAC,EAAE;;gBACb,MAAM,YAAY,GAAG,IAAA,8BAAc,EACjC,IAAI,CAAC,aAAa,EAClB,eAAe,CAChB,CAAC,CAAC,CAAC,CAAA;gBACJ,IAAI,CAAC,YAAY,EAAE;oBACjB,MAAM,IAAI,KAAK,CAAC,iDAAiD,CAAC,CAAA;iBACnE;gBACD,MAAM,YAAY,GAAG,OAAO,CAAC,UAAU,CAAC,IAAI,CAC1C,QAAQ,CAAC,EAAE,CAAC,IAAA,8BAAc,EAAC,QAAQ,EAAE,MAAM,CAAC,KAAK,YAAY,CAC9D,CAAA;gBACD,IAAI,CAAC,YAAY,EAAE;oBACjB,MAAM,IAAI,KAAK,CAAC,aAAa,YAAY,aAAa,CAAC,CAAA;iBACxD;gBACD,MAAM,eAAe,GAAG,IAAA,8BAAc,EAAC,YAAY,EAAE;oBACnD,UAAU;oBACV,SAAS;iBACV,CAAC,CAAA;gBAEF,aAAa;gBACb,MAAM,SAAS,GAAG,MAAA,MAAM,CAAC,MAAM,0CAAE,GAAG,CAAC,QAAQ,CAAC,EAAE;oBAC9C,MAAM,QAAQ,GAAG,IAAA,6BAAkB,EACjC,QAAQ,EACR,MAAM,CAAC,QAAQ,IAAI,EAAE,EACrB,eAAe,CAChB,CAAA;oBAED,aAAa;oBACb,QAAQ,CAAC,aAAa,GAAG,CAAC,YAAY,CAAC,CAAA;oBACvC,OAAO,QAAQ,CAAA;gBACjB,CAAC,CAAC,CAAA;gBAEF,IAAI,CAAC,aAAa,CAAC,SAAS,CAAC,CAAA;YAC/B,CAAC,CAAC;iBACD,KAAK,CAAC,KAAK,CAAC,EAAE;gBACb,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,CAAA;gBACpB,OAAO,CAAC,MAAM,CACZ,mEAAmE,IAAI,CAAC,IAAI,yFAAyF,KAAK,GAAG,EAC7K,OAAO,CACR,CAAA;gBACD,OAAO,CAAC,eAAe,CAAC,IAAI,CAAC,aAAa,CAAC,CAAA;YAC7C,CAAC,CAAC,CAAA;QACN,CAAC;KACF,CAAC,CAAC,CAAA;AACP,CAAC;AA/DD,4BA+DC"}

package/esm/JBrowse1Connection/model.d.ts

@@ -1,14 +1,27 @@
-export default function _default(pluginManager: any): import("mobx-state-tree").IModelType<{
+import PluginManager from '@jbrowse/core/PluginManager';
+export default function (pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
     name: import("mobx-state-tree").ISimpleType<string>;
-    tracks: import("mobx-state-tree").IArrayType<any>;
+    tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
 } & {
     configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
     type: import("mobx-state-tree").ISimpleType<"JBrowse1Connection">;
 }, {
     afterAttach(): void;
-    addTrackConf(trackConf: any): any;
-    addTrackConfs(trackConfs: any): any[];
-    setTrackConfs(trackConfs: any): import("mobx-state-tree").IMSTArray<any> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<any>>;
+    addTrackConf(trackConf: {
+        [x: string]: any;
+    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+        setSubschema(slotName: string, data: unknown): any;
+    } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>): any;
+    addTrackConfs(trackConfs: ({
+        [x: string]: any;
+    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+        setSubschema(slotName: string, data: unknown): any;
+    } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[]): any[];
+    setTrackConfs(trackConfs: ({
+        [x: string]: any;
+    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+        setSubschema(slotName: string, data: unknown): any;
+    } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[]): import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IAnyModelType> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>>;
     clear(): void;
 } & {
     connect(): void;

package/esm/JBrowse1Connection/model.js

@@ -6,28 +6,34 @@ import configSchema from './configSchema';
 import { fetchJb1 } from './jb1ConfigLoad';
 import { convertTrackConfig } from './jb1ToJb2';
 export default function (pluginManager) {
-    return types.compose('JBrowse1Connection', BaseConnectionModelFactory(pluginManager), types
-        .model({
+    return types
+        .compose('JBrowse1Connection', BaseConnectionModelFactory(pluginManager), types.model({
         configuration: ConfigurationReference(configSchema),
         type: types.literal('JBrowse1Connection'),
-    })
+    }))
         .actions(self => ({
         connect() {
             const dataDirLocation = readConfObject(self.configuration, 'dataDirLocation');
             const session = getSession(self);
             fetchJb1(dataDirLocation)
                 .then(config => {
+                var _a;
                 const assemblyName = readConfObject(self.configuration, 'assemblyNames')[0];
                 if (!assemblyName) {
                     throw new Error('assembly name required for JBrowse 1 connection');
                 }
                 const assemblyConf = session.assemblies.find(assembly => readConfObject(assembly, 'name') === assemblyName);
+                if (!assemblyConf) {
+                    throw new Error(`Assembly "${assemblyName}" not found`);
+                }
                 const sequenceAdapter = readConfObject(assemblyConf, [
                     'sequence',
                     'adapter',
                 ]);
-                const jb2Tracks = config.tracks.map(jb1Track => {
-                    const jb2Track = convertTrackConfig(jb1Track, config.dataRoot, sequenceAdapter);
+                // @ts-ignore
+                const jb2Tracks = (_a = config.tracks) === null || _a === void 0 ? void 0 : _a.map(jb1Track => {
+                    const jb2Track = convertTrackConfig(jb1Track, config.dataRoot || '', sequenceAdapter);
+                    // @ts-ignore
                     jb2Track.assemblyNames = [assemblyName];
                     return jb2Track;
                 });
@@ -39,6 +45,6 @@ export default function (pluginManager) {
                 session.breakConnection(self.configuration);
             });
         },
-    })));
+    }));
 }
 //# sourceMappingURL=model.js.map

package/esm/JBrowse1Connection/model.js.map

@@ -1 +1 @@
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+{"version":3,"file":"model.js","sourceRoot":"","sources":["../../src/JBrowse1Connection/model.tsx"],"names":[],"mappings":"AAAA,OAAO,EACL,sBAAsB,EACtB,cAAc,GACf,MAAM,6BAA6B,CAAA;AACpC,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAC/C,OAAO,EAAE,0BAA0B,EAAE,MAAM,4CAA4C,CAAA;AACvF,OAAO,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AACvC,OAAO,YAAY,MAAM,gBAAgB,CAAA;AAEzC,OAAO,EAAE,QAAQ,EAAE,MAAM,iBAAiB,CAAA;AAC1C,OAAO,EAAE,kBAAkB,EAAE,MAAM,YAAY,CAAA;AAG/C,MAAM,CAAC,OAAO,WAAW,aAA4B;IACnD,OAAO,KAAK;SACT,OAAO,CACN,oBAAoB,EACpB,0BAA0B,CAAC,aAAa,CAAC,EACzC,KAAK,CAAC,KAAK,CAAC;QACV,aAAa,EAAE,sBAAsB,CAAC,YAAY,CAAC;QACnD,IAAI,EAAE,KAAK,CAAC,OAAO,CAAC,oBAAoB,CAAC;KAC1C,CAAC,CACH;SAEA,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB,OAAO;YACL,MAAM,eAAe,GAAG,cAAc,CACpC,IAAI,CAAC,aAAa,EAClB,iBAAiB,CAClB,CAAA;YACD,MAAM,OAAO,GAAG,UAAU,CAAC,IAAI,CAAC,CAAA;YAChC,QAAQ,CAAC,eAAe,CAAC;iBACtB,IAAI,CAAC,MAAM,CAAC,EAAE;;gBACb,MAAM,YAAY,GAAG,cAAc,CACjC,IAAI,CAAC,aAAa,EAClB,eAAe,CAChB,CAAC,CAAC,CAAC,CAAA;gBACJ,IAAI,CAAC,YAAY,EAAE;oBACjB,MAAM,IAAI,KAAK,CAAC,iDAAiD,CAAC,CAAA;iBACnE;gBACD,MAAM,YAAY,GAAG,OAAO,CAAC,UAAU,CAAC,IAAI,CAC1C,QAAQ,CAAC,EAAE,CAAC,cAAc,CAAC,QAAQ,EAAE,MAAM,CAAC,KAAK,YAAY,CAC9D,CAAA;gBACD,IAAI,CAAC,YAAY,EAAE;oBACjB,MAAM,IAAI,KAAK,CAAC,aAAa,YAAY,aAAa,CAAC,CAAA;iBACxD;gBACD,MAAM,eAAe,GAAG,cAAc,CAAC,YAAY,EAAE;oBACnD,UAAU;oBACV,SAAS;iBACV,CAAC,CAAA;gBAEF,aAAa;gBACb,MAAM,SAAS,GAAG,MAAA,MAAM,CAAC,MAAM,0CAAE,GAAG,CAAC,QAAQ,CAAC,EAAE;oBAC9C,MAAM,QAAQ,GAAG,kBAAkB,CACjC,QAAQ,EACR,MAAM,CAAC,QAAQ,IAAI,EAAE,EACrB,eAAe,CAChB,CAAA;oBAED,aAAa;oBACb,QAAQ,CAAC,aAAa,GAAG,CAAC,YAAY,CAAC,CAAA;oBACvC,OAAO,QAAQ,CAAA;gBACjB,CAAC,CAAC,CAAA;gBAEF,IAAI,CAAC,aAAa,CAAC,SAAS,CAAC,CAAA;YAC/B,CAAC,CAAC;iBACD,KAAK,CAAC,KAAK,CAAC,EAAE;gBACb,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,CAAA;gBACpB,OAAO,CAAC,MAAM,CACZ,mEAAmE,IAAI,CAAC,IAAI,yFAAyF,KAAK,GAAG,EAC7K,OAAO,CACR,CAAA;gBACD,OAAO,CAAC,eAAe,CAAC,IAAI,CAAC,aAAa,CAAC,CAAA;YAC7C,CAAC,CAAC,CAAA;QACN,CAAC;KACF,CAAC,CAAC,CAAA;AACP,CAAC"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-legacy-jbrowse",
-  "version": "2.1.4",
+  "version": "2.1.5",
   "description": "JBrowse 2 plugin for connecting to and reading JBrowse 1 data",
   "keywords": [
     "jbrowse",
@@ -56,5 +56,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "8f53e016dd83b01a1beea0fc61c33964f5b6c809"
+  "gitHead": "bc5253ecdddeceeb999fffebf6dc6cf5f444e1c9"
 }

package/src/JBrowse1Connection/model.tsx

@@ -0,0 +1,77 @@
+import {
+  ConfigurationReference,
+  readConfObject,
+} from '@jbrowse/core/configuration'
+import { getSession } from '@jbrowse/core/util'
+import { BaseConnectionModelFactory } from '@jbrowse/core/pluggableElementTypes/models'
+import { types } from 'mobx-state-tree'
+import configSchema from './configSchema'
+
+import { fetchJb1 } from './jb1ConfigLoad'
+import { convertTrackConfig } from './jb1ToJb2'
+import PluginManager from '@jbrowse/core/PluginManager'
+
+export default function (pluginManager: PluginManager) {
+  return types
+    .compose(
+      'JBrowse1Connection',
+      BaseConnectionModelFactory(pluginManager),
+      types.model({
+        configuration: ConfigurationReference(configSchema),
+        type: types.literal('JBrowse1Connection'),
+      }),
+    )
+
+    .actions(self => ({
+      connect() {
+        const dataDirLocation = readConfObject(
+          self.configuration,
+          'dataDirLocation',
+        )
+        const session = getSession(self)
+        fetchJb1(dataDirLocation)
+          .then(config => {
+            const assemblyName = readConfObject(
+              self.configuration,
+              'assemblyNames',
+            )[0]
+            if (!assemblyName) {
+              throw new Error('assembly name required for JBrowse 1 connection')
+            }
+            const assemblyConf = session.assemblies.find(
+              assembly => readConfObject(assembly, 'name') === assemblyName,
+            )
+            if (!assemblyConf) {
+              throw new Error(`Assembly "${assemblyName}" not found`)
+            }
+            const sequenceAdapter = readConfObject(assemblyConf, [
+              'sequence',
+              'adapter',
+            ])
+
+            // @ts-ignore
+            const jb2Tracks = config.tracks?.map(jb1Track => {
+              const jb2Track = convertTrackConfig(
+                jb1Track,
+                config.dataRoot || '',
+                sequenceAdapter,
+              )
+
+              // @ts-ignore
+              jb2Track.assemblyNames = [assemblyName]
+              return jb2Track
+            })
+
+            self.setTrackConfs(jb2Tracks)
+          })
+          .catch(error => {
+            console.error(error)
+            session.notify(
+              `There was a problem connecting to the JBrowse 1 data directory "${self.name}". Please make sure you have entered a valid location. The error that was thrown is: "${error}"`,
+              'error',
+            )
+            session.breakConnection(self.configuration)
+          })
+      },
+    }))
+}

package/src/JBrowse1Connection/model.js

@@ -1,69 +0,0 @@
-import {
-  ConfigurationReference,
-  readConfObject,
-} from '@jbrowse/core/configuration'
-import { getSession } from '@jbrowse/core/util'
-import { BaseConnectionModelFactory } from '@jbrowse/core/pluggableElementTypes/models'
-import { types } from 'mobx-state-tree'
-import configSchema from './configSchema'
-
-import { fetchJb1 } from './jb1ConfigLoad'
-import { convertTrackConfig } from './jb1ToJb2'
-
-export default function (pluginManager) {
-  return types.compose(
-    'JBrowse1Connection',
-    BaseConnectionModelFactory(pluginManager),
-    types
-      .model({
-        configuration: ConfigurationReference(configSchema),
-        type: types.literal('JBrowse1Connection'),
-      })
-      .actions(self => ({
-        connect() {
-          const dataDirLocation = readConfObject(
-            self.configuration,
-            'dataDirLocation',
-          )
-          const session = getSession(self)
-          fetchJb1(dataDirLocation)
-            .then(config => {
-              const assemblyName = readConfObject(
-                self.configuration,
-                'assemblyNames',
-              )[0]
-              if (!assemblyName) {
-                throw new Error(
-                  'assembly name required for JBrowse 1 connection',
-                )
-              }
-              const assemblyConf = session.assemblies.find(
-                assembly => readConfObject(assembly, 'name') === assemblyName,
-              )
-              const sequenceAdapter = readConfObject(assemblyConf, [
-                'sequence',
-                'adapter',
-              ])
-              const jb2Tracks = config.tracks.map(jb1Track => {
-                const jb2Track = convertTrackConfig(
-                  jb1Track,
-                  config.dataRoot,
-                  sequenceAdapter,
-                )
-                jb2Track.assemblyNames = [assemblyName]
-                return jb2Track
-              })
-              self.setTrackConfs(jb2Tracks)
-            })
-            .catch(error => {
-              console.error(error)
-              session.notify(
-                `There was a problem connecting to the JBrowse 1 data directory "${self.name}". Please make sure you have entered a valid location. The error that was thrown is: "${error}"`,
-                'error',
-              )
-              session.breakConnection(self.configuration)
-            })
-        },
-      })),
-  )
-}