@jbrowse/plugin-legacy-jbrowse 2.1.4 → 2.1.6

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (14) hide show
  1. package/dist/JBrowse1Connection/jb1ConfigParse.js +1 -1
  2. package/dist/JBrowse1Connection/jb1ConfigParse.js.map +1 -1
  3. package/dist/JBrowse1Connection/model.d.ts +18 -5
  4. package/dist/JBrowse1Connection/model.js +12 -6
  5. package/dist/JBrowse1Connection/model.js.map +1 -1
  6. package/esm/JBrowse1Connection/jb1ConfigParse.js +1 -1
  7. package/esm/JBrowse1Connection/jb1ConfigParse.js.map +1 -1
  8. package/esm/JBrowse1Connection/model.d.ts +18 -5
  9. package/esm/JBrowse1Connection/model.js +12 -6
  10. package/esm/JBrowse1Connection/model.js.map +1 -1
  11. package/package.json +2 -2
  12. package/src/JBrowse1Connection/jb1ConfigParse.ts +1 -1
  13. package/src/JBrowse1Connection/model.tsx +77 -0
  14. package/src/JBrowse1Connection/model.js +0 -69
package/dist/JBrowse1Connection/jb1ConfigParse.js CHANGED
@@ -93,7 +93,7 @@ function parse(text, url) {
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  }
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  }
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  }
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- text.split('\n').forEach((textLine, i) => {
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+ text.split(/\n|\r\n|\r/).forEach((textLine, i) => {
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  lineNumber = i + 1;
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  const line = textLine.replace(/^\s*#.+/, '');
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  // new section
package/dist/JBrowse1Connection/jb1ConfigParse.js.map CHANGED
@@ -1 +1 @@
1
- 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1
+ 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package/dist/JBrowse1Connection/model.d.ts CHANGED
@@ -1,14 +1,27 @@
1
- export default function _default(pluginManager: any): import("mobx-state-tree").IModelType<{
1
+ import PluginManager from '@jbrowse/core/PluginManager';
2
+ export default function (pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
2
3
  name: import("mobx-state-tree").ISimpleType<string>;
3
- tracks: import("mobx-state-tree").IArrayType<any>;
4
+ tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
4
5
  } & {
5
6
  configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
6
7
  type: import("mobx-state-tree").ISimpleType<"JBrowse1Connection">;
7
8
  }, {
8
9
  afterAttach(): void;
9
- addTrackConf(trackConf: any): any;
10
- addTrackConfs(trackConfs: any): any[];
11
- setTrackConfs(trackConfs: any): import("mobx-state-tree").IMSTArray<any> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<any>>;
10
+ addTrackConf(trackConf: {
11
+ [x: string]: any;
12
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
13
+ setSubschema(slotName: string, data: unknown): any;
14
+ } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>): any;
15
+ addTrackConfs(trackConfs: ({
16
+ [x: string]: any;
17
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
18
+ setSubschema(slotName: string, data: unknown): any;
19
+ } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[]): any[];
20
+ setTrackConfs(trackConfs: ({
21
+ [x: string]: any;
22
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
23
+ setSubschema(slotName: string, data: unknown): any;
24
+ } & 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>>;
12
25
  clear(): void;
13
26
  } & {
14
27
  connect(): void;
package/dist/JBrowse1Connection/model.js CHANGED
@@ -11,28 +11,34 @@ const configSchema_1 = __importDefault(require("./configSchema"));
11
11
  const jb1ConfigLoad_1 = require("./jb1ConfigLoad");
12
12
  const jb1ToJb2_1 = require("./jb1ToJb2");
13
13
  function default_1(pluginManager) {
14
- return mobx_state_tree_1.types.compose('JBrowse1Connection', (0, models_1.BaseConnectionModelFactory)(pluginManager), mobx_state_tree_1.types
15
- .model({
14
+ return mobx_state_tree_1.types
15
+ .compose('JBrowse1Connection', (0, models_1.BaseConnectionModelFactory)(pluginManager), mobx_state_tree_1.types.model({
16
16
  configuration: (0, configuration_1.ConfigurationReference)(configSchema_1.default),
17
17
  type: mobx_state_tree_1.types.literal('JBrowse1Connection'),
18
- })
18
+ }))
19
19
  .actions(self => ({
20
20
  connect() {
21
21
  const dataDirLocation = (0, configuration_1.readConfObject)(self.configuration, 'dataDirLocation');
22
22
  const session = (0, util_1.getSession)(self);
23
23
  (0, jb1ConfigLoad_1.fetchJb1)(dataDirLocation)
24
24
  .then(config => {
25
+ var _a;
25
26
  const assemblyName = (0, configuration_1.readConfObject)(self.configuration, 'assemblyNames')[0];
26
27
  if (!assemblyName) {
27
28
  throw new Error('assembly name required for JBrowse 1 connection');
28
29
  }
29
30
  const assemblyConf = session.assemblies.find(assembly => (0, configuration_1.readConfObject)(assembly, 'name') === assemblyName);
31
+ if (!assemblyConf) {
32
+ throw new Error(`Assembly "${assemblyName}" not found`);
33
+ }
30
34
  const sequenceAdapter = (0, configuration_1.readConfObject)(assemblyConf, [
31
35
  'sequence',
32
36
  'adapter',
33
37
  ]);
34
- const jb2Tracks = config.tracks.map(jb1Track => {
35
- const jb2Track = (0, jb1ToJb2_1.convertTrackConfig)(jb1Track, config.dataRoot, sequenceAdapter);
38
+ // @ts-ignore
39
+ const jb2Tracks = (_a = config.tracks) === null || _a === void 0 ? void 0 : _a.map(jb1Track => {
40
+ const jb2Track = (0, jb1ToJb2_1.convertTrackConfig)(jb1Track, config.dataRoot || '', sequenceAdapter);
41
+ // @ts-ignore
36
42
  jb2Track.assemblyNames = [assemblyName];
37
43
  return jb2Track;
38
44
  });
@@ -44,7 +50,7 @@ function default_1(pluginManager) {
44
50
  session.breakConnection(self.configuration);
45
51
  });
46
52
  },
47
- })));
53
+ }));
48
54
  }
49
55
  exports.default = default_1;
50
56
  //# sourceMappingURL=model.js.map
package/dist/JBrowse1Connection/model.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"model.js","sourceRoot":"","sources":["../../src/JBrowse1Connection/model.js"],"names":[],"mappings":";;;;;AAAA,+DAGoC;AACpC,6CAA+C;AAC/C,uEAAuF;AACvF,qDAAuC;AACvC,kEAAyC;AAEzC,mDAA0C;AAC1C,yCAA+C;AAE/C,mBAAyB,aAAa;IACpC,OAAO,uBAAK,CAAC,OAAO,CAClB,oBAAoB,EACpB,IAAA,mCAA0B,EAAC,aAAa,CAAC,EACzC,uBAAK;SACF,KAAK,CAAC;QACL,aAAa,EAAE,IAAA,sCAAsB,EAAC,sBAAY,CAAC;QACnD,IAAI,EAAE,uBAAK,CAAC,OAAO,CAAC,oBAAoB,CAAC;KAC1C,CAAC;SACD,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,CACb,iDAAiD,CAClD,CAAA;iBACF;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,MAAM,eAAe,GAAG,IAAA,8BAAc,EAAC,YAAY,EAAE;oBACnD,UAAU;oBACV,SAAS;iBACV,CAAC,CAAA;gBACF,MAAM,SAAS,GAAG,MAAM,CAAC,MAAM,CAAC,GAAG,CAAC,QAAQ,CAAC,EAAE;oBAC7C,MAAM,QAAQ,GAAG,IAAA,6BAAkB,EACjC,QAAQ,EACR,MAAM,CAAC,QAAQ,EACf,eAAe,CAChB,CAAA;oBACD,QAAQ,CAAC,aAAa,GAAG,CAAC,YAAY,CAAC,CAAA;oBACvC,OAAO,QAAQ,CAAA;gBACjB,CAAC,CAAC,CAAA;gBACF,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,CACN,CAAA;AACH,CAAC;AAxDD,4BAwDC"}
1
+ {"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/jb1ConfigParse.js CHANGED
@@ -85,7 +85,7 @@ function parse(text, url) {
85
85
  }
86
86
  }
87
87
  }
88
- text.split('\n').forEach((textLine, i) => {
88
+ text.split(/\n|\r\n|\r/).forEach((textLine, i) => {
89
89
  lineNumber = i + 1;
90
90
  const line = textLine.replace(/^\s*#.+/, '');
91
91
  // new section
package/esm/JBrowse1Connection/jb1ConfigParse.js.map CHANGED
@@ -1 +1 @@
1
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1
+ 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package/esm/JBrowse1Connection/model.d.ts CHANGED
@@ -1,14 +1,27 @@
1
- export default function _default(pluginManager: any): import("mobx-state-tree").IModelType<{
1
+ import PluginManager from '@jbrowse/core/PluginManager';
2
+ export default function (pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
2
3
  name: import("mobx-state-tree").ISimpleType<string>;
3
- tracks: import("mobx-state-tree").IArrayType<any>;
4
+ tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
4
5
  } & {
5
6
  configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
6
7
  type: import("mobx-state-tree").ISimpleType<"JBrowse1Connection">;
7
8
  }, {
8
9
  afterAttach(): void;
9
- addTrackConf(trackConf: any): any;
10
- addTrackConfs(trackConfs: any): any[];
11
- setTrackConfs(trackConfs: any): import("mobx-state-tree").IMSTArray<any> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<any>>;
10
+ addTrackConf(trackConf: {
11
+ [x: string]: any;
12
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
13
+ setSubschema(slotName: string, data: unknown): any;
14
+ } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>): any;
15
+ addTrackConfs(trackConfs: ({
16
+ [x: string]: any;
17
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
18
+ setSubschema(slotName: string, data: unknown): any;
19
+ } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[]): any[];
20
+ setTrackConfs(trackConfs: ({
21
+ [x: string]: any;
22
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
23
+ setSubschema(slotName: string, data: unknown): any;
24
+ } & 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>>;
12
25
  clear(): void;
13
26
  } & {
14
27
  connect(): void;
package/esm/JBrowse1Connection/model.js CHANGED
@@ -6,28 +6,34 @@ import configSchema from './configSchema';
6
6
  import { fetchJb1 } from './jb1ConfigLoad';
7
7
  import { convertTrackConfig } from './jb1ToJb2';
8
8
  export default function (pluginManager) {
9
- return types.compose('JBrowse1Connection', BaseConnectionModelFactory(pluginManager), types
10
- .model({
9
+ return types
10
+ .compose('JBrowse1Connection', BaseConnectionModelFactory(pluginManager), types.model({
11
11
  configuration: ConfigurationReference(configSchema),
12
12
  type: types.literal('JBrowse1Connection'),
13
- })
13
+ }))
14
14
  .actions(self => ({
15
15
  connect() {
16
16
  const dataDirLocation = readConfObject(self.configuration, 'dataDirLocation');
17
17
  const session = getSession(self);
18
18
  fetchJb1(dataDirLocation)
19
19
  .then(config => {
20
+ var _a;
20
21
  const assemblyName = readConfObject(self.configuration, 'assemblyNames')[0];
21
22
  if (!assemblyName) {
22
23
  throw new Error('assembly name required for JBrowse 1 connection');
23
24
  }
24
25
  const assemblyConf = session.assemblies.find(assembly => readConfObject(assembly, 'name') === assemblyName);
26
+ if (!assemblyConf) {
27
+ throw new Error(`Assembly "${assemblyName}" not found`);
28
+ }
25
29
  const sequenceAdapter = readConfObject(assemblyConf, [
26
30
  'sequence',
27
31
  'adapter',
28
32
  ]);
29
- const jb2Tracks = config.tracks.map(jb1Track => {
30
- const jb2Track = convertTrackConfig(jb1Track, config.dataRoot, sequenceAdapter);
33
+ // @ts-ignore
34
+ const jb2Tracks = (_a = config.tracks) === null || _a === void 0 ? void 0 : _a.map(jb1Track => {
35
+ const jb2Track = convertTrackConfig(jb1Track, config.dataRoot || '', sequenceAdapter);
36
+ // @ts-ignore
31
37
  jb2Track.assemblyNames = [assemblyName];
32
38
  return jb2Track;
33
39
  });
@@ -39,6 +45,6 @@ export default function (pluginManager) {
39
45
  session.breakConnection(self.configuration);
40
46
  });
41
47
  },
42
- })));
48
+ }));
43
49
  }
44
50
  //# sourceMappingURL=model.js.map
package/esm/JBrowse1Connection/model.js.map CHANGED
@@ -1 +1 @@
1
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1
+ {"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 CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/plugin-legacy-jbrowse",
3
- "version": "2.1.4",
3
+ "version": "2.1.6",
4
4
  "description": "JBrowse 2 plugin for connecting to and reading JBrowse 1 data",
5
5
  "keywords": [
6
6
  "jbrowse",
@@ -56,5 +56,5 @@
56
56
  "distModule": "esm/index.js",
57
57
  "srcModule": "src/index.ts",
58
58
  "module": "esm/index.js",
59
- "gitHead": "8f53e016dd83b01a1beea0fc61c33964f5b6c809"
59
+ "gitHead": "df810d2a4f057adcd8f5345d54972508fba007a7"
60
60
  }
package/src/JBrowse1Connection/jb1ConfigParse.ts CHANGED
@@ -99,7 +99,7 @@ function parse(text: string, url: string): Config {
99
99
  }
100
100
  }
101
101
 
102
- text.split('\n').forEach((textLine, i): void => {
102
+ text.split(/\n|\r\n|\r/).forEach((textLine, i): void => {
103
103
  lineNumber = i + 1
104
104
  const line = textLine.replace(/^\s*#.+/, '')
105
105
 
package/src/JBrowse1Connection/model.tsx ADDED
@@ -0,0 +1,77 @@
1
+ import {
2
+ ConfigurationReference,
3
+ readConfObject,
4
+ } from '@jbrowse/core/configuration'
5
+ import { getSession } from '@jbrowse/core/util'
6
+ import { BaseConnectionModelFactory } from '@jbrowse/core/pluggableElementTypes/models'
7
+ import { types } from 'mobx-state-tree'
8
+ import configSchema from './configSchema'
9
+
10
+ import { fetchJb1 } from './jb1ConfigLoad'
11
+ import { convertTrackConfig } from './jb1ToJb2'
12
+ import PluginManager from '@jbrowse/core/PluginManager'
13
+
14
+ export default function (pluginManager: PluginManager) {
15
+ return types
16
+ .compose(
17
+ 'JBrowse1Connection',
18
+ BaseConnectionModelFactory(pluginManager),
19
+ types.model({
20
+ configuration: ConfigurationReference(configSchema),
21
+ type: types.literal('JBrowse1Connection'),
22
+ }),
23
+ )
24
+
25
+ .actions(self => ({
26
+ connect() {
27
+ const dataDirLocation = readConfObject(
28
+ self.configuration,
29
+ 'dataDirLocation',
30
+ )
31
+ const session = getSession(self)
32
+ fetchJb1(dataDirLocation)
33
+ .then(config => {
34
+ const assemblyName = readConfObject(
35
+ self.configuration,
36
+ 'assemblyNames',
37
+ )[0]
38
+ if (!assemblyName) {
39
+ throw new Error('assembly name required for JBrowse 1 connection')
40
+ }
41
+ const assemblyConf = session.assemblies.find(
42
+ assembly => readConfObject(assembly, 'name') === assemblyName,
43
+ )
44
+ if (!assemblyConf) {
45
+ throw new Error(`Assembly "${assemblyName}" not found`)
46
+ }
47
+ const sequenceAdapter = readConfObject(assemblyConf, [
48
+ 'sequence',
49
+ 'adapter',
50
+ ])
51
+
52
+ // @ts-ignore
53
+ const jb2Tracks = config.tracks?.map(jb1Track => {
54
+ const jb2Track = convertTrackConfig(
55
+ jb1Track,
56
+ config.dataRoot || '',
57
+ sequenceAdapter,
58
+ )
59
+
60
+ // @ts-ignore
61
+ jb2Track.assemblyNames = [assemblyName]
62
+ return jb2Track
63
+ })
64
+
65
+ self.setTrackConfs(jb2Tracks)
66
+ })
67
+ .catch(error => {
68
+ console.error(error)
69
+ session.notify(
70
+ `There was a problem connecting to the JBrowse 1 data directory "${self.name}". Please make sure you have entered a valid location. The error that was thrown is: "${error}"`,
71
+ 'error',
72
+ )
73
+ session.breakConnection(self.configuration)
74
+ })
75
+ },
76
+ }))
77
+ }
package/src/JBrowse1Connection/model.js DELETED
@@ -1,69 +0,0 @@
1
- import {
2
- ConfigurationReference,
3
- readConfObject,
4
- } from '@jbrowse/core/configuration'
5
- import { getSession } from '@jbrowse/core/util'
6
- import { BaseConnectionModelFactory } from '@jbrowse/core/pluggableElementTypes/models'
7
- import { types } from 'mobx-state-tree'
8
- import configSchema from './configSchema'
9
-
10
- import { fetchJb1 } from './jb1ConfigLoad'
11
- import { convertTrackConfig } from './jb1ToJb2'
12
-
13
- export default function (pluginManager) {
14
- return types.compose(
15
- 'JBrowse1Connection',
16
- BaseConnectionModelFactory(pluginManager),
17
- types
18
- .model({
19
- configuration: ConfigurationReference(configSchema),
20
- type: types.literal('JBrowse1Connection'),
21
- })
22
- .actions(self => ({
23
- connect() {
24
- const dataDirLocation = readConfObject(
25
- self.configuration,
26
- 'dataDirLocation',
27
- )
28
- const session = getSession(self)
29
- fetchJb1(dataDirLocation)
30
- .then(config => {
31
- const assemblyName = readConfObject(
32
- self.configuration,
33
- 'assemblyNames',
34
- )[0]
35
- if (!assemblyName) {
36
- throw new Error(
37
- 'assembly name required for JBrowse 1 connection',
38
- )
39
- }
40
- const assemblyConf = session.assemblies.find(
41
- assembly => readConfObject(assembly, 'name') === assemblyName,
42
- )
43
- const sequenceAdapter = readConfObject(assemblyConf, [
44
- 'sequence',
45
- 'adapter',
46
- ])
47
- const jb2Tracks = config.tracks.map(jb1Track => {
48
- const jb2Track = convertTrackConfig(
49
- jb1Track,
50
- config.dataRoot,
51
- sequenceAdapter,
52
- )
53
- jb2Track.assemblyNames = [assemblyName]
54
- return jb2Track
55
- })
56
- self.setTrackConfs(jb2Tracks)
57
- })
58
- .catch(error => {
59
- console.error(error)
60
- session.notify(
61
- `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}"`,
62
- 'error',
63
- )
64
- session.breakConnection(self.configuration)
65
- })
66
- },
67
- })),
68
- )
69
- }