@jbrowse/plugin-data-management 2.2.1 → 2.3.0
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.
- package/dist/AddTrackWidget/components/AddTrackWidget.js +28 -5
- package/dist/AddTrackWidget/components/AddTrackWidget.js.map +1 -1
- package/dist/AddTrackWidget/components/ConfirmTrack.d.ts +2 -3
- package/dist/AddTrackWidget/components/ConfirmTrack.js +30 -177
- package/dist/AddTrackWidget/components/ConfirmTrack.js.map +1 -1
- package/dist/AddTrackWidget/components/DefaultAddTrackWorkflow.js.map +1 -1
- package/dist/AddTrackWidget/components/TextIndexingConfig.d.ts +6 -0
- package/dist/AddTrackWidget/components/TextIndexingConfig.js +109 -0
- package/dist/AddTrackWidget/components/TextIndexingConfig.js.map +1 -0
- package/dist/AddTrackWidget/components/TrackAdapterSelector.d.ts +6 -0
- package/dist/AddTrackWidget/components/TrackAdapterSelector.js +50 -0
- package/dist/AddTrackWidget/components/TrackAdapterSelector.js.map +1 -0
- package/dist/AddTrackWidget/components/TrackTypeSelector.d.ts +6 -0
- package/dist/AddTrackWidget/components/TrackTypeSelector.js +27 -0
- package/dist/AddTrackWidget/components/TrackTypeSelector.js.map +1 -0
- package/dist/AssemblyManager/AssemblyAddForm.js +14 -41
- package/dist/AssemblyManager/AssemblyAddForm.js.map +1 -1
- package/dist/AssemblyManager/AssemblyEditor.js +2 -1
- package/dist/AssemblyManager/AssemblyEditor.js.map +1 -1
- package/dist/AssemblyManager/AssemblyManager.js +14 -54
- package/dist/AssemblyManager/AssemblyManager.js.map +1 -1
- package/dist/AssemblyManager/AssemblyTable.js +24 -47
- package/dist/AssemblyManager/AssemblyTable.js.map +1 -1
- package/dist/HierarchicalTrackSelectorWidget/components/HierarchicalTrackSelector.js +3 -4
- package/dist/HierarchicalTrackSelectorWidget/components/HierarchicalTrackSelector.js.map +1 -1
- package/dist/HierarchicalTrackSelectorWidget/components/ManageConnectionsDialog.js +4 -12
- package/dist/HierarchicalTrackSelectorWidget/components/ManageConnectionsDialog.js.map +1 -1
- package/dist/HierarchicalTrackSelectorWidget/components/ToggleConnectionsDialog.js +5 -13
- package/dist/HierarchicalTrackSelectorWidget/components/ToggleConnectionsDialog.js.map +1 -1
- package/dist/HierarchicalTrackSelectorWidget/model.d.ts +2 -1
- package/dist/HierarchicalTrackSelectorWidget/model.js +6 -6
- package/dist/HierarchicalTrackSelectorWidget/model.js.map +1 -1
- package/dist/PluginStoreWidget/components/CustomPluginForm.js +1 -11
- package/dist/PluginStoreWidget/components/CustomPluginForm.js.map +1 -1
- package/dist/PluginStoreWidget/components/PluginStoreWidget.js.map +1 -1
- package/dist/ucsc-trackhub/index.d.ts +2 -2
- package/dist/ucsc-trackhub/index.js.map +1 -1
- package/dist/ucsc-trackhub/model.d.ts +3 -2
- package/dist/ucsc-trackhub/model.js +41 -40
- package/dist/ucsc-trackhub/model.js.map +1 -1
- package/dist/ucsc-trackhub/ucscAssemblies.js.map +1 -1
- package/esm/AddTrackWidget/components/AddTrackWidget.js +6 -6
- package/esm/AddTrackWidget/components/AddTrackWidget.js.map +1 -1
- package/esm/AddTrackWidget/components/ConfirmTrack.d.ts +2 -3
- package/esm/AddTrackWidget/components/ConfirmTrack.js +28 -175
- package/esm/AddTrackWidget/components/ConfirmTrack.js.map +1 -1
- package/esm/AddTrackWidget/components/DefaultAddTrackWorkflow.js.map +1 -1
- package/esm/AddTrackWidget/components/TextIndexingConfig.d.ts +6 -0
- package/esm/AddTrackWidget/components/TextIndexingConfig.js +81 -0
- package/esm/AddTrackWidget/components/TextIndexingConfig.js.map +1 -0
- package/esm/AddTrackWidget/components/TrackAdapterSelector.d.ts +6 -0
- package/esm/AddTrackWidget/components/TrackAdapterSelector.js +45 -0
- package/esm/AddTrackWidget/components/TrackAdapterSelector.js.map +1 -0
- package/esm/AddTrackWidget/components/TrackTypeSelector.d.ts +6 -0
- package/esm/AddTrackWidget/components/TrackTypeSelector.js +22 -0
- package/esm/AddTrackWidget/components/TrackTypeSelector.js.map +1 -0
- package/esm/AssemblyManager/AssemblyAddForm.js +9 -36
- package/esm/AssemblyManager/AssemblyAddForm.js.map +1 -1
- package/esm/AssemblyManager/AssemblyEditor.js +2 -1
- package/esm/AssemblyManager/AssemblyEditor.js.map +1 -1
- package/esm/AssemblyManager/AssemblyManager.js +15 -55
- package/esm/AssemblyManager/AssemblyManager.js.map +1 -1
- package/esm/AssemblyManager/AssemblyTable.js +25 -48
- package/esm/AssemblyManager/AssemblyTable.js.map +1 -1
- package/esm/HierarchicalTrackSelectorWidget/components/HierarchicalTrackSelector.js +3 -4
- package/esm/HierarchicalTrackSelectorWidget/components/HierarchicalTrackSelector.js.map +1 -1
- package/esm/HierarchicalTrackSelectorWidget/components/ManageConnectionsDialog.js +5 -13
- package/esm/HierarchicalTrackSelectorWidget/components/ManageConnectionsDialog.js.map +1 -1
- package/esm/HierarchicalTrackSelectorWidget/components/ToggleConnectionsDialog.js +6 -14
- package/esm/HierarchicalTrackSelectorWidget/components/ToggleConnectionsDialog.js.map +1 -1
- package/esm/HierarchicalTrackSelectorWidget/model.d.ts +2 -1
- package/esm/HierarchicalTrackSelectorWidget/model.js +7 -7
- package/esm/HierarchicalTrackSelectorWidget/model.js.map +1 -1
- package/esm/PluginStoreWidget/components/CustomPluginForm.js +2 -12
- package/esm/PluginStoreWidget/components/CustomPluginForm.js.map +1 -1
- package/esm/PluginStoreWidget/components/PluginStoreWidget.js.map +1 -1
- package/esm/ucsc-trackhub/index.d.ts +2 -2
- package/esm/ucsc-trackhub/index.js.map +1 -1
- package/esm/ucsc-trackhub/model.d.ts +3 -2
- package/esm/ucsc-trackhub/model.js +41 -40
- package/esm/ucsc-trackhub/model.js.map +1 -1
- package/esm/ucsc-trackhub/ucscAssemblies.js.map +1 -1
- package/package.json +4 -5
- package/src/AddTrackWidget/components/AddTrackWidget.test.tsx +3 -4
- package/src/AddTrackWidget/components/AddTrackWidget.tsx +6 -9
- package/src/AddTrackWidget/components/ConfirmTrack.tsx +36 -296
- package/src/AddTrackWidget/components/DefaultAddTrackWorkflow.tsx +0 -1
- package/src/AddTrackWidget/components/TextIndexingConfig.tsx +134 -0
- package/src/AddTrackWidget/components/TrackAdapterSelector.tsx +73 -0
- package/src/AddTrackWidget/components/TrackTypeSelector.tsx +46 -0
- package/src/AssemblyManager/AssemblyAddForm.tsx +147 -182
- package/src/AssemblyManager/AssemblyEditor.tsx +5 -1
- package/src/AssemblyManager/AssemblyManager.test.tsx +1 -1
- package/src/AssemblyManager/AssemblyManager.tsx +70 -137
- package/src/AssemblyManager/AssemblyTable.tsx +65 -97
- package/src/HierarchicalTrackSelectorWidget/components/HierarchicalTrackSelector.tsx +4 -4
- package/src/HierarchicalTrackSelectorWidget/components/ManageConnectionsDialog.tsx +5 -20
- package/src/HierarchicalTrackSelectorWidget/components/ToggleConnectionsDialog.tsx +12 -22
- package/src/HierarchicalTrackSelectorWidget/components/__snapshots__/HierarchicalTrackSelector.test.tsx.snap +1 -1
- package/src/HierarchicalTrackSelectorWidget/model.ts +14 -9
- package/src/PluginStoreWidget/components/CustomPluginForm.tsx +1 -18
- package/src/PluginStoreWidget/components/PluginStoreWidget.tsx +1 -0
- package/src/PluginStoreWidget/components/__snapshots__/PluginStoreWidget.test.js.snap +0 -22
- package/src/ucsc-trackhub/{index.js → index.ts} +0 -0
- package/src/ucsc-trackhub/model.ts +119 -0
- package/src/ucsc-trackhub/{ucscAssemblies.js → ucscAssemblies.ts} +0 -0
- package/src/ucsc-trackhub/model.js +0 -125
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const mui_1 = require("tss-react/mui");
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const IconButton_1 = __importDefault(require("@mui/material/IconButton"));
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const Close_1 = __importDefault(require("@mui/icons-material/Close"));
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const ExpandMore_1 = __importDefault(require("@mui/icons-material/ExpandMore"));
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const useStyles = (0, mui_1.makeStyles)()(theme => ({
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},
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dialogContent: {
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display: 'flex',
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40
|
flexDirection: 'column',
|
|
@@ -108,11 +102,7 @@ function CustomPluginForm({ open, onClose, model, }) {
|
|
|
108
102
|
setCJSPluginUrl('');
|
|
109
103
|
onClose();
|
|
110
104
|
}
|
|
111
|
-
return (react_1.default.createElement(material_1.Dialog, { open: open, onClose: handleClose },
|
|
112
|
-
react_1.default.createElement(material_1.DialogTitle, null,
|
|
113
|
-
"Add custom plugin",
|
|
114
|
-
react_1.default.createElement(IconButton_1.default, { size: "medium", className: classes.closeButton, onClick: () => onClose() },
|
|
115
|
-
react_1.default.createElement(Close_1.default, null))),
|
|
105
|
+
return (react_1.default.createElement(material_1.Dialog, { open: open, onClose: handleClose, title: "Add custom plugin" },
|
|
116
106
|
react_1.default.createElement("form", { onSubmit: handleSubmit },
|
|
117
107
|
react_1.default.createElement(material_1.DialogContent, { className: classes.dialogContent },
|
|
118
108
|
react_1.default.createElement(material_1.DialogContentText, null, "Enter the name of the plugin and its URL. The name should match what is defined in the plugin's build."),
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"CustomPluginForm.js","sourceRoot":"","sources":["../../../src/PluginStoreWidget/components/CustomPluginForm.tsx"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,+CAAuC;AACvC,2CAAqC;AACrC,qDAAyC;AAEzC,
|
|
1
|
+
{"version":3,"file":"CustomPluginForm.js","sourceRoot":"","sources":["../../../src/PluginStoreWidget/components/CustomPluginForm.tsx"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,+CAAuC;AACvC,2CAAqC;AACrC,qDAAyC;AAEzC,4CAQsB;AACtB,uCAA0C;AAE1C,QAAQ;AACR,0EAAiD;AACjD,gFAA2D;AAK3D,MAAM,SAAS,GAAG,IAAA,gBAAU,GAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,aAAa,EAAE;QACb,OAAO,EAAE,MAAM;QACf,aAAa,EAAE,QAAQ;KACxB;IACD,MAAM,EAAE;QACN,SAAS,EAAE,cAAc;QACzB,UAAU,EAAE,MAAM;QAClB,UAAU,EAAE,KAAK,CAAC,WAAW,CAAC,MAAM,CAAC,WAAW,EAAE;YAChD,QAAQ,EAAE,KAAK,CAAC,WAAW,CAAC,QAAQ,CAAC,QAAQ;SAC9C,CAAC;KACH;IACD,UAAU,EAAE;QACV,SAAS,EAAE,gBAAgB;KAC5B;CACF,CAAC,CAAC,CAAA;AAEH,SAAS,gBAAgB,CAAC,EACxB,IAAI,EACJ,OAAO,EACP,KAAK,GAKN;IACC,MAAM,EAAE,OAAO,EAAE,EAAE,EAAE,GAAG,SAAS,EAAE,CAAA;IACnC,MAAM,CAAC,aAAa,EAAE,gBAAgB,CAAC,GAAG,IAAA,gBAAQ,EAAC,EAAE,CAAC,CAAA;IACtD,MAAM,CAAC,YAAY,EAAE,eAAe,CAAC,GAAG,IAAA,gBAAQ,EAAC,EAAE,CAAC,CAAA;IACpD,MAAM,CAAC,YAAY,EAAE,eAAe,CAAC,GAAG,IAAA,gBAAQ,EAAC,EAAE,CAAC,CAAA;IACpD,MAAM,CAAC,YAAY,EAAE,eAAe,CAAC,GAAG,IAAA,gBAAQ,EAAC,EAAE,CAAC,CAAA;IACpD,MAAM,CAAC,mBAAmB,EAAE,sBAAsB,CAAC,GAAG,IAAA,gBAAQ,EAAC,KAAK,CAAC,CAAA;IAErE,SAAS,YAAY,CAAC,KAA6C;QACjE,MAAM,EAAE,IAAI,EAAE,KAAK,EAAE,GAAG,KAAK,CAAC,MAAM,CAAA;QACpC,IAAI,IAAI,KAAK,SAAS,EAAE;YACtB,gBAAgB,CAAC,KAAK,CAAC,CAAA;SACxB;QACD,IAAI,IAAI,KAAK,QAAQ,EAAE;YACrB,eAAe,CAAC,KAAK,CAAC,CAAA;SACvB;QACD,IAAI,IAAI,KAAK,QAAQ,EAAE;YACrB,eAAe,CAAC,KAAK,CAAC,CAAA;SACvB;QACD,IAAI,IAAI,KAAK,QAAQ,EAAE;YACrB,eAAe,CAAC,KAAK,CAAC,CAAA;SACvB;IACH,CAAC;IAED,SAAS,yBAAyB;QAChC,sBAAsB,CAAC,CAAC,mBAAmB,CAAC,CAAA;IAC9C,CAAC;IAED,8DAA8D;IAC9D,MAAM,EAAE,OAAO,EAAE,GAAG,IAAA,yBAAO,EAAM,KAAK,CAAC,CAAA;IAEvC,MAAM,KAAK,GAAG,OAAO,CACnB,CAAC,aAAa,IAAI,YAAY,CAAC,IAAI,YAAY,IAAI,YAAY,CAChE,CAAA;IAED,SAAS,YAAY;QACnB,IAAI,CAAC,KAAK,EAAE;YACV,OAAM;SACP;QACD,MAAM,gBAAgB,GAAqB,EAAE,CAAA;QAC7C,IAAI,aAAa,IAAI,YAAY,EAAE;YACjC,gBAAgB,CAAC,IAAI,GAAG,aAAa,CAAA;YACrC,gBAAgB,CAAC,MAAM,GAAG,YAAY,CAAA;SACvC;QACD,IAAI,YAAY,EAAE;YAChB,gBAAgB,CAAC,MAAM,GAAG,YAAY,CAAA;SACvC;QACD,IAAI,YAAY,EAAE;YAChB,gBAAgB,CAAC,MAAM,GAAG,YAAY,CAAA;SACvC;QACD,OAAO,CAAC,SAAS,CAAC,gBAAgB,CAAC,CAAA;IACrC,CAAC;IAED,SAAS,WAAW;QAClB,gBAAgB,CAAC,EAAE,CAAC,CAAA;QACpB,eAAe,CAAC,EAAE,CAAC,CAAA;QACnB,eAAe,CAAC,EAAE,CAAC,CAAA;QACnB,eAAe,CAAC,EAAE,CAAC,CAAA;QACnB,OAAO,EAAE,CAAA;IACX,CAAC;IAED,OAAO,CACL,8BAAC,iBAAM,IAAC,IAAI,EAAE,IAAI,EAAE,OAAO,EAAE,WAAW,EAAE,KAAK,EAAC,mBAAmB;QACjE,wCAAM,QAAQ,EAAE,YAAY;YAC1B,8BAAC,wBAAa,IAAC,SAAS,EAAE,OAAO,CAAC,aAAa;gBAC7C,8BAAC,4BAAiB,iHAGE;gBACpB,8BAAC,oBAAS,IACR,EAAE,EAAC,gBAAgB,EACnB,IAAI,EAAC,SAAS,EACd,KAAK,EAAC,aAAa,EACnB,OAAO,EAAC,UAAU,EAClB,KAAK,EAAE,aAAa,EACpB,QAAQ,EAAE,YAAY,GACtB;gBACF,8BAAC,oBAAS,IACR,EAAE,EAAC,eAAe,EAClB,IAAI,EAAC,QAAQ,EACb,KAAK,EAAC,YAAY,EAClB,OAAO,EAAC,UAAU,EAClB,KAAK,EAAE,YAAY,EACnB,QAAQ,EAAE,YAAY,GACtB;gBACF,8BAAC,4BAAiB,IAAC,OAAO,EAAE,yBAAyB;oBACnD,8BAAC,oBAAU,IACT,SAAS,EAAE,EAAE,CAAC,OAAO,CAAC,MAAM,EAAE;4BAC5B,CAAC,OAAO,CAAC,UAAU,CAAC,EAAE,mBAAmB;yBAC1C,CAAC,mBACa,mBAAmB,gBACvB,WAAW;wBAEtB,8BAAC,oBAAc,OAAG,CACP;uCAEK;gBACpB,8BAAC,mBAAQ,IAAC,EAAE,EAAE,mBAAmB;oBAC/B,uCAAK,SAAS,EAAE,OAAO,CAAC,aAAa;wBACnC,8BAAC,4BAAiB,oQAKE;wBACpB,8BAAC,oBAAS,IACR,EAAE,EAAC,eAAe,EAClB,IAAI,EAAC,QAAQ,EACb,KAAK,EAAC,eAAe,EACrB,OAAO,EAAC,UAAU,EAClB,KAAK,EAAE,YAAY,EACnB,QAAQ,EAAE,YAAY,GACtB;wBACF,8BAAC,oBAAS,IACR,EAAE,EAAC,eAAe,EAClB,IAAI,EAAC,QAAQ,EACb,KAAK,EAAC,eAAe,EACrB,OAAO,EAAC,UAAU,EAClB,KAAK,EAAE,YAAY,EACnB,QAAQ,EAAE,YAAY,GACtB,CACE,CACG,CACG;YAChB,8BAAC,wBAAa;gBACZ,8BAAC,iBAAM,IAAC,OAAO,EAAC,WAAW,EAAC,OAAO,EAAE,WAAW,aAEvC;gBACT,8BAAC,iBAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,OAAO,EAAE,YAAY,EACrB,QAAQ,EAAE,CAAC,KAAK,aAGT,CACK,CACX,CACA,CACV,CAAA;AACH,CAAC;AAED,kBAAe,IAAA,qBAAQ,EAAC,gBAAgB,CAAC,CAAA"}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"PluginStoreWidget.js","sourceRoot":"","sources":["../../../src/PluginStoreWidget/components/PluginStoreWidget.tsx"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,+CAAkD;AAElD,4CAQsB;AACtB,uCAA0C;AAC1C,2CAAqC;AACrC,qDAAwC;AAExC,yCAAkD;AAClD,6CAA2D;AAE3D,QAAQ;AACR,gFAA2D;AAC3D,sEAAiD;AACjD,oFAA+D;AAE/D,SAAS;AACT,kFAAyD;AACzD,8DAAqC;AACrC,0EAAiD;AAGjD,MAAM,SAAS,GAAG,IAAA,gBAAU,GAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,IAAI,EAAE;QACJ,MAAM,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;KACzB;IACD,UAAU,EAAE;QACV,KAAK,EAAE,MAAM;KACd;IACD,UAAU,EAAE;QACV,MAAM,EAAE,OAAO;QACf,YAAY,EAAE,CAAC;QACf,eAAe,EAAE,KAAK,CAAC,OAAO,CAAC,UAAU,CAAC,IAAI;QAC9C,OAAO,EAAE,KAAK;QACd,OAAO,EAAE,MAAM;QACf,YAAY,EAAE,QAAQ;KACvB;IACD,kBAAkB,EAAE;QAClB,MAAM,EAAE,OAAO;QACf,OAAO,EAAE,MAAM;QACf,cAAc,EAAE,QAAQ;KACzB;CACF,CAAC,CAAC,CAAA;AAEH,SAAS,iBAAiB,CAAC,EAAE,KAAK,EAA+B;IAC/D,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,CAAC,WAAW,EAAE,cAAc,CAAC,GAAG,IAAA,gBAAQ,GAAmB,CAAA;IACjE,MAAM,CAAC,KAAK,EAAE,QAAQ,CAAC,GAAG,IAAA,gBAAQ,GAAW,CAAA;IAC7C,MAAM,CAAC,oBAAoB,EAAE,uBAAuB,CAAC,GAAG,IAAA,gBAAQ,EAAC,KAAK,CAAC,CAAA;IACvE,MAAM,EAAE,SAAS,EAAE,GAAG,IAAA,iBAAU,EAAC,KAAK,CAAC,CAAA;IACvC,MAAM,EAAE,aAAa,EAAE,GAAG,IAAA,wBAAM,EAAC,KAAK,CAAC,CAAA;IAEvC,IAAA,iBAAS,EAAC,GAAG,EAAE;QACb,MAAM,UAAU,GAAG,IAAI,eAAe,EAAE,CAAA;QACxC,MAAM,EAAE,MAAM,EAAE,GAAG,UAAU,
|
|
1
|
+
{"version":3,"file":"PluginStoreWidget.js","sourceRoot":"","sources":["../../../src/PluginStoreWidget/components/PluginStoreWidget.tsx"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,+CAAkD;AAElD,4CAQsB;AACtB,uCAA0C;AAC1C,2CAAqC;AACrC,qDAAwC;AAExC,yCAAkD;AAClD,6CAA2D;AAE3D,QAAQ;AACR,gFAA2D;AAC3D,sEAAiD;AACjD,oFAA+D;AAE/D,SAAS;AACT,kFAAyD;AACzD,8DAAqC;AACrC,0EAAiD;AAGjD,MAAM,SAAS,GAAG,IAAA,gBAAU,GAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,IAAI,EAAE;QACJ,MAAM,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;KACzB;IACD,UAAU,EAAE;QACV,KAAK,EAAE,MAAM;KACd;IACD,UAAU,EAAE;QACV,MAAM,EAAE,OAAO;QACf,YAAY,EAAE,CAAC;QACf,eAAe,EAAE,KAAK,CAAC,OAAO,CAAC,UAAU,CAAC,IAAI;QAC9C,OAAO,EAAE,KAAK;QACd,OAAO,EAAE,MAAM;QACf,YAAY,EAAE,QAAQ;KACvB;IACD,kBAAkB,EAAE;QAClB,MAAM,EAAE,OAAO;QACf,OAAO,EAAE,MAAM;QACf,cAAc,EAAE,QAAQ;KACzB;CACF,CAAC,CAAC,CAAA;AAEH,SAAS,iBAAiB,CAAC,EAAE,KAAK,EAA+B;IAC/D,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,CAAC,WAAW,EAAE,cAAc,CAAC,GAAG,IAAA,gBAAQ,GAAmB,CAAA;IACjE,MAAM,CAAC,KAAK,EAAE,QAAQ,CAAC,GAAG,IAAA,gBAAQ,GAAW,CAAA;IAC7C,MAAM,CAAC,oBAAoB,EAAE,uBAAuB,CAAC,GAAG,IAAA,gBAAQ,EAAC,KAAK,CAAC,CAAA;IACvE,MAAM,EAAE,SAAS,EAAE,GAAG,IAAA,iBAAU,EAAC,KAAK,CAAC,CAAA;IACvC,MAAM,EAAE,aAAa,EAAE,GAAG,IAAA,wBAAM,EAAC,KAAK,CAAC,CAAA;IAEvC,IAAA,iBAAS,EAAC,GAAG,EAAE;QACb,MAAM,UAAU,GAAG,IAAI,eAAe,EAAE,CAAA;QACxC,MAAM,EAAE,MAAM,EAAE,GAAG,UAAU,CAG5B;QAAA,CAAC,KAAK,IAAI,EAAE;YACX,IAAI;gBACF,MAAM,QAAQ,GAAG,MAAM,KAAK,CAC1B,+CAA+C,EAC/C,EAAE,MAAM,EAAE,CACX,CAAA;gBACD,IAAI,CAAC,QAAQ,CAAC,EAAE,EAAE;oBAChB,MAAM,GAAG,GAAG,MAAM,QAAQ,CAAC,IAAI,EAAE,CAAA;oBACjC,MAAM,IAAI,KAAK,CACb,gCAAgC,QAAQ,CAAC,MAAM,IAAI,QAAQ,CAAC,UAAU,IAAI,GAAG,EAAE,CAChF,CAAA;iBACF;gBACD,MAAM,KAAK,GAAG,MAAM,QAAQ,CAAC,IAAI,EAAE,CAAA;gBACnC,IAAI,CAAC,MAAM,CAAC,OAAO,EAAE;oBACnB,cAAc,CAAC,KAAK,CAAC,OAAO,CAAC,CAAA;iBAC9B;aACF;YAAC,OAAO,CAAC,EAAE;gBACV,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;gBAChB,QAAQ,CAAC,CAAC,CAAC,CAAA;aACZ;QACH,CAAC,CAAC,EAAE,CAAA;QAEJ,OAAO,GAAG,EAAE;YACV,UAAU,CAAC,KAAK,EAAE,CAAA;QACpB,CAAC,CAAA;IACH,CAAC,EAAE,EAAE,CAAC,CAAA;IAEN,OAAO,CACL,uCAAK,SAAS,EAAE,OAAO,CAAC,IAAI;QACzB,SAAS,IAAI,CACZ;YACG,CAAC,iBAAU,IAAI,CACd,uCAAK,SAAS,EAAE,OAAO,CAAC,UAAU;gBAChC,8BAAC,sBAAgB,IAAC,KAAK,EAAE,EAAE,WAAW,EAAE,OAAO,EAAE,GAAI;gBACrD,8BAAC,qBAAU;;oBACS,2DAAyB;kKAGhC,CACT,CACP;YACD,uCAAK,SAAS,EAAE,OAAO,CAAC,kBAAkB;gBACxC,8BAAC,iBAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,OAAO,EAAE,GAAG,EAAE,CAAC,uBAAuB,CAAC,IAAI,CAAC,wBAGrC,CACL;YACN,8BAAC,0BAAgB,IACf,IAAI,EAAE,oBAAoB,EAC1B,OAAO,EAAE,GAAG,EAAE,CAAC,uBAAuB,CAAC,KAAK,CAAC,EAC7C,KAAK,EAAE,KAAK,GACZ,CACD,CACJ;QACD,8BAAC,oBAAS,IACR,KAAK,EAAC,gBAAgB,EACtB,KAAK,EAAE,KAAK,CAAC,UAAU,EACvB,QAAQ,EAAE,KAAK,CAAC,EAAE,CAAC,KAAK,CAAC,aAAa,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,EAC1D,SAAS,QACT,UAAU,EAAE;gBACV,YAAY,EAAE,CACZ,8BAAC,yBAAc,IAAC,QAAQ,EAAC,KAAK;oBAC5B,8BAAC,qBAAU,IACT,KAAK,EAAC,WAAW,EACjB,OAAO,EAAE,GAAG,EAAE,CAAC,KAAK,CAAC,eAAe,EAAE;wBAEtC,8BAAC,eAAS,OAAG,CACF,CACE,CAClB;aACF,GACD;QACF,8BAAC,oBAAS,IAAC,eAAe;YACxB,8BAAC,2BAAgB,IACf,UAAU,EAAE,8BAAC,oBAAc,IAAC,SAAS,EAAE,OAAO,CAAC,UAAU,GAAI;gBAE7D,8BAAC,qBAAU,IAAC,OAAO,EAAC,IAAI,wBAA+B,CACtC;YACnB,uCAAK,KAAK,EAAE,EAAE,MAAM,EAAE,KAAK,EAAE;gBAC3B,8BAAC,8BAAoB,IAAC,aAAa,EAAE,aAAa,EAAE,KAAK,EAAE,KAAK,GAAI,CAChE,CACI;QACZ,8BAAC,oBAAS,IAAC,eAAe;YACxB,8BAAC,2BAAgB,IACf,UAAU,EAAE,8BAAC,oBAAc,IAAC,SAAS,EAAE,OAAO,CAAC,UAAU,GAAI;gBAE7D,8BAAC,qBAAU,IAAC,OAAO,EAAC,IAAI,wBAA+B,CACtC;YAClB,KAAK,CAAC,CAAC,CAAC,CACP,8BAAC,qBAAU,IAAC,KAAK,EAAC,OAAO,IAAE,GAAG,KAAK,EAAE,CAAc,CACpD,CAAC,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,CAChB,WAAW;iBACR,MAAM,CAAC,MAAM,CAAC,EAAE;gBACf,0DAA0D;gBAC1D,IACE,CAAC,iBAAU;oBACX,CAAC,CAAC,MAAM,CAAC,MAAM,IAAI,MAAM,CAAC,GAAG,IAAI,MAAM,CAAC,MAAM,CAAC,EAC/C;oBACA,OAAO,KAAK,CAAA;iBACb;gBACD,OAAO,MAAM,CAAC,IAAI;qBACf,WAAW,EAAE;qBACb,QAAQ,CAAC,KAAK,CAAC,UAAU,CAAC,WAAW,EAAE,CAAC,CAAA;YAC7C,CAAC,CAAC;iBACD,GAAG,CAAC,MAAM,CAAC,EAAE,CAAC,CACb,8BAAC,oBAAU,IACT,GAAG,EAAG,MAAwB,CAAC,IAAI,EACnC,MAAM,EAAE,MAAM,EACd,KAAK,EAAE,KAAK,EACZ,SAAS,EAAE,CAAC,CAAC,SAAS,GACtB,CACH,CAAC,CACL,CAAC,CAAC,CAAC,CACF,8BAAC,oBAAe,OAAG,CACpB,CACS,CACR,CACP,CAAA;AACH,CAAC;AAED,kBAAe,IAAA,qBAAQ,EAAC,iBAAiB,CAAC,CAAA"}
|
|
@@ -1,2 +1,2 @@
|
|
|
1
|
-
export { default as modelFactory } from
|
|
2
|
-
export { default as configSchema } from
|
|
1
|
+
export { default as modelFactory } from './model';
|
|
2
|
+
export { default as configSchema } from './configSchema';
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/ucsc-trackhub/index.
|
|
1
|
+
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/ucsc-trackhub/index.ts"],"names":[],"mappings":";;;;;;AAAA,iCAAiD;AAAxC,sHAAA,OAAO,OAAgB;AAChC,+CAAwD;AAA/C,6HAAA,OAAO,OAAgB"}
|
|
@@ -1,4 +1,5 @@
|
|
|
1
|
-
|
|
1
|
+
import PluginManager from '@jbrowse/core/PluginManager';
|
|
2
|
+
export default function UCSCTrackHubConnection(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
|
|
2
3
|
name: import("mobx-state-tree").ISimpleType<string>;
|
|
3
4
|
tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
|
|
4
5
|
} & {
|
|
@@ -23,5 +24,5 @@ export default function UCSCTrackHubConnection(pluginManager: any): import("mobx
|
|
|
23
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>>;
|
|
24
25
|
clear(): void;
|
|
25
26
|
} & {
|
|
26
|
-
connect(): void
|
|
27
|
+
connect(): Promise<void>;
|
|
27
28
|
}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
|
|
@@ -7,82 +7,83 @@ const models_1 = require("@jbrowse/core/pluggableElementTypes/models");
|
|
|
7
7
|
const configuration_1 = require("@jbrowse/core/configuration");
|
|
8
8
|
const util_1 = require("@jbrowse/core/util");
|
|
9
9
|
const mobx_state_tree_1 = require("mobx-state-tree");
|
|
10
|
+
// locals
|
|
10
11
|
const configSchema_1 = __importDefault(require("./configSchema"));
|
|
11
12
|
const ucscTrackHub_1 = require("./ucscTrackHub");
|
|
12
13
|
function UCSCTrackHubConnection(pluginManager) {
|
|
13
|
-
return mobx_state_tree_1.types
|
|
14
|
-
.model({
|
|
14
|
+
return mobx_state_tree_1.types
|
|
15
|
+
.compose('UCSCTrackHubConnection', (0, models_1.BaseConnectionModelFactory)(pluginManager), mobx_state_tree_1.types.model({
|
|
15
16
|
configuration: (0, configuration_1.ConfigurationReference)(configSchema_1.default),
|
|
16
17
|
type: mobx_state_tree_1.types.literal('UCSCTrackHubConnection'),
|
|
17
|
-
})
|
|
18
|
+
}))
|
|
18
19
|
.actions(self => ({
|
|
19
|
-
connect() {
|
|
20
|
-
const connectionName = (0, configuration_1.getConf)(self, 'name');
|
|
21
|
-
const hubFileLocation = (0, configuration_1.getConf)(self, 'hubTxtLocation');
|
|
20
|
+
async connect() {
|
|
22
21
|
const session = (0, util_1.getSession)(self);
|
|
23
|
-
|
|
24
|
-
.
|
|
25
|
-
const
|
|
22
|
+
try {
|
|
23
|
+
const connectionName = (0, configuration_1.getConf)(self, 'name');
|
|
24
|
+
const hubFileLocation = (0, configuration_1.getConf)(self, 'hubTxtLocation');
|
|
25
|
+
const hubFile = await (0, ucscTrackHub_1.fetchHubFile)(hubFileLocation);
|
|
26
|
+
const genomeFile = hubFile.get('genomesFile');
|
|
27
|
+
if (!genomeFile) {
|
|
28
|
+
throw new Error('genomesFile not found on hub');
|
|
29
|
+
}
|
|
30
|
+
const hubUri = new URL(hubFileLocation.uri, hubFileLocation.baseUri);
|
|
31
|
+
const genomesFileLocation = hubUri
|
|
26
32
|
? {
|
|
27
|
-
uri: new URL(
|
|
33
|
+
uri: new URL(genomeFile, hubUri).href,
|
|
28
34
|
locationType: 'UriLocation',
|
|
29
35
|
}
|
|
30
36
|
: {
|
|
31
|
-
localPath:
|
|
37
|
+
localPath: genomeFile,
|
|
32
38
|
locationType: 'LocalPathLocation',
|
|
33
39
|
};
|
|
34
|
-
|
|
35
|
-
hubFile,
|
|
36
|
-
(0, ucscTrackHub_1.fetchGenomesFile)(genomesFileLocation),
|
|
37
|
-
]);
|
|
38
|
-
})
|
|
39
|
-
.then(([hubFile, genomesFile]) => {
|
|
40
|
+
const genomesFile = await (0, ucscTrackHub_1.fetchGenomesFile)(genomesFileLocation);
|
|
40
41
|
const trackDbData = [];
|
|
41
42
|
for (const [genomeName, genome] of genomesFile) {
|
|
42
43
|
const assemblyNames = (0, configuration_1.getConf)(self, 'assemblyNames');
|
|
43
44
|
if (assemblyNames.length > 0 &&
|
|
44
45
|
!assemblyNames.includes(genomeName)) {
|
|
45
|
-
|
|
46
|
+
continue;
|
|
46
47
|
}
|
|
47
|
-
const
|
|
48
|
-
if (!
|
|
48
|
+
const conf = session.assemblies.find(a => (0, configuration_1.readConfObject)(a, 'name') === genomeName);
|
|
49
|
+
if (!conf) {
|
|
49
50
|
throw new Error(`Cannot find assembly for "${genomeName}" from the genomes file for connection "${connectionName}"`);
|
|
50
51
|
}
|
|
51
|
-
const
|
|
52
|
+
const trackDb = genome.get('trackDb');
|
|
53
|
+
if (!trackDb) {
|
|
54
|
+
throw new Error('genomesFile not found on hub');
|
|
55
|
+
}
|
|
56
|
+
const trackDbFileLocation = hubUri
|
|
52
57
|
? {
|
|
53
|
-
uri: new URL(
|
|
58
|
+
uri: new URL(trackDb, new URL(genomeFile, hubUri)).href,
|
|
54
59
|
locationType: 'UriLocation',
|
|
55
60
|
}
|
|
56
61
|
: {
|
|
57
|
-
localPath:
|
|
62
|
+
localPath: trackDb,
|
|
58
63
|
locationType: 'LocalPathLocation',
|
|
59
64
|
};
|
|
60
|
-
trackDbData.push(
|
|
65
|
+
trackDbData.push([
|
|
61
66
|
trackDbFileLocation,
|
|
62
|
-
(0, ucscTrackHub_1.fetchTrackDbFile)(trackDbFileLocation),
|
|
67
|
+
await (0, ucscTrackHub_1.fetchTrackDbFile)(trackDbFileLocation),
|
|
63
68
|
genomeName,
|
|
64
|
-
|
|
65
|
-
])
|
|
69
|
+
conf,
|
|
70
|
+
]);
|
|
66
71
|
}
|
|
67
|
-
|
|
68
|
-
|
|
69
|
-
.then(trackDbData => {
|
|
70
|
-
for (const [trackDbFileLocation, trackDbFile, genomeName, assemblyConf,] of trackDbData) {
|
|
71
|
-
const sequenceAdapter = (0, configuration_1.readConfObject)(assemblyConf, [
|
|
72
|
+
for (const [trackDbFileLocation, trackDbFile, genomeName, conf,] of trackDbData) {
|
|
73
|
+
const sequenceAdapter = (0, configuration_1.readConfObject)(conf, [
|
|
72
74
|
'sequence',
|
|
73
75
|
'adapter',
|
|
74
76
|
]);
|
|
75
|
-
|
|
76
|
-
self.addTrackConfs(tracks);
|
|
77
|
+
self.addTrackConfs((0, ucscTrackHub_1.generateTracks)(trackDbFile, trackDbFileLocation, genomeName, sequenceAdapter));
|
|
77
78
|
}
|
|
78
|
-
}
|
|
79
|
-
|
|
80
|
-
console.error(
|
|
81
|
-
session.notify(`There was a problem connecting to the UCSC Track Hub "${self.name}". Please make sure you have entered a valid hub.txt file. The error that was thrown is: "${
|
|
79
|
+
}
|
|
80
|
+
catch (e) {
|
|
81
|
+
console.error(e);
|
|
82
|
+
session.notify(`There was a problem connecting to the UCSC Track Hub "${self.configuration.name}". Please make sure you have entered a valid hub.txt file. The error that was thrown is: "${e}"`, 'error');
|
|
82
83
|
session.breakConnection(self.configuration);
|
|
83
|
-
}
|
|
84
|
+
}
|
|
84
85
|
},
|
|
85
|
-
}))
|
|
86
|
+
}));
|
|
86
87
|
}
|
|
87
88
|
exports.default = UCSCTrackHubConnection;
|
|
88
89
|
//# sourceMappingURL=model.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"model.js","sourceRoot":"","sources":["../../src/ucsc-trackhub/model.
|
|
1
|
+
{"version":3,"file":"model.js","sourceRoot":"","sources":["../../src/ucsc-trackhub/model.ts"],"names":[],"mappings":";;;;;AACA,uEAAuF;AACvF,+DAIoC;AACpC,6CAA+C;AAC/C,qDAAuC;AAEvC,SAAS;AACT,kEAAyC;AACzC,iDAKuB;AAEvB,SAAwB,sBAAsB,CAAC,aAA4B;IACzE,OAAO,uBAAK;SACT,OAAO,CACN,wBAAwB,EACxB,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,wBAAwB,CAAC;KAC9C,CAAC,CACH;SACA,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB,KAAK,CAAC,OAAO;YACX,MAAM,OAAO,GAAG,IAAA,iBAAU,EAAC,IAAI,CAAC,CAAA;YAChC,IAAI;gBACF,MAAM,cAAc,GAAG,IAAA,uBAAO,EAAC,IAAI,EAAE,MAAM,CAAC,CAAA;gBAC5C,MAAM,eAAe,GAAG,IAAA,uBAAO,EAAC,IAAI,EAAE,gBAAgB,CAAC,CAAA;gBACvD,MAAM,OAAO,GAAG,MAAM,IAAA,2BAAY,EAAC,eAAe,CAAC,CAAA;gBACnD,MAAM,UAAU,GAAG,OAAO,CAAC,GAAG,CAAC,aAAa,CAAC,CAAA;gBAC7C,IAAI,CAAC,UAAU,EAAE;oBACf,MAAM,IAAI,KAAK,CAAC,8BAA8B,CAAC,CAAA;iBAChD;gBAED,MAAM,MAAM,GAAG,IAAI,GAAG,CAAC,eAAe,CAAC,GAAG,EAAE,eAAe,CAAC,OAAO,CAAC,CAAA;gBACpE,MAAM,mBAAmB,GAAG,MAAM;oBAChC,CAAC,CAAC;wBACE,GAAG,EAAE,IAAI,GAAG,CAAC,UAAU,EAAE,MAAM,CAAC,CAAC,IAAI;wBACrC,YAAY,EAAE,aAAa;qBAC5B;oBACH,CAAC,CAAC;wBACE,SAAS,EAAE,UAAU;wBACrB,YAAY,EAAE,mBAAmB;qBAClC,CAAA;gBACL,MAAM,WAAW,GAAG,MAAM,IAAA,+BAAgB,EAAC,mBAAmB,CAAC,CAAA;gBAC/D,MAAM,WAAW,GAAG,EAAE,CAAA;gBACtB,KAAK,MAAM,CAAC,UAAU,EAAE,MAAM,CAAC,IAAI,WAAW,EAAE;oBAC9C,MAAM,aAAa,GAAG,IAAA,uBAAO,EAAC,IAAI,EAAE,eAAe,CAAC,CAAA;oBACpD,IACE,aAAa,CAAC,MAAM,GAAG,CAAC;wBACxB,CAAC,aAAa,CAAC,QAAQ,CAAC,UAAU,CAAC,EACnC;wBACA,SAAQ;qBACT;oBACD,MAAM,IAAI,GAAG,OAAO,CAAC,UAAU,CAAC,IAAI,CAClC,CAAC,CAAC,EAAE,CAAC,IAAA,8BAAc,EAAC,CAAC,EAAE,MAAM,CAAC,KAAK,UAAU,CAC9C,CAAA;oBACD,IAAI,CAAC,IAAI,EAAE;wBACT,MAAM,IAAI,KAAK,CACb,6BAA6B,UAAU,2CAA2C,cAAc,GAAG,CACpG,CAAA;qBACF;oBACD,MAAM,OAAO,GAAG,MAAM,CAAC,GAAG,CAAC,SAAS,CAAC,CAAA;oBACrC,IAAI,CAAC,OAAO,EAAE;wBACZ,MAAM,IAAI,KAAK,CAAC,8BAA8B,CAAC,CAAA;qBAChD;oBACD,MAAM,mBAAmB,GAAG,MAAM;wBAChC,CAAC,CAAC;4BACE,GAAG,EAAE,IAAI,GAAG,CAAC,OAAO,EAAE,IAAI,GAAG,CAAC,UAAU,EAAE,MAAM,CAAC,CAAC,CAAC,IAAI;4BACvD,YAAY,EAAE,aAAa;yBAC5B;wBACH,CAAC,CAAC;4BACE,SAAS,EAAE,OAAO;4BAClB,YAAY,EAAE,mBAAmB;yBAClC,CAAA;oBACL,WAAW,CAAC,IAAI,CAAC;wBACf,mBAAmB;wBACnB,MAAM,IAAA,+BAAgB,EAAC,mBAAmB,CAAC;wBAC3C,UAAU;wBACV,IAAI;qBACI,CAAC,CAAA;iBACZ;gBACD,KAAK,MAAM,CACT,mBAAmB,EACnB,WAAW,EACX,UAAU,EACV,IAAI,EACL,IAAI,WAAW,EAAE;oBAChB,MAAM,eAAe,GAAG,IAAA,8BAAc,EAAC,IAAI,EAAE;wBAC3C,UAAU;wBACV,SAAS;qBACV,CAAC,CAAA;oBACF,IAAI,CAAC,aAAa,CAChB,IAAA,6BAAc,EACZ,WAAW,EACX,mBAAmB,EACnB,UAAU,EACV,eAAe,CAChB,CACF,CAAA;iBACF;aACF;YAAC,OAAO,CAAC,EAAE;gBACV,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;gBAChB,OAAO,CAAC,MAAM,CACZ,yDAAyD,IAAI,CAAC,aAAa,CAAC,IAAI,6FAA6F,CAAC,GAAG,EACjL,OAAO,CACR,CAAA;gBACD,OAAO,CAAC,eAAe,CAAC,IAAI,CAAC,aAAa,CAAC,CAAA;aAC5C;QACH,CAAC;KACF,CAAC,CAAC,CAAA;AACP,CAAC;AAnGD,yCAmGC"}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"ucscAssemblies.js","sourceRoot":"","sources":["../../src/ucsc-trackhub/ucscAssemblies.
|
|
1
|
+
{"version":3,"file":"ucscAssemblies.js","sourceRoot":"","sources":["../../src/ucsc-trackhub/ucscAssemblies.ts"],"names":[],"mappings":";AAAA,yEAAyE;AACzE,yFAAyF;AACzF,oDAAoD;;AAEpD,kBAAe;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;QAoMP,CAAC,KAAK,CAAC,OAAO,CAAC,CAAA"}
|
|
@@ -1,20 +1,20 @@
|
|
|
1
|
-
import React from 'react';
|
|
1
|
+
import React, { useState } from 'react';
|
|
2
2
|
import { observer } from 'mobx-react';
|
|
3
3
|
import { FormControl, FormHelperText, Select, MenuItem } from '@mui/material';
|
|
4
|
-
import { getEnv
|
|
4
|
+
import { getEnv } from '@jbrowse/core/util';
|
|
5
5
|
import DefaultAddTrackWorkflow from './DefaultAddTrackWorkflow';
|
|
6
6
|
import PasteConfigWorkflow from './PasteConfigWorkflow';
|
|
7
7
|
function AddTrackSelector({ model }) {
|
|
8
|
-
const [val, setVal] =
|
|
8
|
+
const [val, setVal] = useState('Default add track workflow');
|
|
9
9
|
const { pluginManager } = getEnv(model);
|
|
10
|
-
const widgets = pluginManager.
|
|
10
|
+
const widgets = pluginManager.getAddTrackWorkflowElements();
|
|
11
11
|
const ComponentMap = {
|
|
12
|
-
Default: DefaultAddTrackWorkflow,
|
|
12
|
+
'Default add track workflow': DefaultAddTrackWorkflow,
|
|
13
13
|
'Add track JSON': PasteConfigWorkflow,
|
|
14
14
|
...Object.fromEntries(widgets.map(w => [w.name, w.ReactComponent])),
|
|
15
15
|
};
|
|
16
16
|
// make sure the selected value is in the list
|
|
17
|
-
const val2 = ComponentMap[val] ? val : 'Default';
|
|
17
|
+
const val2 = ComponentMap[val] ? val : 'Default add track workflow';
|
|
18
18
|
const Component = ComponentMap[val2];
|
|
19
19
|
return (React.createElement(React.Fragment, null,
|
|
20
20
|
React.createElement(FormControl, null,
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"AddTrackWidget.js","sourceRoot":"","sources":["../../../src/AddTrackWidget/components/AddTrackWidget.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;
|
|
1
|
+
{"version":3,"file":"AddTrackWidget.js","sourceRoot":"","sources":["../../../src/AddTrackWidget/components/AddTrackWidget.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AACvC,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,WAAW,EAAE,cAAc,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AAC7E,OAAO,EAAE,MAAM,EAAE,MAAM,oBAAoB,CAAA;AAI3C,OAAO,uBAAuB,MAAM,2BAA2B,CAAA;AAC/D,OAAO,mBAAmB,MAAM,uBAAuB,CAAA;AAEvD,SAAS,gBAAgB,CAAC,EAAE,KAAK,EAA4B;IAC3D,MAAM,CAAC,GAAG,EAAE,MAAM,CAAC,GAAG,QAAQ,CAAC,4BAA4B,CAAC,CAAA;IAC5D,MAAM,EAAE,aAAa,EAAE,GAAG,MAAM,CAAC,KAAK,CAAC,CAAA;IACvC,MAAM,OAAO,GAAG,aAAa,CAAC,2BAA2B,EAAE,CAAA;IAC3D,MAAM,YAAY,GAAG;QACnB,4BAA4B,EAAE,uBAAuB;QACrD,gBAAgB,EAAE,mBAAmB;QACrC,GAAG,MAAM,CAAC,WAAW,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC,cAAc,CAAC,CAAC,CAAC;KACX,CAAA;IAE1D,8CAA8C;IAC9C,MAAM,IAAI,GAAG,YAAY,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,4BAA4B,CAAA;IACnE,MAAM,SAAS,GAAG,YAAY,CAAC,IAAI,CAAC,CAAA;IACpC,OAAO,CACL;QACE,oBAAC,WAAW;YACV,oBAAC,MAAM,IAAC,KAAK,EAAE,IAAI,EAAE,QAAQ,EAAE,KAAK,CAAC,EAAE,CAAC,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,IAC/D,MAAM,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAClC,oBAAC,QAAQ,IAAC,GAAG,EAAE,CAAC,EAAE,KAAK,EAAE,CAAC,IACvB,CAAC,CACO,CACZ,CAAC,CACK;YACT,oBAAC,cAAc,qCAA4C,CAC/C;QAEd,+BAAM;QACN,oBAAC,SAAS,IAAC,KAAK,EAAE,KAAK,GAAI,CAC1B,CACJ,CAAA;AACH,CAAC;AAED,eAAe,QAAQ,CAAC,gBAAgB,CAAC,CAAA"}
|
|
@@ -1,7 +1,6 @@
|
|
|
1
1
|
/// <reference types="react" />
|
|
2
2
|
import { AddTrackModel } from '../model';
|
|
3
|
-
declare
|
|
3
|
+
declare const _default: ({ model, }: {
|
|
4
4
|
model: AddTrackModel;
|
|
5
|
-
})
|
|
6
|
-
declare const _default: typeof ConfirmTrack;
|
|
5
|
+
}) => JSX.Element;
|
|
7
6
|
export default _default;
|
|
@@ -1,169 +1,36 @@
|
|
|
1
1
|
import React, { useEffect, useState } from 'react';
|
|
2
|
-
import {
|
|
2
|
+
import { Checkbox, FormControl, FormControlLabel, Link, TextField, Typography, } from '@mui/material';
|
|
3
3
|
import { makeStyles } from 'tss-react/mui';
|
|
4
|
-
import {
|
|
5
|
-
import { supportedIndexingAdapters, getSession, getEnv, isElectron, } from '@jbrowse/core/util';
|
|
4
|
+
import { supportedIndexingAdapters, getSession, isElectron, } from '@jbrowse/core/util';
|
|
6
5
|
import { observer } from 'mobx-react';
|
|
7
6
|
import { UNKNOWN } from '@jbrowse/core/util/tracks';
|
|
8
|
-
|
|
9
|
-
import
|
|
10
|
-
import
|
|
7
|
+
import { AssemblySelector } from '@jbrowse/core/ui';
|
|
8
|
+
import TextIndexingConfig from './TextIndexingConfig';
|
|
9
|
+
import TrackTypeSelector from './TrackTypeSelector';
|
|
10
|
+
import TrackAdapterSelector from './TrackAdapterSelector';
|
|
11
11
|
const useStyles = makeStyles()(theme => ({
|
|
12
12
|
spacing: {
|
|
13
13
|
marginBottom: theme.spacing(3),
|
|
14
14
|
},
|
|
15
|
-
paper: {
|
|
16
|
-
display: 'flex',
|
|
17
|
-
flexDirection: 'column',
|
|
18
|
-
padding: theme.spacing(1),
|
|
19
|
-
},
|
|
20
|
-
spacer: {
|
|
21
|
-
height: theme.spacing(8),
|
|
22
|
-
},
|
|
23
|
-
card: {
|
|
24
|
-
marginTop: theme.spacing(1),
|
|
25
|
-
},
|
|
26
15
|
}));
|
|
27
16
|
function StatusMessage({ trackAdapter, trackType, }) {
|
|
28
|
-
var _a;
|
|
29
17
|
const { classes } = useStyles();
|
|
30
|
-
|
|
18
|
+
const { type, subadapter } = trackAdapter;
|
|
19
|
+
return type === 'SNPCoverageAdapter' ? (React.createElement(Typography, { className: classes.spacing },
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"Selected ",
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React.createElement("code", null, trackType),
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". Using adapter",
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"
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' ',
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React.createElement("code", null, (_a = trackAdapter.subadapter) === null || _a === void 0 ? void 0 : _a.type),
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". Using adapter ",
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React.createElement("code", null, type),
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" with subadapter ",
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React.createElement("code", null, subadapter === null || subadapter === void 0 ? void 0 : subadapter.type),
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". Please enter a track name and, if necessary, update the track type.")) : (React.createElement(Typography, { className: classes.spacing },
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"Using adapter ",
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React.createElement("code", null,
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React.createElement("code", null, type),
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" and guessing track type",
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' ',
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React.createElement("code", null, trackType),
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". Please enter a track name and, if necessary, update the track type."));
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}
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/**
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* categorizeAdapters takes a list of adapters and sorts their menu item elements under an appropriate ListSubheader
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* element. In this way, adapters that are from external plugins can have headers that differentiate them from the
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* out-of-the-box plugins.
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* @param adaptersList - a list of adapters found in the PluginManager
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* @returns a series of JSX elements that are ListSubheaders followed by the adapters
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* found under that subheader
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*/
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function categorizeAdapters(adaptersList) {
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let currentCategory = '';
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// eslint-disable-next-line @typescript-eslint/no-explicit-any
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const items = [];
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adaptersList.forEach(adapter => {
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var _a, _b, _c, _d, _e, _f, _g, _h;
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if ((_a = adapter.adapterMetadata) === null || _a === void 0 ? void 0 : _a.category) {
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if (currentCategory !== ((_b = adapter.adapterMetadata) === null || _b === void 0 ? void 0 : _b.category)) {
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currentCategory = (_c = adapter.adapterMetadata) === null || _c === void 0 ? void 0 : _c.category;
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items.push(React.createElement(ListSubheader, { key: (_d = adapter.adapterMetadata) === null || _d === void 0 ? void 0 : _d.category, value: (_e = adapter.adapterMetadata) === null || _e === void 0 ? void 0 : _e.category }, (_f = adapter.adapterMetadata) === null || _f === void 0 ? void 0 : _f.category));
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}
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items.push(React.createElement(MenuItem, { key: adapter.name, value: adapter.name }, ((_g = adapter.adapterMetadata) === null || _g === void 0 ? void 0 : _g.displayName)
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? (_h = adapter.adapterMetadata) === null || _h === void 0 ? void 0 : _h.displayName
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: adapter.name));
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}
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});
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return items;
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}
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function getAdapterTypes(pluginManager) {
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|
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return pluginManager.getElementTypesInGroup('adapter');
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|
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}
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function getTrackTypes(pluginManager) {
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return pluginManager.getElementTypesInGroup('track');
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|
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}
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|
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const TextIndexingConfig = observer(({ model }) => {
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const { classes } = useStyles();
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|
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const [value1, setValue1] = useState('');
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const [value2, setValue2] = useState('');
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|
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const [attributes, setAttributes] = useState(['Name', 'ID']);
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|
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const [exclude, setExclude] = useState(['CDS', 'exon']);
|
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|
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const sections = [
|
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|
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{
|
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|
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label: 'Indexing attributes',
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|
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values: attributes,
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|
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},
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|
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{
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|
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label: 'Feature types to exclude',
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values: exclude,
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|
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},
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|
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];
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|
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useEffect(() => {
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|
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model.setTextIndexingConf({ attributes, exclude });
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|
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}, [model, attributes, exclude]);
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|
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return (React.createElement(Paper, { className: classes.paper },
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|
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React.createElement(InputLabel, null, "Indexing configuration"),
|
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|
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sections.map((section, index) => (React.createElement(Card, { raised: true, key: section.label, className: classes.card },
|
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|
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React.createElement(CardContent, null,
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|
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React.createElement(InputLabel, null, section.label),
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|
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React.createElement(List, { disablePadding: true },
|
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|
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section.values.map((val, idx) => (React.createElement(ListItem, { key: idx, disableGutters: true },
|
|
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|
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React.createElement(TextField, { value: val, InputProps: {
|
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|
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endAdornment: (React.createElement(InputAdornment, { position: "end" },
|
|
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|
-
React.createElement(IconButton, { color: "secondary", onClick: () => {
|
|
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|
-
const newAttr = section.values.filter((a, i) => {
|
|
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|
-
return i !== idx;
|
|
110
|
-
});
|
|
111
|
-
index === 0
|
|
112
|
-
? setAttributes(newAttr)
|
|
113
|
-
: setExclude(newAttr);
|
|
114
|
-
} },
|
|
115
|
-
React.createElement(DeleteIcon, null)))),
|
|
116
|
-
} })))),
|
|
117
|
-
React.createElement(ListItem, { disableGutters: true },
|
|
118
|
-
React.createElement(TextField, { value: index === 0 ? value1 : value2, placeholder: "add new", onChange: event => {
|
|
119
|
-
index === 0
|
|
120
|
-
? setValue1(event.target.value)
|
|
121
|
-
: setValue2(event.target.value);
|
|
122
|
-
}, InputProps: {
|
|
123
|
-
endAdornment: (React.createElement(InputAdornment, { position: "end" },
|
|
124
|
-
React.createElement(IconButton, { onClick: () => {
|
|
125
|
-
if (index === 0) {
|
|
126
|
-
const newAttr = attributes;
|
|
127
|
-
newAttr.push(value1);
|
|
128
|
-
setAttributes(newAttr);
|
|
129
|
-
setValue1('');
|
|
130
|
-
}
|
|
131
|
-
else {
|
|
132
|
-
const newFeat = exclude;
|
|
133
|
-
newFeat.push(value2);
|
|
134
|
-
setExclude(newFeat);
|
|
135
|
-
setValue2('');
|
|
136
|
-
}
|
|
137
|
-
}, disabled: index === 0 ? value1 === '' : value2 === '', color: "secondary", "data-testid": `stringArrayAdd-Feat` },
|
|
138
|
-
React.createElement(AddIcon, null)))),
|
|
139
|
-
} })))))))));
|
|
140
|
-
});
|
|
141
|
-
const TrackAdapterSelector = observer(({ model }) => {
|
|
142
|
-
const { classes } = useStyles();
|
|
143
|
-
const { trackAdapter } = model;
|
|
144
|
-
const { pluginManager } = getEnv(model);
|
|
145
|
-
const adapters = getAdapterTypes(pluginManager);
|
|
146
|
-
return (React.createElement(TextField, { className: classes.spacing, value: (trackAdapter === null || trackAdapter === void 0 ? void 0 : trackAdapter.type) !== 'UNKNOWN' ? trackAdapter === null || trackAdapter === void 0 ? void 0 : trackAdapter.type : '', label: "adapterType", helperText: "Select an adapter type", select: true, fullWidth: true, onChange: event => model.setAdapterHint(event.target.value), SelectProps: {
|
|
147
|
-
// @ts-ignore
|
|
148
|
-
SelectDisplayProps: { 'data-testid': 'adapterTypeSelect' },
|
|
149
|
-
} },
|
|
150
|
-
adapters
|
|
151
|
-
// Excludes any adapter with the 'adapterMetadata.hiddenFromGUI' property, and anything with the 'adapterMetadata.category' property
|
|
152
|
-
.filter(elt => {
|
|
153
|
-
var _a, _b;
|
|
154
|
-
return !((_a = elt.adapterMetadata) === null || _a === void 0 ? void 0 : _a.hiddenFromGUI) &&
|
|
155
|
-
!((_b = elt.adapterMetadata) === null || _b === void 0 ? void 0 : _b.category);
|
|
156
|
-
})
|
|
157
|
-
.map(elt => {
|
|
158
|
-
var _a, _b;
|
|
159
|
-
return (React.createElement(MenuItem, { key: elt.name, value: elt.name }, ((_a = elt.adapterMetadata) === null || _a === void 0 ? void 0 : _a.displayName)
|
|
160
|
-
? (_b = elt.adapterMetadata) === null || _b === void 0 ? void 0 : _b.displayName
|
|
161
|
-
: elt.name));
|
|
162
|
-
}),
|
|
163
|
-
// adapters with the 'adapterMetadata.category' property are categorized
|
|
164
|
-
// by the value of the property here
|
|
165
|
-
categorizeAdapters(adapters.filter(elt => { var _a; return !((_a = elt.adapterMetadata) === null || _a === void 0 ? void 0 : _a.hiddenFromGUI); }))));
|
|
166
|
-
});
|
|
167
34
|
function UnknownAdapterPrompt({ model }) {
|
|
168
35
|
const { classes } = useStyles();
|
|
169
36
|
return (React.createElement(React.Fragment, null,
|
|
@@ -179,32 +46,16 @@ function UnknownAdapterPrompt({ model }) {
|
|
|
179
46
|
"and add a feature request for this data type."),
|
|
180
47
|
React.createElement(TrackAdapterSelector, { model: model })));
|
|
181
48
|
}
|
|
182
|
-
|
|
183
|
-
const { classes } = useStyles();
|
|
184
|
-
const session = getSession(model);
|
|
185
|
-
const { trackType } = model;
|
|
186
|
-
const trackTypes = getTrackTypes(getEnv(session).pluginManager);
|
|
187
|
-
return (React.createElement(TextField, { className: classes.spacing, value: trackType, label: "trackType", helperText: "Select a track type", select: true, fullWidth: true, onChange: event => {
|
|
188
|
-
model.setTrackType(event.target.value);
|
|
189
|
-
}, SelectProps: {
|
|
190
|
-
// @ts-ignore
|
|
191
|
-
SelectDisplayProps: { 'data-testid': 'trackTypeSelect' },
|
|
192
|
-
} }, trackTypes.map(({ name }) => (React.createElement(MenuItem, { key: name, value: name }, name)))));
|
|
193
|
-
});
|
|
194
|
-
const TrackAssemblySelector = observer(({ model }) => {
|
|
195
|
-
const session = getSession(model);
|
|
196
|
-
const { assembly } = model;
|
|
197
|
-
return (React.createElement(TextField, { value: assembly, label: "assemblyName", helperText: "Assembly to which the track will be added", select: true, fullWidth: true, onChange: event => model.setAssembly(event.target.value), SelectProps: {
|
|
198
|
-
// @ts-ignore
|
|
199
|
-
SelectDisplayProps: { 'data-testid': 'assemblyNameSelect' },
|
|
200
|
-
} }, session.assemblies
|
|
201
|
-
.map(conf => readConfObject(conf, 'name'))
|
|
202
|
-
.map(name => (React.createElement(MenuItem, { key: name, value: name }, name)))));
|
|
203
|
-
});
|
|
204
|
-
function ConfirmTrack({ model }) {
|
|
49
|
+
export default observer(function ConfirmTrack({ model, }) {
|
|
205
50
|
const { classes } = useStyles();
|
|
206
51
|
const [check, setCheck] = useState(true);
|
|
52
|
+
const session = getSession(model);
|
|
207
53
|
const { trackName, trackAdapter, trackType, warningMessage, adapterHint } = model;
|
|
54
|
+
useEffect(() => {
|
|
55
|
+
if (adapterHint === '' && trackAdapter) {
|
|
56
|
+
model.setAdapterHint(trackAdapter.type);
|
|
57
|
+
}
|
|
58
|
+
}, [adapterHint, trackAdapter, trackAdapter === null || trackAdapter === void 0 ? void 0 : trackAdapter.type, model]);
|
|
208
59
|
if (model.unsupported) {
|
|
209
60
|
return (React.createElement(Typography, { className: classes.spacing },
|
|
210
61
|
"This version of JBrowse cannot display data of this type. It is possible, however, that there is a newer version that can display them. You can",
|
|
@@ -220,9 +71,6 @@ function ConfirmTrack({ model }) {
|
|
|
220
71
|
if ((trackAdapter === null || trackAdapter === void 0 ? void 0 : trackAdapter.type) === UNKNOWN) {
|
|
221
72
|
return React.createElement(UnknownAdapterPrompt, { model: model });
|
|
222
73
|
}
|
|
223
|
-
if (adapterHint === '' && trackAdapter) {
|
|
224
|
-
model.setAdapterHint(trackAdapter.type);
|
|
225
|
-
}
|
|
226
74
|
if (!(trackAdapter === null || trackAdapter === void 0 ? void 0 : trackAdapter.type)) {
|
|
227
75
|
return React.createElement(Typography, null, "Could not recognize this data type.");
|
|
228
76
|
}
|
|
@@ -233,13 +81,18 @@ function ConfirmTrack({ model }) {
|
|
|
233
81
|
React.createElement(TextField, { className: classes.spacing, label: "trackName", helperText: "A name for this track", fullWidth: true, value: trackName, onChange: event => model.setTrackName(event.target.value), inputProps: { 'data-testid': 'trackNameInput' } }),
|
|
234
82
|
React.createElement(TrackAdapterSelector, { model: model }),
|
|
235
83
|
React.createElement(TrackTypeSelector, { model: model }),
|
|
236
|
-
React.createElement(
|
|
84
|
+
React.createElement(AssemblySelector, { session: session, helperText: "Select assembly to add track to", selected: model.assembly, onChange: asm => model.setAssembly(asm), TextFieldProps: {
|
|
85
|
+
fullWidth: true,
|
|
86
|
+
SelectProps: {
|
|
87
|
+
// @ts-ignore
|
|
88
|
+
SelectDisplayProps: { 'data-testid': 'assemblyNameSelect' },
|
|
89
|
+
},
|
|
90
|
+
} }),
|
|
237
91
|
isElectron && supportedForIndexing && (React.createElement(FormControl, null,
|
|
238
92
|
React.createElement(FormControlLabel, { label: 'Index track for text searching?', control: React.createElement(Checkbox, { checked: check, onChange: e => {
|
|
239
93
|
setCheck(e.target.checked);
|
|
240
94
|
model.setTextIndexTrack(e.target.checked);
|
|
241
95
|
} }) }))),
|
|
242
96
|
isElectron && check && supportedForIndexing ? (React.createElement(TextIndexingConfig, { model: model })) : null));
|
|
243
|
-
}
|
|
244
|
-
export default observer(ConfirmTrack);
|
|
97
|
+
});
|
|
245
98
|
//# sourceMappingURL=ConfirmTrack.js.map
|