@jbrowse/plugin-data-management 3.1.0 → 3.2.0

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Files changed (11) hide show
  1. package/dist/AddTrackWidget/components/PasteConfigWorkflow.js +4 -4
  2. package/dist/HierarchicalTrackSelectorWidget/components/ShoppingCart.d.ts +5 -2
  3. package/dist/HierarchicalTrackSelectorWidget/components/ShoppingCart.js +4 -1
  4. package/dist/UCSCTrackHub/configSchema.js +11 -0
  5. package/dist/UCSCTrackHub/doConnect.js +10 -0
  6. package/esm/AddTrackWidget/components/PasteConfigWorkflow.js +4 -4
  7. package/esm/HierarchicalTrackSelectorWidget/components/ShoppingCart.d.ts +5 -2
  8. package/esm/HierarchicalTrackSelectorWidget/components/ShoppingCart.js +4 -1
  9. package/esm/UCSCTrackHub/configSchema.js +11 -0
  10. package/esm/UCSCTrackHub/doConnect.js +10 -0
  11. package/package.json +5 -5
package/dist/AddTrackWidget/components/PasteConfigWorkflow.js CHANGED
@@ -33,12 +33,12 @@ const PasteConfigAddTrackWorkflow = (0, mobx_react_1.observer)(function ({ model
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  if ((0, util_1.isSessionWithAddTracks)(session) &&
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  (0, util_1.isSessionModelWithWidgets)(session)) {
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  (0, mobx_1.transaction)(() => {
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- confs.forEach(c => {
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+ for (const c of confs) {
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  session.addTrackConf(c);
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- });
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- confs.forEach(c => {
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+ }
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+ for (const c of confs) {
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  model.view.showTrack(c.trackId);
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- });
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+ }
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  model.clearData();
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  });
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  session.hideWidget(model);
package/dist/HierarchicalTrackSelectorWidget/components/ShoppingCart.d.ts CHANGED
@@ -1,5 +1,8 @@
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- import type { HierarchicalTrackSelectorModel } from '../model';
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+ import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
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  declare const ShoppingCart: ({ model, }: {
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- model: HierarchicalTrackSelectorModel;
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+ model: {
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+ clearSelection: () => void;
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+ selection: AnyConfigurationModel[];
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+ };
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  }) => import("react/jsx-runtime").JSX.Element | null;
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  export default ShoppingCart;
package/dist/HierarchicalTrackSelectorWidget/components/ShoppingCart.js CHANGED
@@ -29,7 +29,10 @@ const ShoppingCart = (0, mobx_react_1.observer)(function ({ model, }) {
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  {
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  label: 'Delete tracks',
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  onClick: () => {
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- selection.forEach(s => { var _a; return (_a = session.deleteTrackConf) === null || _a === void 0 ? void 0 : _a.call(session, s); });
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+ var _a;
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+ for (const s of selection) {
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+ (_a = session.deleteTrackConf) === null || _a === void 0 ? void 0 : _a.call(session, s);
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+ }
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  },
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  },
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  ]
package/dist/UCSCTrackHub/configSchema.js CHANGED
@@ -19,5 +19,16 @@ const UCSCTrackHubConnection = (0, configuration_1.ConfigurationSchema)('UCSCTra
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  },
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  }, {
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  baseConfiguration: models_1.baseConnectionConfig,
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+ preProcessSnapshot: snap => {
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+ return snap.uri
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+ ? {
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+ ...snap,
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+ hubTxtLocation: {
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+ uri: snap.uri,
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+ baseUri: snap.baseUri,
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+ },
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+ }
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+ : snap;
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+ },
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  });
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  exports.default = UCSCTrackHubConnection;
package/dist/UCSCTrackHub/doConnect.js CHANGED
@@ -49,6 +49,16 @@ async function doConnect(self) {
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  },
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  },
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  },
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+ ...(genome.data.chromAliasBb
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+ ? {
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+ refNameAliases: {
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+ adapter: {
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+ type: 'BigBedAdapter',
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+ uri: (0, util_2.resolve)(genome.data.chromAliasBb, hubUri),
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+ },
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+ },
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+ }
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+ : {}),
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  });
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  }
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  const asm2 = assemblyManager.get(genomeName);
package/esm/AddTrackWidget/components/PasteConfigWorkflow.js CHANGED
@@ -31,12 +31,12 @@ const PasteConfigAddTrackWorkflow = observer(function ({ model, }) {
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  if (isSessionWithAddTracks(session) &&
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  isSessionModelWithWidgets(session)) {
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  transaction(() => {
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- confs.forEach(c => {
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+ for (const c of confs) {
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  session.addTrackConf(c);
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- });
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- confs.forEach(c => {
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+ }
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+ for (const c of confs) {
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  model.view.showTrack(c.trackId);
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- });
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+ }
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  model.clearData();
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  });
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  session.hideWidget(model);
package/esm/HierarchicalTrackSelectorWidget/components/ShoppingCart.d.ts CHANGED
@@ -1,5 +1,8 @@
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- import type { HierarchicalTrackSelectorModel } from '../model';
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+ import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
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  declare const ShoppingCart: ({ model, }: {
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- model: HierarchicalTrackSelectorModel;
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+ model: {
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+ clearSelection: () => void;
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+ selection: AnyConfigurationModel[];
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+ };
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  }) => import("react/jsx-runtime").JSX.Element | null;
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  export default ShoppingCart;
package/esm/HierarchicalTrackSelectorWidget/components/ShoppingCart.js CHANGED
@@ -24,7 +24,10 @@ const ShoppingCart = observer(function ({ model, }) {
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  {
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  label: 'Delete tracks',
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  onClick: () => {
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- selection.forEach(s => { var _a; return (_a = session.deleteTrackConf) === null || _a === void 0 ? void 0 : _a.call(session, s); });
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+ var _a;
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+ for (const s of selection) {
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+ (_a = session.deleteTrackConf) === null || _a === void 0 ? void 0 : _a.call(session, s);
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+ }
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  },
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  },
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  ]
package/esm/UCSCTrackHub/configSchema.js CHANGED
@@ -17,5 +17,16 @@ const UCSCTrackHubConnection = ConfigurationSchema('UCSCTrackHubConnection', {
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  },
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  }, {
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  baseConfiguration: baseConnectionConfig,
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+ preProcessSnapshot: snap => {
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+ return snap.uri
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+ ? {
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+ ...snap,
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+ hubTxtLocation: {
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+ uri: snap.uri,
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+ baseUri: snap.baseUri,
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+ },
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+ }
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+ : snap;
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+ },
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  });
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  export default UCSCTrackHubConnection;
package/esm/UCSCTrackHub/doConnect.js CHANGED
@@ -46,6 +46,16 @@ export async function doConnect(self) {
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  },
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  },
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  },
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+ ...(genome.data.chromAliasBb
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+ ? {
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+ refNameAliases: {
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+ adapter: {
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+ type: 'BigBedAdapter',
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+ uri: resolve(genome.data.chromAliasBb, hubUri),
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+ },
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+ },
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+ }
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+ : {}),
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  });
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  }
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  const asm2 = assemblyManager.get(genomeName);
package/package.json CHANGED
@@ -1,6 +1,6 @@
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  {
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  "name": "@jbrowse/plugin-data-management",
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- "version": "3.1.0",
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+ "version": "3.2.0",
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  "description": "JBrowse 2 linear genome view",
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  "keywords": [
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  "jbrowse",
@@ -37,9 +37,9 @@
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  },
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  "dependencies": {
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  "@gmod/ucsc-hub": "^1.0.0",
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- "@jbrowse/core": "^3.1.0",
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- "@jbrowse/plugin-config": "^3.1.0",
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- "@jbrowse/product-core": "^3.1.0",
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+ "@jbrowse/core": "^3.2.0",
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+ "@jbrowse/plugin-config": "^3.2.0",
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+ "@jbrowse/product-core": "^3.2.0",
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  "@mui/icons-material": "^6.0.0",
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  "@mui/material": "^6.0.0",
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  "@mui/x-data-grid": "^7.0.0",
@@ -61,5 +61,5 @@
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  "distModule": "esm/index.js",
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  "srcModule": "src/index.ts",
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  "module": "esm/index.js",
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- "gitHead": "91492049ddea0aed90eb24d3c066c2d9f5a6b189"
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+ "gitHead": "c750e3f56706a490c19ba75abd807fec5e38aebf"
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  }