@jbrowse/plugin-legacy-jbrowse 5.0.0-beta.13 → 5.0.0-beta.14

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Files changed (9) hide show
  1. package/esm/JBrowse1Connection/configSchema.d.ts +2 -0
  2. package/esm/JBrowse1Connection/configSchema.js +2 -0
  3. package/esm/JBrowse1Connection/jb1ToJb2.js +1 -1
  4. package/esm/JBrowse1TextSearchAdapter/JBrowse1TextSearchAdapter.js +1 -2
  5. package/esm/JBrowse1TextSearchAdapter/configSchema.d.ts +3 -1
  6. package/esm/JBrowse1TextSearchAdapter/configSchema.js +3 -1
  7. package/esm/NCListAdapter/configSchema.d.ts +2 -0
  8. package/esm/NCListAdapter/configSchema.js +3 -0
  9. package/package.json +6 -6
package/esm/JBrowse1Connection/configSchema.d.ts CHANGED
@@ -1,5 +1,7 @@
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  /**
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  * #config JBrowse1Connection
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+ * Adds the tracks of a JBrowse 1 data directory to the session, translated to
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+ * their JBrowse 2 equivalents.
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  *
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  * #example
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  * An entry in the config's `connections`, pointing at a JBrowse 1 data
package/esm/JBrowse1Connection/configSchema.js CHANGED
@@ -2,6 +2,8 @@ import { ConfigurationSchema } from '@jbrowse/core/configuration';
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  import { baseConnectionConfig } from '@jbrowse/core/pluggableElementTypes/models';
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  /**
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  * #config JBrowse1Connection
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+ * Adds the tracks of a JBrowse 1 data directory to the session, translated to
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+ * their JBrowse 2 equivalents.
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  *
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  * #example
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  * An entry in the config's `connections`, pointing at a JBrowse 1 data
package/esm/JBrowse1Connection/jb1ToJb2.js CHANGED
@@ -47,7 +47,7 @@ const NO_ADAPTER = {
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  */
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  function wiggleDisplays(jb1TrackConfig, jb2TrackConfig) {
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  const mark = jb1TrackConfig.type?.endsWith('Density')
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- ? 'heatmap'
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+ ? 'span'
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  : jb1TrackConfig.type?.endsWith('XYPlot')
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  ? 'bar'
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  : undefined;
package/esm/JBrowse1TextSearchAdapter/JBrowse1TextSearchAdapter.js CHANGED
@@ -7,8 +7,7 @@ export default class JBrowse1TextSearchAdapter extends BaseAdapter {
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  httpMap;
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  constructor(config, getSubAdapter, pluginManager) {
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  super(config, getSubAdapter, pluginManager);
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- const namesIndex = readConfObject(config, 'namesIndexLocation');
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- const { baseUri, uri } = namesIndex;
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+ const { baseUri, uri } = readConfObject(config, 'namesIndexLocation');
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  this.httpMap = new HttpMap({
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  url: baseUri ? new URL(uri, baseUri).href : uri,
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  });
package/esm/JBrowse1TextSearchAdapter/configSchema.d.ts CHANGED
@@ -2,7 +2,9 @@
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  * #config JBrowse1TextSearchAdapter
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  * #trackType TextSearchAdapter
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  * #fileFormat textsearch | JBrowse 1 names index | From JBrowse 1 `generate-names.pl`
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- * note: metadata about tracks and assemblies covered by text search adapter
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+ * Searches a names index written by JBrowse 1's `generate-names.pl`. The
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+ * `tracks` and `assemblyNames` slots list the tracks and assemblies the index
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+ * covers.
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  *
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  * #example
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  * An entry in `aggregateTextSearchAdapters`, pointing at the `names/`
package/esm/JBrowse1TextSearchAdapter/configSchema.js CHANGED
@@ -3,7 +3,9 @@ import { ConfigurationSchema } from '@jbrowse/core/configuration';
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  * #config JBrowse1TextSearchAdapter
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  * #trackType TextSearchAdapter
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  * #fileFormat textsearch | JBrowse 1 names index | From JBrowse 1 `generate-names.pl`
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- * note: metadata about tracks and assemblies covered by text search adapter
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+ * Searches a names index written by JBrowse 1's `generate-names.pl`. The
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+ * `tracks` and `assemblyNames` slots list the tracks and assemblies the index
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+ * covers.
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  *
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  * #example
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  * An entry in `aggregateTextSearchAdapters`, pointing at the `names/`
package/esm/NCListAdapter/configSchema.d.ts CHANGED
@@ -1,6 +1,8 @@
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  /**
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  * #config NCListAdapter
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  * #trackType FeatureTrack
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+ * Reads a JBrowse 1 NCList feature store, the per-reference `trackData.json`
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+ * files that the JBrowse 1 formatting scripts write.
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  *
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  * #example
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  * Reads a JBrowse 1 NCList store in place, so an existing JBrowse 1 instance's
package/esm/NCListAdapter/configSchema.js CHANGED
@@ -2,6 +2,8 @@ import { ConfigurationSchema } from '@jbrowse/core/configuration';
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  /**
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  * #config NCListAdapter
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  * #trackType FeatureTrack
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+ * Reads a JBrowse 1 NCList feature store, the per-reference `trackData.json`
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+ * files that the JBrowse 1 formatting scripts write.
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  *
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  * #example
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  * Reads a JBrowse 1 NCList store in place, so an existing JBrowse 1 instance's
@@ -40,5 +42,6 @@ const NCListAdapter = ConfigurationSchema('NCListAdapter', {
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  },
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  }, {
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  explicitlyTyped: true,
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+ closed: true,
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  });
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  export default NCListAdapter;
package/package.json CHANGED
@@ -1,6 +1,6 @@
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  {
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  "name": "@jbrowse/plugin-legacy-jbrowse",
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- "version": "5.0.0-beta.13",
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+ "version": "5.0.0-beta.14",
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  "type": "module",
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  "description": "JBrowse 2 plugin for connecting to and reading JBrowse 1 data",
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  "keywords": [
@@ -21,13 +21,13 @@
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  "esm"
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  ],
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  "dependencies": {
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- "@gmod/nclist": "^3.0.14",
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- "@jbrowse/mobx-state-tree": "^6.7.0",
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- "generic-filehandle2": "^2.5.0",
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+ "@gmod/nclist": "^3.0.15",
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+ "@jbrowse/mobx-state-tree": "^6.9.0",
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+ "generic-filehandle2": "^2.5.1",
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  "mobx": "^7.0.6",
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  "rxjs": "^7.8.2",
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- "@jbrowse/add-track-core": "^5.0.0-beta.13",
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- "@jbrowse/core": "^5.0.0-beta.13"
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+ "@jbrowse/add-track-core": "^5.0.0-beta.14",
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+ "@jbrowse/core": "^5.0.0-beta.14"
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  },
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  "peerDependencies": {
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  "react": ">=19.0.0",