@jbrowse/plugin-rdf 5.0.0-beta.8 → 5.0.0-beta.9

package/esm/SPARQLAdapter/SPARQLAdapter.js

@@ -1,8 +1,8 @@
 import { readConfObject } from '@jbrowse/core/configuration';
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { checkAbortSignal } from '@jbrowse/core/util/aborting';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import SimpleFeature from '@jbrowse/core/util/simpleFeature';
-import { checkStopToken } from '@jbrowse/core/util/stopToken';
 // fill `{name}` placeholders from data; `{{name}}` is an escaped literal.
 // replaces the `string-template` dependency
 const templateRegex = /\{([0-9a-zA-Z_]+)\}/g;
@@ -51,14 +51,14 @@ export default class SPARQLAdapter extends BaseFeatureDataAdapter {
                 observer.next(feature);
             }
             observer.complete();
-        }, opts.stopToken);
+        }, opts.signal);
     }
     async querySparql(query, opts) {
         let additionalQueryParams = '';
         if (this.additionalQueryParams.length) {
             additionalQueryParams = `&${this.additionalQueryParams.join('&')}`;
         }
-        checkStopToken(opts?.stopToken);
+        checkAbortSignal(opts?.signal);
         const url = `${this.endpoint}?query=${query}${additionalQueryParams}`;
         const response = await fetch(url, {
             headers: {
@@ -68,7 +68,7 @@ export default class SPARQLAdapter extends BaseFeatureDataAdapter {
         if (!response.ok) {
             throw new Error(`SPARQL query failed: ${response.status} ${response.statusText}`);
         }
-        checkStopToken(opts?.stopToken);
+        checkAbortSignal(opts?.signal);
         return response.json();
     }
     resultsToRefNames(response) {

package/esm/SPARQLAdapter/configSchema.d.ts

@@ -24,49 +24,36 @@ import type { Instance } from '@jbrowse/mobx-state-tree';
  * ```
  */
 declare const SPARQLAdapterConfigSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
+    type: {
+        type: "string";
+    } & {
+        defaultValue: string;
+    };
     readonly endpoint: {
-        readonly type: "fileLocation";
-        readonly defaultValue: {
-            readonly uri: "https://somesite.com/sparql";
-            readonly locationType: "UriLocation";
-        };
-        readonly description: "URL of the SPARQL endpoint";
+        type: "fileLocation";
+    } & {
+        defaultValue: unknown;
     };
-    /**
-     * #slot
-     */
     readonly queryTemplate: {
-        readonly type: "text";
-        readonly defaultValue: "";
-        readonly description: "SPARQL query where {start} {end} and {refName} will get replaced for each call";
+        type: "text";
+    } & {
+        defaultValue: string;
     };
-    /**
-     * #slot
-     */
     readonly refNamesQueryTemplate: {
-        readonly type: "text";
-        readonly defaultValue: "";
-        readonly description: "SPARQL query that returns the possible refNames in a ?refName column";
+        type: "text";
+    } & {
+        defaultValue: string;
     };
-    /**
-     * #slot
-     */
     readonly refNames: {
-        readonly type: "stringArray";
-        readonly defaultValue: readonly [];
-        readonly description: "Possible refNames used by the SPARQL endpoint (ignored if \"refNamesQueryTemplate\" is provided)";
+        type: "stringArray";
+    } & {
+        defaultValue: unknown;
     };
-    /**
-     * #slot
-     */
     readonly additionalQueryParams: {
-        readonly type: "stringArray";
-        readonly defaultValue: readonly [];
-        readonly description: "Additional parameters to add to the query, e.g. \"format=JSON\"";
+        type: "stringArray";
+    } & {
+        defaultValue: unknown;
     };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, true, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>>>;
 export default SPARQLAdapterConfigSchema;
 export type SPARQLAdapterConfig = Instance<typeof SPARQLAdapterConfigSchema>;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-rdf",
-  "version": "5.0.0-beta.8",
+  "version": "5.0.0-beta.9",
   "type": "module",
   "description": "JBrowse 2 RDF resources",
   "keywords": [
@@ -21,10 +21,10 @@
     "esm"
   ],
   "dependencies": {
-    "@jbrowse/mobx-state-tree": "^6.5.1",
+    "@jbrowse/mobx-state-tree": "^6.5.2",
     "mobx": "^7.0.3",
     "rxjs": "^7.8.2",
-    "@jbrowse/core": "^5.0.0-beta.8"
+    "@jbrowse/core": "^5.0.0-beta.9"
   },
   "publishConfig": {
     "access": "public"