@jbrowse/plugin-rdf 2.13.0 → 2.14.0

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Files changed (5) hide show
  1. package/dist/SPARQLAdapter/SPARQLAdapter.d.ts +1 -1
  2. package/dist/SPARQLAdapter/SPARQLAdapter.js +14 -25
  3. package/esm/SPARQLAdapter/SPARQLAdapter.d.ts +1 -1
  4. package/esm/SPARQLAdapter/SPARQLAdapter.js +14 -25
  5. package/package.json +3 -3
package/dist/SPARQLAdapter/SPARQLAdapter.d.ts CHANGED
@@ -2,9 +2,9 @@ import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters
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  import { NoAssemblyRegion } from '@jbrowse/core/util/types';
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  import { Feature } from '@jbrowse/core/util/simpleFeature';
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  import { Instance } from 'mobx-state-tree';
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- import MyConfigSchema from './configSchema';
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  import PluginManager from '@jbrowse/core/PluginManager';
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  import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
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+ import type MyConfigSchema from './configSchema';
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  export default class SPARQLAdapter extends BaseFeatureDataAdapter {
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  private endpoint;
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  private queryTemplate;
package/dist/SPARQLAdapter/SPARQLAdapter.js CHANGED
@@ -21,17 +21,15 @@ class SPARQLAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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  if (this.refNames) {
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  return this.refNames;
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  }
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- let refNames = [];
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  if (this.refNamesQueryTemplate) {
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  const queryTemplate = encodeURIComponent(this.refNamesQueryTemplate);
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  const results = await this.querySparql(queryTemplate, opts);
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- refNames = this.resultsToRefNames(results);
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+ this.refNames = this.resultsToRefNames(results);
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  }
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- else if (this.configRefNames) {
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- refNames = this.configRefNames;
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+ else {
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+ this.refNames = this.configRefNames;
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  }
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- this.refNames = refNames;
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- return refNames;
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+ return this.refNames;
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  }
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  getFeatures(query, opts = {}) {
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  return (0, rxjs_1.ObservableCreate)(async (observer) => {
@@ -44,7 +42,6 @@ class SPARQLAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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  observer.complete();
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  }, opts.signal);
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  }
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- // eslint-disable-next-line @typescript-eslint/no-explicit-any
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  async querySparql(query, opts) {
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  let additionalQueryParams = '';
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  if (this.additionalQueryParams.length) {
@@ -58,11 +55,7 @@ class SPARQLAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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  return response.json();
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  }
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  resultsToRefNames(response) {
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- var _a;
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- const rows = ((_a = response === null || response === void 0 ? void 0 : response.results) === null || _a === void 0 ? void 0 : _a.bindings) || [];
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- if (!rows.length) {
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- return [];
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- }
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+ const rows = response.results.bindings || [];
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  const fields = response.head.vars;
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  if (!fields.includes('refName')) {
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  throw new Error('"refName" not found in refNamesQueryTemplate response');
@@ -70,11 +63,7 @@ class SPARQLAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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  return rows.map(row => row.refName.value);
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  }
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  resultsToFeatures(results, refName) {
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- var _a;
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- const rows = ((_a = results === null || results === void 0 ? void 0 : results.results) === null || _a === void 0 ? void 0 : _a.bindings) || [];
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- if (!rows.length) {
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- return [];
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- }
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+ const rows = results.results.bindings || [];
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  const fields = results.head.vars;
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  const requiredFields = ['start', 'end', 'uniqueId'];
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  requiredFields.forEach(requiredField => {
@@ -100,18 +89,18 @@ class SPARQLAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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  }
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  });
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  rawData.forEach((rd, idx) => {
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- const { uniqueId } = rd;
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+ const { uniqueId, start, end, strand } = rd;
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  if (idx < rawData.length - 1) {
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  rawData[idx + 1].parentUniqueId = uniqueId;
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  }
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  seenFeatures[uniqueId] = {
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  data: {
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  ...rd,
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- uniqueId,
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+ uniqueId: uniqueId,
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  refName,
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- start: parseInt(rd.start, 10),
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- end: parseInt(rd.end, 10),
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- strand: parseInt(rd.strand, 10) || 0,
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+ start: Number.parseInt(start, 10),
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+ end: Number.parseInt(end, 10),
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+ strand: Number.parseInt(strand, 10) || 0,
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  },
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  };
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  });
@@ -119,7 +108,7 @@ class SPARQLAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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  // resolve subfeatures, keeping only top-level features in seenFeatures
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  for (const [uniqueId, f] of Object.entries(seenFeatures)) {
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  const pid = f.data.parentUniqueId;
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- delete f.data.parentUniqueId;
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+ f.data.parentUniqueId = undefined;
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  if (pid) {
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  const p = seenFeatures[pid];
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  if (p) {
@@ -139,7 +128,7 @@ class SPARQLAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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  .flat();
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  let found = false;
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  for (const subfeature of subfeatures) {
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- if (subfeature && subfeature.uniqueId === pid) {
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+ if (subfeature.uniqueId === pid) {
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  if (!subfeature.subfeatures) {
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  subfeature.subfeatures = [];
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  }
@@ -151,7 +140,7 @@ class SPARQLAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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  found = true;
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  break;
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  }
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- else if (subfeature === null || subfeature === void 0 ? void 0 : subfeature.subfeatures) {
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+ if (subfeature.subfeatures) {
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  subfeatures.push(...subfeature.subfeatures);
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  }
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  }
package/esm/SPARQLAdapter/SPARQLAdapter.d.ts CHANGED
@@ -2,9 +2,9 @@ import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters
2
2
  import { NoAssemblyRegion } from '@jbrowse/core/util/types';
3
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  import { Feature } from '@jbrowse/core/util/simpleFeature';
4
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  import { Instance } from 'mobx-state-tree';
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- import MyConfigSchema from './configSchema';
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  import PluginManager from '@jbrowse/core/PluginManager';
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  import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
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+ import type MyConfigSchema from './configSchema';
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  export default class SPARQLAdapter extends BaseFeatureDataAdapter {
9
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  private endpoint;
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  private queryTemplate;
package/esm/SPARQLAdapter/SPARQLAdapter.js CHANGED
@@ -16,17 +16,15 @@ export default class SPARQLAdapter extends BaseFeatureDataAdapter {
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  if (this.refNames) {
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  return this.refNames;
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  }
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- let refNames = [];
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  if (this.refNamesQueryTemplate) {
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  const queryTemplate = encodeURIComponent(this.refNamesQueryTemplate);
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  const results = await this.querySparql(queryTemplate, opts);
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- refNames = this.resultsToRefNames(results);
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+ this.refNames = this.resultsToRefNames(results);
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  }
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- else if (this.configRefNames) {
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- refNames = this.configRefNames;
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+ else {
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+ this.refNames = this.configRefNames;
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  }
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- this.refNames = refNames;
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- return refNames;
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+ return this.refNames;
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  }
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  getFeatures(query, opts = {}) {
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  return ObservableCreate(async (observer) => {
@@ -39,7 +37,6 @@ export default class SPARQLAdapter extends BaseFeatureDataAdapter {
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  observer.complete();
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  }, opts.signal);
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  }
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- // eslint-disable-next-line @typescript-eslint/no-explicit-any
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  async querySparql(query, opts) {
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  let additionalQueryParams = '';
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  if (this.additionalQueryParams.length) {
@@ -53,11 +50,7 @@ export default class SPARQLAdapter extends BaseFeatureDataAdapter {
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  return response.json();
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  }
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  resultsToRefNames(response) {
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- var _a;
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- const rows = ((_a = response === null || response === void 0 ? void 0 : response.results) === null || _a === void 0 ? void 0 : _a.bindings) || [];
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- if (!rows.length) {
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- return [];
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- }
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+ const rows = response.results.bindings || [];
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  const fields = response.head.vars;
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  if (!fields.includes('refName')) {
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  throw new Error('"refName" not found in refNamesQueryTemplate response');
@@ -65,11 +58,7 @@ export default class SPARQLAdapter extends BaseFeatureDataAdapter {
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  return rows.map(row => row.refName.value);
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  }
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  resultsToFeatures(results, refName) {
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- var _a;
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- const rows = ((_a = results === null || results === void 0 ? void 0 : results.results) === null || _a === void 0 ? void 0 : _a.bindings) || [];
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- if (!rows.length) {
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- return [];
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- }
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+ const rows = results.results.bindings || [];
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  const fields = results.head.vars;
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  const requiredFields = ['start', 'end', 'uniqueId'];
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  requiredFields.forEach(requiredField => {
@@ -95,18 +84,18 @@ export default class SPARQLAdapter extends BaseFeatureDataAdapter {
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  }
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  });
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  rawData.forEach((rd, idx) => {
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- const { uniqueId } = rd;
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+ const { uniqueId, start, end, strand } = rd;
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  if (idx < rawData.length - 1) {
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  rawData[idx + 1].parentUniqueId = uniqueId;
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  }
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  seenFeatures[uniqueId] = {
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  data: {
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  ...rd,
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- uniqueId,
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+ uniqueId: uniqueId,
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  refName,
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- start: parseInt(rd.start, 10),
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- end: parseInt(rd.end, 10),
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- strand: parseInt(rd.strand, 10) || 0,
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+ start: Number.parseInt(start, 10),
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+ end: Number.parseInt(end, 10),
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+ strand: Number.parseInt(strand, 10) || 0,
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  },
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  };
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  });
@@ -114,7 +103,7 @@ export default class SPARQLAdapter extends BaseFeatureDataAdapter {
114
103
  // resolve subfeatures, keeping only top-level features in seenFeatures
115
104
  for (const [uniqueId, f] of Object.entries(seenFeatures)) {
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  const pid = f.data.parentUniqueId;
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- delete f.data.parentUniqueId;
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+ f.data.parentUniqueId = undefined;
118
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  if (pid) {
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  const p = seenFeatures[pid];
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  if (p) {
@@ -134,7 +123,7 @@ export default class SPARQLAdapter extends BaseFeatureDataAdapter {
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  .flat();
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  let found = false;
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  for (const subfeature of subfeatures) {
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- if (subfeature && subfeature.uniqueId === pid) {
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+ if (subfeature.uniqueId === pid) {
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  if (!subfeature.subfeatures) {
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  subfeature.subfeatures = [];
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  }
@@ -146,7 +135,7 @@ export default class SPARQLAdapter extends BaseFeatureDataAdapter {
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  found = true;
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  break;
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  }
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- else if (subfeature === null || subfeature === void 0 ? void 0 : subfeature.subfeatures) {
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+ if (subfeature.subfeatures) {
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  subfeatures.push(...subfeature.subfeatures);
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  }
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  }
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
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  "name": "@jbrowse/plugin-rdf",
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- "version": "2.13.0",
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+ "version": "2.14.0",
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  "description": "JBrowse 2 RDF resources",
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  "keywords": [
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  "jbrowse",
@@ -24,7 +24,7 @@
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  ],
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  "scripts": {
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  "build": "npm-run-all build:*",
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- "test": "cd ../..; jest plugins/rdf",
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+ "test": "cd ../..; jest --passWithNoTests plugins/rdf",
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  "prepublishOnly": "yarn test",
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  "prepack": "yarn build && yarn useDist",
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  "postpack": "yarn useSrc",
@@ -51,5 +51,5 @@
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  "publishConfig": {
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  "access": "public"
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  },
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- "gitHead": "efe02fb9616e20e929cceeed46eb96420c1b6923"
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+ "gitHead": "9fb8231d932db40adf0a283081765431756c66ff"
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  }