@jbrowse/plugin-rdf 2.6.1

package/esm/SPARQLAdapter/SPARQLAdapter.js

@@ -0,0 +1,172 @@
+import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { ObservableCreate } from '@jbrowse/core/util/rxjs';
+import SimpleFeature from '@jbrowse/core/util/simpleFeature';
+import format from 'string-template';
+import { readConfObject } from '@jbrowse/core/configuration';
+export default class SPARQLAdapter extends BaseFeatureDataAdapter {
+    constructor(config, getSubAdapter, pluginManager) {
+        super(config, getSubAdapter, pluginManager);
+        this.endpoint = readConfObject(config, 'endpoint').uri;
+        this.queryTemplate = readConfObject(config, 'queryTemplate');
+        this.additionalQueryParams = readConfObject(config, 'additionalQueryParams');
+        this.refNamesQueryTemplate = readConfObject(config, 'refNamesQueryTemplate');
+        this.configRefNames = readConfObject(config, 'refNames');
+    }
+    async getRefNames(opts = {}) {
+        if (this.refNames) {
+            return this.refNames;
+        }
+        let refNames = [];
+        if (this.refNamesQueryTemplate) {
+            const queryTemplate = encodeURIComponent(this.refNamesQueryTemplate);
+            const results = await this.querySparql(queryTemplate, opts);
+            refNames = this.resultsToRefNames(results);
+        }
+        else if (this.configRefNames) {
+            refNames = this.configRefNames;
+        }
+        this.refNames = refNames;
+        return refNames;
+    }
+    getFeatures(query, opts = {}) {
+        return ObservableCreate(async (observer) => {
+            const filledTemplate = encodeURIComponent(format(this.queryTemplate, query));
+            const { refName } = query;
+            const results = await this.querySparql(filledTemplate, opts);
+            this.resultsToFeatures(results, refName).forEach(feature => {
+                observer.next(feature);
+            });
+            observer.complete();
+        }, opts.signal);
+    }
+    // eslint-disable-next-line @typescript-eslint/no-explicit-any
+    async querySparql(query, opts) {
+        let additionalQueryParams = '';
+        if (this.additionalQueryParams.length) {
+            additionalQueryParams = `&${this.additionalQueryParams.join('&')}`;
+        }
+        const signal = opts && opts.signal;
+        const response = await fetch(`${this.endpoint}?query=${query}${additionalQueryParams}`, {
+            headers: { accept: 'application/json,application/sparql-results+json' },
+            signal,
+        });
+        return response.json();
+    }
+    resultsToRefNames(response) {
+        const rows = ((response || {}).results || {}).bindings || [];
+        if (!rows.length) {
+            return [];
+        }
+        const fields = response.head.vars;
+        if (!fields.includes('refName')) {
+            throw new Error('"refName" not found in refNamesQueryTemplate response');
+        }
+        return rows.map(row => row.refName.value);
+    }
+    resultsToFeatures(results, refName) {
+        const rows = ((results || {}).results || {}).bindings || [];
+        if (!rows.length) {
+            return [];
+        }
+        const fields = results.head.vars;
+        const requiredFields = ['start', 'end', 'uniqueId'];
+        requiredFields.forEach(requiredField => {
+            if (!fields.includes(requiredField)) {
+                console.error(`Required field ${requiredField} missing from feature data`);
+            }
+        });
+        const seenFeatures = {};
+        rows.forEach(row => {
+            const rawData = [{}];
+            fields.forEach(field => {
+                if (field in row) {
+                    const { value } = row[field];
+                    let idx = 0;
+                    while (field.startsWith('sub_')) {
+                        field = field.slice(4);
+                        idx += 1;
+                    }
+                    while (idx > rawData.length - 1) {
+                        rawData.push({});
+                    }
+                    rawData[idx][field] = value;
+                }
+            });
+            rawData.forEach((rd, idx) => {
+                const { uniqueId } = rd;
+                if (idx < rawData.length - 1) {
+                    rawData[idx + 1].parentUniqueId = uniqueId;
+                }
+                seenFeatures[uniqueId] = {
+                    data: {
+                        ...rd,
+                        uniqueId,
+                        refName,
+                        start: parseInt(rd.start, 10),
+                        end: parseInt(rd.end, 10),
+                        strand: parseInt(rd.strand, 10) || 0,
+                    },
+                };
+            });
+        });
+        // resolve subfeatures, keeping only top-level features in seenFeatures
+        for (const [uniqueId, f] of Object.entries(seenFeatures)) {
+            const pid = f.data.parentUniqueId;
+            delete f.data.parentUniqueId;
+            if (pid) {
+                const p = seenFeatures[pid];
+                if (p) {
+                    if (!p.data.subfeatures) {
+                        p.data.subfeatures = [];
+                    }
+                    p.data.subfeatures.push({
+                        ...f.data,
+                        uniqueId,
+                    });
+                    delete seenFeatures[uniqueId];
+                }
+                else {
+                    const subfeatures = Object.values(seenFeatures)
+                        .map(sf => sf.data.subfeatures)
+                        .filter(sf => !!sf)
+                        .flat();
+                    let found = false;
+                    for (const subfeature of subfeatures) {
+                        if (subfeature && subfeature.uniqueId === pid) {
+                            if (!subfeature.subfeatures) {
+                                subfeature.subfeatures = [];
+                            }
+                            subfeature.subfeatures.push({
+                                ...f.data,
+                                uniqueId,
+                            });
+                            delete seenFeatures[uniqueId];
+                            found = true;
+                            break;
+                        }
+                        else if (subfeature && subfeature.subfeatures) {
+                            subfeatures.push(...subfeature.subfeatures);
+                        }
+                    }
+                    if (!found) {
+                        console.error(`Could not find parentID ${pid}`);
+                    }
+                }
+            }
+        }
+        return Object.keys(seenFeatures).map(seenFeature => new SimpleFeature({
+            ...seenFeatures[seenFeature].data,
+            uniqueId: seenFeature,
+            subfeatures: seenFeatures[seenFeature].data.subfeatures,
+        }));
+    }
+    async hasDataForRefName(refName, opts = {}) {
+        const refNames = await this.getRefNames(opts);
+        if (refNames.length && !refNames.includes(refName)) {
+            return false;
+        }
+        return true;
+    }
+    freeResources( /* { region } */) { }
+}
+//# sourceMappingURL=SPARQLAdapter.js.map

package/esm/SPARQLAdapter/SPARQLAdapter.js.map

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package/esm/SPARQLAdapter/configSchema.d.ts

@@ -0,0 +1,31 @@
+declare const _default: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    endpoint: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+        description: string;
+    };
+    queryTemplate: {
+        type: string;
+        defaultValue: string;
+        description: string;
+    };
+    refNamesQueryTemplate: {
+        type: string;
+        defaultValue: string;
+        description: string;
+    };
+    refNames: {
+        type: string;
+        defaultValue: never[];
+        description: string;
+    };
+    additionalQueryParams: {
+        type: string;
+        defaultValue: never[];
+        description: string;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+export default _default;

package/esm/SPARQLAdapter/configSchema.js

@@ -0,0 +1,32 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+export default ConfigurationSchema('SPARQLAdapter', {
+    endpoint: {
+        type: 'fileLocation',
+        defaultValue: {
+            uri: 'https://somesite.com/sparql',
+            locationType: 'UriLocation',
+        },
+        description: 'URL of the SPARQL endpoint',
+    },
+    queryTemplate: {
+        type: 'text',
+        defaultValue: '',
+        description: 'SPARQL query where {start} {end} and {refName} will get replaced for each call',
+    },
+    refNamesQueryTemplate: {
+        type: 'text',
+        defaultValue: '',
+        description: 'SPARQL query that returns the possible refNames in a ?refName column',
+    },
+    refNames: {
+        type: 'stringArray',
+        defaultValue: [],
+        description: 'Possible refNames used by the SPARQL endpoint (ignored if "refNamesQueryTemplate" is provided)',
+    },
+    additionalQueryParams: {
+        type: 'stringArray',
+        defaultValue: [],
+        description: 'Additional parameters to add to the query, e.g. "format=JSON"',
+    },
+}, { explicitlyTyped: true });
+//# sourceMappingURL=configSchema.js.map

package/esm/SPARQLAdapter/configSchema.js.map

@@ -0,0 +1 @@
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package/esm/SPARQLAdapter/index.d.ts

@@ -0,0 +1,2 @@
+export { default as AdapterClass } from './SPARQLAdapter';
+export { default as configSchema } from './configSchema';

package/esm/SPARQLAdapter/index.js

@@ -0,0 +1,3 @@
+export { default as AdapterClass } from './SPARQLAdapter';
+export { default as configSchema } from './configSchema';
+//# sourceMappingURL=index.js.map

package/esm/SPARQLAdapter/index.js.map

@@ -0,0 +1 @@
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package/esm/index.d.ts

@@ -0,0 +1,6 @@
+import Plugin from '@jbrowse/core/Plugin';
+import PluginManager from '@jbrowse/core/PluginManager';
+export default class RdfPlugin extends Plugin {
+    name: string;
+    install(pluginManager: PluginManager): void;
+}

package/esm/index.js

@@ -0,0 +1,33 @@
+import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
+import Plugin from '@jbrowse/core/Plugin';
+import { AdapterClass as SPARQLAdapterClass, configSchema as sparqlAdapterConfigSchema, } from './SPARQLAdapter';
+import { getFileName } from '@jbrowse/core/util/tracks';
+export default class RdfPlugin extends Plugin {
+    constructor() {
+        super(...arguments);
+        this.name = 'RdfPlugin';
+    }
+    install(pluginManager) {
+        pluginManager.addAdapterType(() => new AdapterType({
+            name: 'SPARQLAdapter',
+            displayName: 'SPARQL adapter',
+            configSchema: sparqlAdapterConfigSchema,
+            AdapterClass: SPARQLAdapterClass,
+        }));
+        pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
+            return (file, index, adapterHint) => {
+                const regexGuess = /\/sparql$/i;
+                const adapterName = 'SPARQLAdapter';
+                const fileName = getFileName(file);
+                if (regexGuess.test(fileName) || adapterHint === adapterName) {
+                    return {
+                        type: adapterName,
+                        endpoint: file,
+                    };
+                }
+                return adapterGuesser(file, index, adapterHint);
+            };
+        });
+    }
+}
+//# sourceMappingURL=index.js.map

package/esm/index.js.map

@@ -0,0 +1 @@
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package/package.json

@@ -0,0 +1,56 @@
+{
+  "name": "@jbrowse/plugin-rdf",
+  "version": "2.6.1",
+  "description": "JBrowse 2 RDF resources",
+  "keywords": [
+    "jbrowse",
+    "jbrowse2"
+  ],
+  "license": "Apache-2.0",
+  "homepage": "https://jbrowse.org",
+  "bugs": "https://github.com/GMOD/jbrowse-components/issues",
+  "repository": {
+    "type": "git",
+    "url": "https://github.com/GMOD/jbrowse-components.git",
+    "directory": "plugins/rdf"
+  },
+  "author": "JBrowse Team",
+  "distMain": "dist/index.js",
+  "srcMain": "src/index.ts",
+  "main": "dist/index.js",
+  "files": [
+    "dist",
+    "src",
+    "esm"
+  ],
+  "scripts": {
+    "build": "npm-run-all build:*",
+    "test": "cd ../..; jest plugins/rdf",
+    "prepublishOnly": "yarn test",
+    "prepack": "yarn build && yarn useDist",
+    "postpack": "yarn useSrc",
+    "useDist": "node ../../scripts/useDist.js",
+    "useSrc": "node ../../scripts/useSrc.js",
+    "prebuild": "npm run clean",
+    "build:esm": "tsc --build tsconfig.build.esm.json",
+    "build:es5": "tsc --build tsconfig.build.es5.json",
+    "clean": "rimraf dist esm *.tsbuildinfo"
+  },
+  "dependencies": {
+    "string-template": "^1.0.0"
+  },
+  "peerDependencies": {
+    "@jbrowse/core": "^2.0.0",
+    "mobx": "^6.0.0",
+    "mobx-react": "^7.0.0",
+    "mobx-state-tree": "^5.0.0",
+    "rxjs": "^7.0.0"
+  },
+  "distModule": "esm/index.js",
+  "srcModule": "src/index.ts",
+  "module": "esm/index.js",
+  "publishConfig": {
+    "access": "public"
+  },
+  "gitHead": "1cbe7ba097fb2d2763c776e5e429e4670cdd583c"
+}

package/src/SPARQLAdapter/README.md

@@ -0,0 +1,115 @@
+# SPARQL Adapter
+
+JBrowse can display genomic information stored in RDF data stores by accessing
+them via a SPARQL endpoint. This is done by configuring a SPARQL adapter.
+
+## Query template
+
+The most basic configuration starts with a SPARQL query that returns features in
+a genomic range, i.e. on a particular chromosome/contig and between a start and
+end position. In such a query, replace the chromosome/contig name with
+`{refName}` and the start and end with `{start}` and `{end}`. For example
+
+```sparql
+PREFIX  rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX  rdf:  <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX  faldo: <http://biohackathon.org/resource/faldo#>
+PREFIX  dc:   <http://purl.org/dc/elements/1.1/>
+
+SELECT DISTINCT  ?gene (?id AS ?uniqueId) (?label AS ?name) (?desc AS ?note) ?strand ?start ?end
+WHERE
+  { VALUES ?location_type { faldo:ForwardStrandPosition faldo:ReverseStrandPosition faldo:BothStrandsPosition }
+    ?location  faldo:begin     _:b0 .
+    _:b0      rdf:type         ?location_type ;
+              faldo:position   ?faldo_begin .
+    ?location  faldo:end       _:b1 .
+    _:b1      rdf:type         ?location_type ;
+              faldo:position   ?faldo_end .
+    ?location  faldo:reference  <http://rdf.ebi.ac.uk/resource/ensembl/97/homo_sapiens/GRCh38/{refName}> .
+    ?gene     rdf:type         ?type ;
+              rdfs:label       ?label ;
+              dc:description   ?desc ;
+              dc:identifier    ?id ;
+              faldo:location   ?location
+    BIND(if(( ?location_type = faldo:ForwardStrandPosition ), 1, if(( ?location_type = faldo:ReverseStrandPosition ), -1, 0)) AS ?strand)
+    BIND(if(( ?strand = -1 ), ?faldo_end, ?faldo_begin) AS ?start)
+    BIND(if(( ?strand = -1 ), ?faldo_begin, ?faldo_end) AS ?end)
+    FILTER ( ( ?start >= {start} ) && ( ?end <= {end} ) )
+  }
+```
+
+The SELECT in the the query must provide at least the variables `?start`,
+`?end`, and `?uniqueId`. Any other variables will be added to the feature data.
+
+## Adding a track
+
+From a JBrowse track selector, click the "+" icon and choose "Add track". When
+asked for the location of the data source, enter the SPARQL endpoint. If the
+endpoint ends with `/sparql`, JBrowse will automatically choose the SPARQL
+adapter. If not, choose "SPARQL adapter" in the resulting dialog. (You can use
+https://www.ebi.ac.uk/rdf/services/sparql as the endpoint to demonstrate the
+above example.)
+
+You will then be able to choose a track name and type as well as the assembly to
+which the track should be added. BasicTrack is suggested for most
+configurations, and using other track types is covered below. Click the "Add"
+button to add the track.
+
+Next, in the track selector click the settings icon next to the track which was
+just added. Paste the query template (see above) in the "queryTemplate" section.
+You can also configure other aspects of the track such as a description,
+category, etc.
+
+## Advanced configuration
+
+### Subfeatures
+
+There are two ways to provide subfeature information. The first is to include a
+`?parentUniqueId` variable with a feature. It will be created as a subfeature of
+the feature with a matching `?uniqueId`.
+
+The second way is useful if a single query response line contains information
+for more than one feature, e.g. gene, transcript, and exon information on a
+single line. For this type of data prefix all variables for the subfeature with
+`sub_`, which will allow you to define multiple features from the same line. It
+also works for deeper nested features, too, by using `sub_sub_`, etc. Parent
+features that are duplicated across lines will be resolved into a single
+feature. For example, take the following SPARQL query result lines:
+
+| uniqueId   | type | start    | end      | sub_uniqueId     | sub_type   | sub_start | sub_end  | sub_sub_uniqueId | sub_sub_type | sub_sub_start | sub_sub_end |
+| ---------- | ---- | -------- | -------- | ---------------- | ---------- | --------- | -------- | ---------------- | ------------ | ------------- | ----------- |
+| geneId0001 | gene | 10430102 | 10452003 | transcriptId0001 | transcript | 10430518  | 10442405 | exonId0001       | exon         | 10430518      | 10430568    |
+| geneId0001 | gene | 10430102 | 10452003 | transcriptId0001 | transcript | 10430518  | 10442405 | exonId0002       | exon         | 10432568      | 10433965    |
+
+These two lines will resolve into a singe feature "geneId0001" with one child
+feature "transcriptId0001", which will then itself have two child features
+"exonId0001" and "exonId0002".
+
+### Additional query parameters
+
+JBrowse will automatically send a header stating that it expects responses to be
+in the `application/json` or `application/sparql-results+json` format. Some
+SPARQL endpoints, however, require additional query parameters to be passed in
+order for the results be returned in JSON format, for example `format=json`.
+These can be added to the "additionalQueryParams" section and will be appended
+to each SPARQL request.
+
+### Reference sequence renaming
+
+In order for the track to take advantage of JBrowse's reference name aliasing,
+it must know what reference name the SPARQL store uses. These can be entered in
+one of two ways. The first is by entering a SPARQL query in the
+"refNamesQueryTemplate" config section. This query should return a line for each
+reference name in a `refName` column.
+
+The second option is to enumerate the reference names explicitly in the
+"refNames" config section. These will be ignored if a "refNamesQueryTemplate" is
+defined.
+
+### Other track types
+
+BasicTracks are flexible because they don't require any additional information,
+any any additional info provided in the query is just added to the feature. You
+can use other tracks as well, though, as long as you make sure the SPARQL query
+provides any info the track requires. For example, if you want to use a
+VariantTrack, the SPARQL query must provide REF, ALT, QUAL, etc.

package/src/SPARQLAdapter/SPARQLAdapter.test.ts

@@ -0,0 +1,84 @@
+import { toArray } from 'rxjs/operators'
+import 'whatwg-fetch'
+import Adapter from './SPARQLAdapter'
+import emptyQueryResponse from './test_data/emptyQueryResponse.json'
+import queryResponse from './test_data/queryResponse.json'
+import refNamesResponse from './test_data/refNamesResponse.json'
+
+import configSchema from './configSchema'
+
+// window.fetch = jest.fn(url => new Promise(resolve => resolve()))
+
+test('adapter can fetch variants from volvox.vcf.gz', async () => {
+  function mockFetch(url: RequestInfo | URL) {
+    let response = {}
+    if (`${url}`.includes('chr1')) {
+      response = queryResponse
+    }
+    if (`${url}`.includes('chr80')) {
+      response = emptyQueryResponse
+    } else if (`${url}`.includes('fakeRefNamesQuery')) {
+      response = refNamesResponse
+    }
+
+    return Promise.resolve(new Response(JSON.stringify(response)))
+  }
+
+  const spy = jest.spyOn(global, 'fetch')
+  spy.mockImplementation(mockFetch)
+  const adapter = new Adapter(
+    configSchema.create({
+      endpoint: {
+        uri: 'http://somesite.com/sparql',
+        locationType: 'UriLocation',
+      },
+      queryTemplate: 'fakeSPARQLQuery-start{start}-end{end}-{refName}',
+      refNamesQueryTemplate: 'fakeRefNamesQuery',
+      additionalQueryParams: ['format=json'],
+      refNames: [],
+    }),
+  )
+
+  const refNames = await adapter.getRefNames()
+  expect(spy).toHaveBeenLastCalledWith(
+    'http://somesite.com/sparql?query=fakeRefNamesQuery&format=json',
+    {
+      headers: { accept: 'application/json,application/sparql-results+json' },
+      signal: undefined,
+    },
+  )
+  expect(refNames.length).toBe(17)
+  expect(refNames[0]).toBe('NC_004353.4')
+
+  const features = adapter.getFeatures({
+    refName: 'chr1',
+    start: 0,
+    end: 20000,
+  })
+  const featuresArray = await features.pipe(toArray()).toPromise()
+  expect(featuresArray).toMatchSnapshot()
+  expect(spy).toHaveBeenLastCalledWith(
+    'http://somesite.com/sparql?query=fakeSPARQLQuery-start0-end20000-chr1&format=json',
+    {
+      headers: { accept: 'application/json,application/sparql-results+json' },
+      signal: undefined,
+    },
+  )
+
+  const featuresNonExist = adapter.getFeatures({
+    refName: 'chr80',
+    start: 0,
+    end: 20000,
+  })
+  const featuresArrayNonExist = await featuresNonExist
+    .pipe(toArray())
+    .toPromise()
+  expect(featuresArrayNonExist).toEqual([])
+  expect(spy).toHaveBeenLastCalledWith(
+    'http://somesite.com/sparql?query=fakeSPARQLQuery-start0-end20000-chr80&format=json',
+    {
+      headers: { accept: 'application/json,application/sparql-results+json' },
+      signal: undefined,
+    },
+  )
+})