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Fix RDF neighbor expansion (#870)
* Move parseEdgeId logic * Fix sparql neighbor expansion * Fix limit * Update changelog * Update comments * Performance and readability * Remove drafts * Remove need for indentLinesBeyondFirst * Add unit tests for more scenarios * Fix trailing space in queries * Update helpers * Move getLimit up to common area * Use getLimit in more places
1 parent 91bd960 commit 01daa72

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+1078
-290
lines changed

‎Changelog.md‎

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@@ -27,6 +27,8 @@
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([#828](https://github.com/aws/graph-explorer/pull/828))
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- **Updated** namespaces sidebar to use tabs instead of dropdown
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([#830](https://github.com/aws/graph-explorer/pull/830))
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- **Fixed** issues with filtered neighbor expansion and neighbor counts in RDF
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databases ([#870](https://github.com/aws/graph-explorer/pull/870))
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- **Fixed** issue with table exports
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([#860](https://github.com/aws/graph-explorer/pull/860))
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- **Fixed** issue with long node titles or descriptions pushing the "add to

‎packages/graph-explorer/src/connector/sparql/edgeDetails.ts‎

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@@ -1,7 +1,6 @@
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import { createEdge } from "@/core";
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import { EdgeDetailsRequest, EdgeDetailsResponse } from "../useGEFetchTypes";
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import {
4-
parseEdgeId,
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SparqlFetch,
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sparqlResponseSchema,
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sparqlUriValueSchema,
@@ -10,6 +9,7 @@ import { logger, query } from "@/utils";
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import { z } from "zod";
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import isErrorResponse from "../utils/isErrorResponse";
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import { idParam } from "./idParam";
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import { parseEdgeId } from "./parseEdgeId";
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const responseSchema = sparqlResponseSchema(
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z.object({

‎packages/graph-explorer/src/connector/sparql/fetchNeighbors/helpers.test.ts‎

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@@ -0,0 +1,62 @@
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import { query } from "@/utils";
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import { getFilters, getSubjectClasses } from "./helpers";
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import { normalizeWithNewlines as normalize } from "@/utils/testing";
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describe("getSubjectClasses", () => {
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it("should return empty string if no subject classes", () => {
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const result = getSubjectClasses([]);
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expect(result).toEqual("");
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});
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it("should create values with one class", () => {
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const result = getSubjectClasses(["http://example.org/class"]);
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expect(result).toEqual(
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`VALUES ?subjectClass { <http://example.org/class> }`
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);
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});
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18+
it("should create values with multiple classes", () => {
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const result = getSubjectClasses([
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"http://example.org/class1",
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"http://example.org/class2",
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]);
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expect(result).toEqual(
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`VALUES ?subjectClass { <http://example.org/class1> <http://example.org/class2> }`
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);
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});
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});
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describe("getFilters", () => {
30+
it("should return empty string if no filters", () => {
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const result = getFilters([]);
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expect(normalize(result)).toEqual("");
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});
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35+
it("should create filter with one criteria", () => {
36+
const result = getFilters([
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{ predicate: "http://example.org/predicate", object: "value" },
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]);
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expect(normalize(result)).toEqual(
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normalize(query`
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FILTER (
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(?sPred=<http://example.org/predicate> && regex(str(?sValue), "value", "i"))
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)
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`)
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);
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});
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48+
it("should create filter with multiple criteria", () => {
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const result = getFilters([
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{ predicate: "http://example.org/predicate", object: "value" },
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{ predicate: "http://example.org/predicate2", object: "value2" },
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]);
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expect(normalize(result)).toEqual(
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normalize(query`
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FILTER (
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(?sPred=<http://example.org/predicate> && regex(str(?sValue), "value", "i")) ||
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(?sPred=<http://example.org/predicate2> && regex(str(?sValue), "value2", "i"))
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)
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`)
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);
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});
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});

‎packages/graph-explorer/src/connector/sparql/fetchNeighbors/helpers.ts‎

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Original file line numberDiff line numberDiff line change
@@ -1,6 +1,7 @@
11
import { SPARQLCriterion } from "../types";
2+
import { query } from "@/utils";
23

3-
export const getSubjectClasses = (subjectClasses: string[]) => {
4+
export function getSubjectClasses(subjectClasses: string[]) {
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if (!subjectClasses?.length) {
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return "";
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}
@@ -11,28 +12,23 @@ export const getSubjectClasses = (subjectClasses: string[]) => {
1112
});
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classesValues += " }";
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return classesValues;
14-
};
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}
1516

16-
export const getFilters = (filterCriteria: SPARQLCriterion[]) => {
17+
export function getFilters(filterCriteria: SPARQLCriterion[]) {
1718
if (!filterCriteria?.length) {
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return "";
1920
}
2021

21-
let filter = "FILTER(";
22-
filterCriteria.forEach((criterion, cI) => {
23-
filter += `(?sPred=<${criterion.predicate}> && regex(str(?sValue), "${criterion.object}", "i"))`;
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const filtersTemplate = filterCriteria
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.map(
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c =>
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`(?sPred=<${c.predicate}> && regex(str(?sValue), "${c.object}", "i"))`
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)
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.join(" ||\n");
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25-
if (cI < filterCriteria.length - 1) {
26-
filter += " || ";
27-
}
28-
});
29-
filter += ")";
30-
return filter;
31-
};
32-
33-
export const getLimit = (limit?: number, offset?: number) => {
34-
if (limit === 0) {
35-
return "";
36-
}
37-
return `LIMIT ${limit} OFFSET ${offset}`;
38-
};
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return query`
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FILTER (
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${filtersTemplate}
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)
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`;
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}

‎packages/graph-explorer/src/connector/sparql/fetchNeighbors/index.ts‎

Lines changed: 16 additions & 144 deletions
Original file line numberDiff line numberDiff line change
@@ -1,134 +1,12 @@
1-
import groupBy from "lodash/groupBy";
2-
import { Edge, Vertex, VertexId } from "@/core";
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import {
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toMappedQueryResults,
53
type NeighborsResponse,
64
} from "@/connector/useGEFetchTypes";
7-
import mapIncomingToEdge, {
8-
IncomingPredicate,
9-
isIncomingPredicate,
10-
} from "../mappers/mapIncomingToEdge";
11-
import mapOutgoingToEdge, {
12-
OutgoingPredicate,
13-
} from "../mappers/mapOutgoingToEdge";
14-
import mapRawResultToVertex from "../mappers/mapRawResultToVertex";
15-
import oneHopNeighborsTemplate from "./oneHopNeighborsTemplate";
16-
import subjectPredicatesTemplate from "./subjectPredicatesTemplate";
17-
import {
18-
RawResult,
19-
RawValue,
20-
SparqlFetch,
21-
SPARQLNeighborsRequest,
22-
} from "../types";
23-
import { logger } from "@/utils";
24-
25-
type RawOneHopNeighborsResponse = {
26-
results: {
27-
bindings: Array<{
28-
subject: RawValue;
29-
pred: RawValue;
30-
value: RawValue;
31-
subjectClass: RawValue;
32-
pToSubject?: RawValue;
33-
pFromSubject?: RawValue;
34-
}>;
35-
};
36-
};
37-
38-
type RawNeighborsPredicatesResponse = {
39-
results: {
40-
bindings: Array<OutgoingPredicate | IncomingPredicate>;
41-
};
42-
};
43-
44-
const isBlank = (result: RawValue) => {
45-
return result.type === "bnode";
46-
};
5+
import { oneHopNeighborsTemplate } from "./oneHopNeighborsTemplate";
476

48-
const fetchOneHopNeighbors = async (
49-
sparqlFetch: SparqlFetch,
50-
req: SPARQLNeighborsRequest
51-
) => {
52-
const oneHopTemplate = oneHopNeighborsTemplate(req);
53-
logger.log("[SPARQL Explorer] Fetching oneHopNeighbors...", req);
54-
const data = await sparqlFetch<RawOneHopNeighborsResponse>(oneHopTemplate);
55-
56-
const groupBySubject = groupBy(
57-
data.results.bindings,
58-
result => result.subject.value
59-
);
60-
61-
const mappedResults: Record<string, RawResult> = {};
62-
const bNodesEdges: Edge[] = [];
63-
64-
Object.entries(groupBySubject).forEach(([uri, result]) => {
65-
// Create outgoing predicates to blank nodes
66-
if (isBlank(result[0].subject) && result[0].pToSubject) {
67-
const edge = mapOutgoingToEdge(req.resourceURI, req.resourceClasses, {
68-
subject: result[0].subject,
69-
subjectClass: result[0].subjectClass,
70-
predToSubject: result[0].pToSubject,
71-
});
72-
bNodesEdges.push(edge);
73-
}
74-
75-
// Create incoming predicates from blank nodes
76-
if (isBlank(result[0].subject) && result[0].pFromSubject) {
77-
const edge = mapIncomingToEdge(req.resourceURI, req.resourceClasses, {
78-
subject: result[0].subject,
79-
subjectClass: result[0].subjectClass,
80-
predFromSubject: result[0].pFromSubject,
81-
});
82-
bNodesEdges.push(edge);
83-
}
84-
85-
mappedResults[uri] = {
86-
uri: uri,
87-
class: result[0].subjectClass.value,
88-
isBlank: isBlank(result[0].subject),
89-
attributes: {},
90-
};
91-
92-
result.forEach(attr => {
93-
mappedResults[uri].attributes[attr.pred.value] = attr.value.value;
94-
});
95-
});
96-
97-
const vertices = Object.values(mappedResults).map(result => {
98-
return mapRawResultToVertex(result);
99-
});
100-
101-
return {
102-
vertices,
103-
bNodesEdges,
104-
};
105-
};
106-
107-
export const fetchNeighborsPredicates = async (
108-
sparqlFetch: SparqlFetch,
109-
resourceURI: VertexId,
110-
resourceClasses: Vertex["types"],
111-
subjectURIs: VertexId[]
112-
) => {
113-
const template = subjectPredicatesTemplate({
114-
resourceURI,
115-
subjectURIs,
116-
});
117-
118-
logger.log("[SPARQL Explorer] Fetching neighbor predicates...", {
119-
resourceURI,
120-
resourceClasses,
121-
subjectURIs,
122-
});
123-
const response = await sparqlFetch<RawNeighborsPredicatesResponse>(template);
124-
return response.results.bindings.map(result => {
125-
if (isIncomingPredicate(result)) {
126-
return mapIncomingToEdge(resourceURI, resourceClasses, result);
127-
}
128-
129-
return mapOutgoingToEdge(resourceURI, resourceClasses, result);
130-
});
131-
};
7+
import { SparqlFetch, SPARQLNeighborsRequest } from "../types";
8+
import { logger } from "@/utils";
9+
import { mapToResults, RawOneHopNeighborsResponse } from "./mapToResults";
13210

13311
/**
13412
* Given a subject URI, it returns a set of subjects (with their properties)
@@ -144,26 +22,20 @@ export const fetchNeighborsPredicates = async (
14422
*
14523
* It does not return neighbors counts.
14624
*/
147-
const fetchNeighbors = async (
25+
export default async function fetchNeighbors(
14826
sparqlFetch: SparqlFetch,
14927
req: SPARQLNeighborsRequest
150-
): Promise<NeighborsResponse> => {
151-
const { vertices, bNodesEdges } = await fetchOneHopNeighbors(
152-
sparqlFetch,
153-
req
154-
);
155-
const subjectsURIs = vertices.map(v => v.id);
156-
const edges = await fetchNeighborsPredicates(
157-
sparqlFetch,
158-
req.resourceURI,
159-
req.resourceClasses,
160-
subjectsURIs
161-
);
28+
): Promise<NeighborsResponse> {
29+
const oneHopTemplate = oneHopNeighborsTemplate(req);
30+
logger.log("[SPARQL Explorer] Fetching oneHopNeighbors...", req);
31+
const data = await sparqlFetch<RawOneHopNeighborsResponse>(oneHopTemplate);
32+
logger.log("[SPARQL Explorer] Fetched oneHopNeighbors", data);
33+
34+
const results = mapToResults(data.results.bindings);
16235

16336
return toMappedQueryResults({
164-
vertices,
165-
edges: [...edges, ...bNodesEdges],
37+
// Filter out the source vertex since it is already in the graph and this one is missing the attributes
38+
vertices: results.vertices.filter(v => v.id !== req.resourceURI),
39+
edges: results.edges,
16640
});
167-
};
168-
169-
export default fetchNeighbors;
41+
}

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