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Merge branch 'fix-846-bte' of https://github.com/biothings/bte_trapi_…
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…query_graph_handler into dev
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@tokebe
tokebe committed Aug 19, 2024
2 parents 654fffc + ed1f237 commit 658050f
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Showing 7 changed files with 84 additions and 38 deletions.
12 changes: 11 additions & 1 deletion .github/workflows/test_ws_codecov.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -13,11 +13,21 @@ jobs:
id: branch-name
uses: tj-actions/branch-names@v6

- uses: actions/checkout@v3
- name: Checkout to specific branch
uses: actions/checkout@v3
id: specific-checkout
continue-on-error: true
with:
repository: biothings/biothings_explorer
ref: ${{ steps.branch-name.outputs.current_branch }}

- name: Checkout to main if above failed
if: steps.specific-checkout.outcome == 'failure'
uses: actions/checkout@v3
with:
repository: biothings/biothings_explorer
ref: main

- name: Use Node.js 18.x
uses: actions/setup-node@v3
with:
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2 changes: 1 addition & 1 deletion __test__/integration/KnowledgeGraph.test.ts
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
import KGEdge from '../../src/graph/kg_edge';
import KGNode from '../../src/graph/kg_node';
import KnowledgeGraph from '../../src/graph/knowledge_graph';
import { TrapiAttribute } from '../../src/types';
import { TrapiAttribute } from '@biothings-explorer/types';

describe('Testing KnowledgeGraph Module', () => {
const nodeInput = new KGNode('PUBCHEM.COMPOUND:2662-n0', {
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1 change: 0 additions & 1 deletion __test__/integration/QueryEdge.test.ts
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Expand Up @@ -143,7 +143,6 @@ describe('Testing QueryEdge Module', () => {
expect(res).toContain('contributes_to');
expect(res).toContain('causes');
expect(res).toContain('ameliorates');
expect(res).toContain('treats');
});

test('Predicates not in biolink model should return itself', () => {
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35 changes: 35 additions & 0 deletions __test__/integration/QueryResult.test.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -43,6 +43,11 @@ describe('Testing QueryResults Module', () => {
predicate: 'biolink:physically_interacts_with',
source: 'DGIdb',
api_name: 'BioThings DGIDB API',
"x-translator": {
infores: "infores:biothings-dgidb",
component: "KP",
team: ["Service Provider"]
}
},
edge1,
);
Expand Down Expand Up @@ -98,6 +103,11 @@ describe('Testing QueryResults Module', () => {
{
predicate: 'biolink:gene_associated_with_condition',
api_name: 'Automat Pharos',
"x-translator": {
infores: "infores:automat-pharos",
component: "KP",
team: ["Ranking Agent"]
}
},
edge1,
);
Expand Down Expand Up @@ -197,6 +207,11 @@ describe('Testing QueryResults Module', () => {
{
predicate: 'biolink:gene_associated_with_condition',
api_name: 'Automat Pharos',
"x-translator": {
infores: "infores:automat-pharos",
component: "KP",
team: ["Ranking Agent"]
}
},
edge1,
);
Expand Down Expand Up @@ -295,6 +310,11 @@ describe('Testing QueryResults Module', () => {
{
predicate: 'biolink:gene_associated_with_condition',
api_name: 'Automat Pharos',
"x-translator": {
infores: "infores:automat-pharos",
component: "KP",
team: ["Ranking Agent"]
}
},
edge1,
);
Expand Down Expand Up @@ -393,6 +413,11 @@ describe('Testing QueryResults Module', () => {
{
predicate: 'biolink:gene_associated_with_condition',
api_name: 'Automat Pharos',
"x-translator": {
infores: "infores:automat-pharos",
component: "KP",
team: ["Ranking Agent"]
}
},
edge1,
);
Expand Down Expand Up @@ -493,6 +518,11 @@ describe('Testing QueryResults Module', () => {
{
predicate: 'biolink:gene_associated_with_condition',
api_name: 'Automat Pharos',
"x-translator": {
infores: "infores:automat-pharos",
component: "KP",
team: ["Ranking Agent"]
}
},
edge1,
);
Expand Down Expand Up @@ -594,6 +624,11 @@ describe('Testing QueryResults Module', () => {
{
predicate: 'biolink:gene_associated_with_condition',
api_name: 'Automat Pharos',
"x-translator": {
infores: "infores:automat-pharos",
component: "KP",
team: ["Ranking Agent"]
}
},
edge1,
);
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66 changes: 33 additions & 33 deletions __test__/integration/graph/graph.test.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -109,11 +109,11 @@ describe('Test graph class', () => {
expect(g.nodes['inputPrimaryCurie'].qNodeID).toEqual('qg1');
expect(Array.from(g.nodes['inputPrimaryCurie'].targetNodes)).toEqual(['outputPrimaryCurie']);
expect(Array.from(g.nodes['inputPrimaryCurie'].targetQNodeIDs)).toEqual(['qg2']);
expect(g.edges).toHaveProperty('95fe2a8089c0d79ea093b97c5991f7ba');
expect(Array.from(g.edges['95fe2a8089c0d79ea093b97c5991f7ba'].apis)).toEqual(['API1']);
expect(g.edges['95fe2a8089c0d79ea093b97c5991f7ba'].sources).toHaveProperty('source1');
expect(Array.from(g.edges['95fe2a8089c0d79ea093b97c5991f7ba'].publications)).toEqual(['PMID:1', 'PMID:2']);
expect(g.edges['95fe2a8089c0d79ea093b97c5991f7ba'].attributes).toHaveProperty('relation', new Set(['relation1']));
expect(g.edges).toHaveProperty('2c826c3663b91f65a1cba70f06c7fc65');
expect(Array.from(g.edges['2c826c3663b91f65a1cba70f06c7fc65'].apis)).toEqual(['API1']);
expect(g.edges['2c826c3663b91f65a1cba70f06c7fc65'].sources).toHaveProperty('source1');
expect(Array.from(g.edges['2c826c3663b91f65a1cba70f06c7fc65'].publications)).toEqual(['PMID:1', 'PMID:2']);
expect(g.edges['2c826c3663b91f65a1cba70f06c7fc65'].attributes).toHaveProperty('relation', new Set(['relation1']));
});

test('Multiple query results are correctly updated for two edges having same input, predicate and output', () => {
Expand All @@ -130,17 +130,17 @@ describe('Test graph class', () => {
expect(Array.from(g.nodes['inputPrimaryCurie'].targetNodes)).toEqual(['outputPrimaryCurie']);
expect(Array.from(g.nodes['inputPrimaryCurie'].targetQNodeIDs)).toEqual(['qg2']);

expect(g.edges).toHaveProperty('95fe2a8089c0d79ea093b97c5991f7ba');
expect(Array.from(g.edges['95fe2a8089c0d79ea093b97c5991f7ba'].apis)).toEqual(['API1']);
expect(g.edges['95fe2a8089c0d79ea093b97c5991f7ba'].sources).toHaveProperty('source1');
expect(Array.from(g.edges['95fe2a8089c0d79ea093b97c5991f7ba'].publications)).toEqual(['PMID:1', 'PMID:2']);
expect(g.edges['95fe2a8089c0d79ea093b97c5991f7ba'].attributes).toHaveProperty('relation', new Set(['relation1']));
expect(g.edges).toHaveProperty('2c826c3663b91f65a1cba70f06c7fc65');
expect(Array.from(g.edges['2c826c3663b91f65a1cba70f06c7fc65'].apis)).toEqual(['API1']);
expect(g.edges['2c826c3663b91f65a1cba70f06c7fc65'].sources).toHaveProperty('source1');
expect(Array.from(g.edges['2c826c3663b91f65a1cba70f06c7fc65'].publications)).toEqual(['PMID:1', 'PMID:2']);
expect(g.edges['2c826c3663b91f65a1cba70f06c7fc65'].attributes).toHaveProperty('relation', new Set(['relation1']));

expect(g.edges).toHaveProperty('9d334cb674d5671364c45cc8403184c6');
expect(Array.from(g.edges['9d334cb674d5671364c45cc8403184c6'].apis)).toEqual(['API2']);
expect(g.edges['9d334cb674d5671364c45cc8403184c6'].sources).toHaveProperty('source2');
expect(Array.from(g.edges['9d334cb674d5671364c45cc8403184c6'].publications)).toEqual(['PMC:1', 'PMC:2']);
expect(g.edges['9d334cb674d5671364c45cc8403184c6'].attributes).toHaveProperty('relation', new Set(['relation2']));
expect(g.edges).toHaveProperty('827c366e2e3088b3f4a90dd88a524f15');
expect(Array.from(g.edges['827c366e2e3088b3f4a90dd88a524f15'].apis)).toEqual(['API2']);
expect(g.edges['827c366e2e3088b3f4a90dd88a524f15'].sources).toHaveProperty('source2');
expect(Array.from(g.edges['827c366e2e3088b3f4a90dd88a524f15'].publications)).toEqual(['PMC:1', 'PMC:2']);
expect(g.edges['827c366e2e3088b3f4a90dd88a524f15'].attributes).toHaveProperty('relation', new Set(['relation2']));
});

test('Multiple query results for different edges are correctly updated', () => {
Expand All @@ -157,37 +157,37 @@ describe('Test graph class', () => {
expect(Array.from(g.nodes['inputPrimaryCurie'].targetNodes)).toEqual(['outputPrimaryCurie']);
expect(Array.from(g.nodes['inputPrimaryCurie'].targetQNodeIDs)).toEqual(['qg2']);

expect(g.edges).toHaveProperty('95fe2a8089c0d79ea093b97c5991f7ba');
expect(Array.from(g.edges['95fe2a8089c0d79ea093b97c5991f7ba'].apis)).toEqual(['API1']);
expect(g.edges['95fe2a8089c0d79ea093b97c5991f7ba'].sources).toHaveProperty('source1');
expect(Array.from(g.edges['95fe2a8089c0d79ea093b97c5991f7ba'].publications)).toEqual(['PMID:1', 'PMID:2']);
expect(g.edges['95fe2a8089c0d79ea093b97c5991f7ba'].attributes).toHaveProperty('relation', new Set(['relation1']));
expect(g.edges).toHaveProperty('2c826c3663b91f65a1cba70f06c7fc65');
expect(Array.from(g.edges['2c826c3663b91f65a1cba70f06c7fc65'].apis)).toEqual(['API1']);
expect(g.edges['2c826c3663b91f65a1cba70f06c7fc65'].sources).toHaveProperty('source1');
expect(Array.from(g.edges['2c826c3663b91f65a1cba70f06c7fc65'].publications)).toEqual(['PMID:1', 'PMID:2']);
expect(g.edges['2c826c3663b91f65a1cba70f06c7fc65'].attributes).toHaveProperty('relation', new Set(['relation1']));

expect(g.edges).toHaveProperty('9d334cb674d5671364c45cc8403184c6');
expect(Array.from(g.edges['9d334cb674d5671364c45cc8403184c6'].apis)).toEqual(['API2']);
expect(g.edges['9d334cb674d5671364c45cc8403184c6'].sources).toHaveProperty('source2');
expect(Array.from(g.edges['9d334cb674d5671364c45cc8403184c6'].publications)).toEqual(['PMC:1', 'PMC:2']);
expect(g.edges['9d334cb674d5671364c45cc8403184c6'].attributes).toHaveProperty('relation', new Set(['relation2']));
expect(g.edges).toHaveProperty('827c366e2e3088b3f4a90dd88a524f15');
expect(Array.from(g.edges['827c366e2e3088b3f4a90dd88a524f15'].apis)).toEqual(['API2']);
expect(g.edges['827c366e2e3088b3f4a90dd88a524f15'].sources).toHaveProperty('source2');
expect(Array.from(g.edges['827c366e2e3088b3f4a90dd88a524f15'].publications)).toEqual(['PMC:1', 'PMC:2']);
expect(g.edges['827c366e2e3088b3f4a90dd88a524f15'].attributes).toHaveProperty('relation', new Set(['relation2']));

expect(g.edges).toHaveProperty('4fe2d5d3e03e0f78f272745caf6b627d');
expect(Array.from(g.edges['4fe2d5d3e03e0f78f272745caf6b627d'].apis)).toEqual(['API3']);
expect(g.edges['4fe2d5d3e03e0f78f272745caf6b627d'].sources).toHaveProperty('source3');
expect(Array.from(g.edges['4fe2d5d3e03e0f78f272745caf6b627d'].publications)).toEqual(['PMC:3', 'PMC:4']);
expect(g.edges['4fe2d5d3e03e0f78f272745caf6b627d'].attributes).toHaveProperty('relation', new Set(['relation3']));
expect(g.edges).toHaveProperty('3138ca0afca791770ed38c243dea2116');
expect(Array.from(g.edges['3138ca0afca791770ed38c243dea2116'].apis)).toEqual(['API3']);
expect(g.edges['3138ca0afca791770ed38c243dea2116'].sources).toHaveProperty('source3');
expect(Array.from(g.edges['3138ca0afca791770ed38c243dea2116'].publications)).toEqual(['PMC:3', 'PMC:4']);
expect(g.edges['3138ca0afca791770ed38c243dea2116'].attributes).toHaveProperty('relation', new Set(['relation3']));
});

test('Multiple attributes with the same name are merged', () => {
const g = new graph();
g.update([record3, record3a]);

expect(g.edges).toHaveProperty('4fe2d5d3e03e0f78f272745caf6b627d');
expect(Array.from(g.edges['4fe2d5d3e03e0f78f272745caf6b627d'].publications)).toEqual([
expect(g.edges).toHaveProperty('3138ca0afca791770ed38c243dea2116');
expect(Array.from(g.edges['3138ca0afca791770ed38c243dea2116'].publications)).toEqual([
'PMC:3',
'PMC:4',
'PMC:6',
'PMC:7',
]);
expect(g.edges['4fe2d5d3e03e0f78f272745caf6b627d'].attributes).toHaveProperty(
expect(g.edges['3138ca0afca791770ed38c243dea2116'].attributes).toHaveProperty(
'relation',
new Set(['relation3', 'relation3a', 'relation3b']),
);
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5 changes: 3 additions & 2 deletions __test__/unittest/inferred_mode.test.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -201,6 +201,7 @@ describe('Test InferredQueryHandler', () => {
},
},
template: 'Chem-treats-DoP.json',
qualifiers: {}
},
];

Expand Down Expand Up @@ -549,7 +550,7 @@ describe('Test InferredQueryHandler', () => {
expect(creativeLimitHit).toBeTruthy();
expect(Object.keys(combinedResponse.message.results)).toHaveLength(3);
expect(combinedResponse.message.results['fakeCompound1-fakeDisease1'].analyses[0].score).toEqual(
0.8421052631578949,
0.7836531040612146,
);
expect(combinedResponse.message.results['fakeCompound3-fakeDisease1'].analyses[0].score).toEqual(0.2);
expect(combinedResponse.logs).toHaveLength(3);
Expand Down Expand Up @@ -712,7 +713,7 @@ describe('Test InferredQueryHandler', () => {
expect(Object.keys(mergedResults1)).toHaveLength(1);
expect(creativeLimitHit1).toBeTruthy();
expect(combinedResponse.message.results['fakeCompound1-fakeDisease1'].analyses[0].score).toEqual(
0.8421052631578949,
0.7836531040612146,
);
});

Expand Down
1 change: 1 addition & 0 deletions src/index.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -40,6 +40,7 @@ export { default as QEdge } from './query_edge';
export { default as QNode } from './query_node';
export { default as InvalidQueryGraphError } from './exceptions/invalid_query_graph_error';
export * from './qedge2apiedge';
export {TrapiQueryGraph, TrapiResponse, TrapiResult}; // better readability

export default class TRAPIQueryHandler {
logs: StampedLog[];
Expand Down

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