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fix: use sources passed from node expansion
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@tokebe
tokebe committed Aug 21, 2024
1 parent 7d5d1db commit 05d7b46
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Showing 3 changed files with 98 additions and 68 deletions.
48 changes: 28 additions & 20 deletions src/edge_manager.ts
View file
Original file line number Diff line number Diff line change
Expand Up @@ -110,7 +110,7 @@ export default class QueryEdgeManager {
}
debug(
`(5) Sending next edge '${nextQEdge.getID()}' ` +
`WITH entity count...(${nextQEdge.subject.entity_count || nextQEdge.object.entity_count})`,
`WITH entity count...(${nextQEdge.subject.entity_count || nextQEdge.object.entity_count})`,
);
return this.preSendOffCheck(nextQEdge);
}
Expand All @@ -119,18 +119,19 @@ export default class QueryEdgeManager {
this._qEdges.forEach((qEdge) => {
debug(
`'${qEdge.getID()}'` +
` : (${qEdge.subject.entity_count || 0}) ` +
`${qEdge.reverse ? '<--' : '-->'}` +
` (${qEdge.object.entity_count || 0})`,
` : (${qEdge.subject.entity_count || 0}) ` +
`${qEdge.reverse ? '<--' : '-->'}` +
` (${qEdge.object.entity_count || 0})`,
);
});
}

_logSkippedQueries(unavailableAPIs: UnavailableAPITracker): void {
Object.entries(unavailableAPIs).forEach(([api, { skippedQueries }]) => {
if (skippedQueries > 0) {
const skipMessage = `${skippedQueries} additional quer${skippedQueries > 1 ? 'ies' : 'y'} to ${api} ${skippedQueries > 1 ? 'were' : 'was'
} skipped as the API was unavailable.`;
const skipMessage = `${skippedQueries} additional quer${skippedQueries > 1 ? 'ies' : 'y'} to ${api} ${
skippedQueries > 1 ? 'were' : 'was'
} skipped as the API was unavailable.`;
debug(skipMessage);
this.logs.push(new LogEntry('WARNING', null, skipMessage).getLog());
}
Expand Down Expand Up @@ -196,7 +197,7 @@ export default class QueryEdgeManager {
const objectCuries = qEdge.object.curie;
debug(
`'${qEdge.getID()}' Reversed[${qEdge.reverse}] (${JSON.stringify(subjectCuries.length || 0)})` +
`--(${JSON.stringify(objectCuries.length || 0)}) entities / (${records.length}) records.`,
`--(${JSON.stringify(objectCuries.length || 0)}) entities / (${records.length}) records.`,
);
// debug(`IDS SUB ${JSON.stringify(sub_count)}`)
// debug(`IDS OBJ ${JSON.stringify(obj_count)}`)
Expand All @@ -209,18 +210,24 @@ export default class QueryEdgeManager {
let objectIDs = [record.object.original, record.object.curie, ...record.object.equivalentCuries];

// check if IDs will be resolved to a parent
subjectIDs = [...subjectIDs, ...subjectIDs.reduce((set, subjectID) => {
Object.entries(this._subclassEdges[subjectID] ?? {}).forEach(([id, qNodes]) => {
if (qNodes.includes(qEdge.reverse ? qEdge.object.id : qEdge.subject.id)) set.add(id);
});
return set;
}, new Set<string>())];
objectIDs = [...objectIDs, ...objectIDs.reduce((set, objectID) => {
Object.entries(this._subclassEdges[objectID] ?? {}).forEach(([id, qNodes]) => {
if (qNodes.includes(qEdge.reverse ? qEdge.subject.id : qEdge.object.id)) set.add(id);
});
return set;
}, new Set<string>())];
subjectIDs = [
...subjectIDs,
...subjectIDs.reduce((set, subjectID) => {
Object.entries(this._subclassEdges[subjectID] ?? {}).forEach(([id, { qNodes }]) => {
if (qNodes.includes(qEdge.reverse ? qEdge.object.id : qEdge.subject.id)) set.add(id);
});
return set;
}, new Set<string>()),
];
objectIDs = [
...objectIDs,
...objectIDs.reduce((set, objectID) => {
Object.entries(this._subclassEdges[objectID] ?? {}).forEach(([id, { qNodes }]) => {
if (qNodes.includes(qEdge.reverse ? qEdge.subject.id : qEdge.object.id)) set.add(id);
});
return set;
}, new Set<string>()),
];

// there must be at least a minimal intersection
const subjectMatch = subjectIDs.some((curie) => execSubjectCuries.includes(curie));
Expand Down Expand Up @@ -409,7 +416,8 @@ export default class QueryEdgeManager {
new LogEntry(
'INFO',
null,
`Executing ${currentQEdge.getID()}${currentQEdge.isReversed() ? ' (reversed)' : ''}: ${currentQEdge.subject.id
`Executing ${currentQEdge.getID()}${currentQEdge.isReversed() ? ' (reversed)' : ''}: ${
currentQEdge.subject.id
} ${currentQEdge.isReversed() ? '<--' : '-->'} ${currentQEdge.object.id}`,
).getLog(),
);
Expand Down
107 changes: 63 additions & 44 deletions src/index.ts
View file
Original file line number Diff line number Diff line change
Expand Up @@ -79,7 +79,7 @@ export default class TRAPIQueryHandler {
if (this.options.smartapi) {
smartapiRegistry = this.options.smartapi;
} else {
const file = await fs.readFile(this.path, "utf-8");
const file = await fs.readFile(this.path, 'utf-8');
smartapiRegistry = JSON.parse(file);
}

Expand Down Expand Up @@ -109,8 +109,8 @@ export default class TRAPIQueryHandler {
`Query options are: ${JSON.stringify({
...this.options,
schema: this.options.schema ? this.options.schema.info.version : 'not included',
metakg: "",
smartapi: ""
metakg: '',
smartapi: '',
})}`,
);

Expand Down Expand Up @@ -172,9 +172,13 @@ export default class TRAPIQueryHandler {
const nodesToRebind: { [nodeID: string]: { [qEdgeID: string]: { newNode: string; subclassEdgeID: string } } } = {};
Object.keys(this.bteGraph.nodes).forEach((nodeID) => {
const subclassCuries = [];
expandedIDsbyPrimaryID[nodeID]?.forEach((expandedID) => Object.keys(this.subclassEdges[expandedID]).forEach((parentID) => subclassCuries.push({ original: parentID, expanded: expandedID })));
expandedIDsbyPrimaryID[nodeID]?.forEach((expandedID) =>
Object.keys(this.subclassEdges[expandedID]).forEach((parentID) =>
subclassCuries.push({ original: parentID, expanded: expandedID }),
),
);
if (!subclassCuries.length) return; // Nothing to rebind
subclassCuries.forEach(({original, expanded}) => {
subclassCuries.forEach(({ original, expanded }) => {
const subject = nodeID;
const object = primaryIDsByOriginalID[original];
// Don't keep self-subclass
Expand All @@ -186,11 +190,9 @@ export default class TRAPIQueryHandler {
subject,
object,
});
const source = Object.entries(ontologyKnowledgeSourceMapping).find(([prefix]) => {
return expanded.includes(prefix);
})[1];
subclassEdge.addAdditionalAttributes('biolink:knowledge_level', 'knowledge_assertion')
subclassEdge.addAdditionalAttributes('biolink:agent_type', 'manual_agent')
const source = ontologyKnowledgeSourceMapping[this.subclassEdges[expanded][original].source] ?? 'error-not-provided';
subclassEdge.addAdditionalAttributes('biolink:knowledge_level', 'knowledge_assertion');
subclassEdge.addAdditionalAttributes('biolink:agent_type', 'manual_agent');
subclassEdge.addSource([
{ resource_id: source, resource_role: 'primary_knowledge_source' },
{
Expand All @@ -202,39 +204,47 @@ export default class TRAPIQueryHandler {
]);
this.bteGraph.edges[subclassEdgeID] = subclassEdge;
if (!nodesToRebind[subject]) nodesToRebind[subject] = {};
this.subclassEdges[expanded][original].forEach((qNodeID) => nodesToRebind[subject][qNodeID] = { newNode: object, subclassEdgeID });
this.subclassEdges[expanded][original].qNodes.forEach(
(qNodeID) => (nodesToRebind[subject][qNodeID] = { newNode: object, subclassEdgeID }),
);
});
});

// Create new constructed edges and aux graphs for edges that used subclass edges
let auxGraphs: { [supportGraphID: string]: TrapiAuxiliaryGraph } = {};
const edgesToRebind: { [edgeID: string]: { [originalSubject: string]: { [originalObject: string]: string /* re-bound edge ID */ } } } = {};
const edgesToRebind: {
[edgeID: string]: { [originalSubject: string]: { [originalObject: string]: string /* re-bound edge ID */ } };
} = {};
const edgesIDsByAuxGraphID = {};
Object.entries(this.bteGraph.edges).forEach(([edgeID, bteEdge]) => {
if (edgeID.includes('expanded')) return;
const combos: {subject: string, object: string, supportGraph: string[]}[] = [];
const subjectToSupportGraphs: {[sbj: string]: Set<string>} = {
[bteEdge.subject]: new Set(),
const combos: { subject: string; object: string; supportGraph: string[] }[] = [];
const subjectToSupportGraphs: { [sbj: string]: Set<string> } = {
[bteEdge.subject]: new Set(),
...Object.values(nodesToRebind[bteEdge.subject] ?? {}).reduce((acc, x) => {
x.newNode in acc ? acc[x.newNode].add(x.subclassEdgeID) : acc[x.newNode] = new Set([x.subclassEdgeID])
x.newNode in acc ? acc[x.newNode].add(x.subclassEdgeID) : (acc[x.newNode] = new Set([x.subclassEdgeID]));
return acc;
}, {})
}, {}),
};
const objectToSupportGraphs: {[obj: string]: Set<string>} = {
[bteEdge.object]: new Set(),
const objectToSupportGraphs: { [obj: string]: Set<string> } = {
[bteEdge.object]: new Set(),
...Object.values(nodesToRebind[bteEdge.object] ?? {}).reduce((acc, x) => {
x.newNode in acc ? acc[x.newNode].add(x.subclassEdgeID) : acc[x.newNode] = new Set([x.subclassEdgeID]);
x.newNode in acc ? acc[x.newNode].add(x.subclassEdgeID) : (acc[x.newNode] = new Set([x.subclassEdgeID]));
return acc;
}, {})
}, {}),
};
for (const subject in subjectToSupportGraphs) {
for (const object in objectToSupportGraphs) {
if (subject == bteEdge.subject && object == bteEdge.object) continue; // no nodes are rebound
combos.push({ subject, object, supportGraph: [...subjectToSupportGraphs[subject], ...objectToSupportGraphs[object], edgeID] });
combos.push({
subject,
object,
supportGraph: [...subjectToSupportGraphs[subject], ...objectToSupportGraphs[object], edgeID],
});
}
}

combos.forEach(({subject, object, supportGraph}) => {
combos.forEach(({ subject, object, supportGraph }) => {
const boundEdgeID = `${subject}-${bteEdge.predicate.replace('biolink:', '')}-${object}-via_subclass`;
let suffix = 0;
while (Object.keys(auxGraphs).includes(`support${suffix}-${boundEdgeID}`)) {
Expand All @@ -253,8 +263,8 @@ export default class TRAPIQueryHandler {
object: object,
});
boundEdge.addAdditionalAttributes('biolink:support_graphs', [supportGraphID]);
boundEdge.addAdditionalAttributes('biolink:knowledge_level', 'logical_entailment')
boundEdge.addAdditionalAttributes('biolink:agent_type', 'automated_agent')
boundEdge.addAdditionalAttributes('biolink:knowledge_level', 'logical_entailment');
boundEdge.addAdditionalAttributes('biolink:agent_type', 'automated_agent');
boundEdge.addSource([
{
resource_id: this.options.provenanceUsesServiceProvider
Expand All @@ -270,7 +280,7 @@ export default class TRAPIQueryHandler {
if (!edgesToRebind[edgeID]) edgesToRebind[edgeID] = {};
if (!edgesToRebind[edgeID][subject]) edgesToRebind[edgeID][subject] = {};
edgesToRebind[edgeID][subject][object] = boundEdgeID;
})
});
});

const resultBoundEdgesWithAuxGraphs = new Set();
Expand Down Expand Up @@ -343,15 +353,18 @@ export default class TRAPIQueryHandler {
}

appendOriginalCuriesToResults(results: TrapiResult[]): void {
results.forEach(result => {
results.forEach((result) => {
Object.entries(result.node_bindings).forEach(([_, bindings]) => {
bindings.forEach(binding => {
if (this.bteGraph.nodes[binding.id].originalCurie && this.bteGraph.nodes[binding.id].originalCurie !== binding.id) {
bindings.forEach((binding) => {
if (
this.bteGraph.nodes[binding.id].originalCurie &&
this.bteGraph.nodes[binding.id].originalCurie !== binding.id
) {
binding.query_id = this.bteGraph.nodes[binding.id].originalCurie;
}
})
})
})
});
});
});
}

async addQueryNodes(): Promise<void> {
Expand Down Expand Up @@ -412,8 +425,10 @@ export default class TRAPIQueryHandler {
for (const nodeId in queryGraph.nodes) {
// perform node expansion
if (queryGraph.nodes[nodeId].ids && !this._queryUsesInferredMode()) {
const descendantsByCurie: { [curie: string]: string[] } = getDescendants(queryGraph.nodes[nodeId].ids);
let expanded = Object.values(descendantsByCurie).flat();
const descendantsByCurie: { [curie: string]: { [descendants: string]: string } } = getDescendants(
queryGraph.nodes[nodeId].ids,
);
let expanded = Object.values(descendantsByCurie).map(descendants => Object.keys(descendants)).flat()

expanded = _.uniq([...queryGraph.nodes[nodeId].ids, ...expanded]);

Expand All @@ -425,11 +440,11 @@ export default class TRAPIQueryHandler {

if (foundExpandedIds) {
Object.entries(descendantsByCurie).forEach(([curie, descendants]) => {
descendants.forEach((descendant) => {
Object.entries(descendants).forEach(([ descendant, source ]) => {
if (queryGraph.nodes[nodeId].ids.includes(descendant)) return;
if (!this.subclassEdges[descendant]) this.subclassEdges[descendant] = {};
if (!this.subclassEdges[descendant][curie]) this.subclassEdges[descendant][curie] = [];
this.subclassEdges[descendant][curie].push(nodeId);
if (!this.subclassEdges[descendant][curie]) this.subclassEdges[descendant][curie] = { source, qNodes: [] };
this.subclassEdges[descendant][curie].qNodes.push(nodeId);
});
});
}
Expand Down Expand Up @@ -492,11 +507,13 @@ export default class TRAPIQueryHandler {

let log_msg: string;
if (currentQEdge.reverse) {
log_msg = `qEdge ${currentQEdge.id} (reversed): ${currentQEdge.object.categories} > ${currentQEdge.predicate ? `${currentQEdge.predicate} > ` : ''
}${currentQEdge.subject.categories}`;
log_msg = `qEdge ${currentQEdge.id} (reversed): ${currentQEdge.object.categories} > ${
currentQEdge.predicate ? `${currentQEdge.predicate} > ` : ''
}${currentQEdge.subject.categories}`;
} else {
log_msg = `qEdge ${currentQEdge.id}: ${currentQEdge.subject.categories} > ${currentQEdge.predicate ? `${currentQEdge.predicate} > ` : ''
}${currentQEdge.object.categories}`;
log_msg = `qEdge ${currentQEdge.id}: ${currentQEdge.subject.categories} > ${
currentQEdge.predicate ? `${currentQEdge.predicate} > ` : ''
}${currentQEdge.object.categories}`;
}
this.logs.push(new LogEntry('INFO', null, log_msg).getLog());

Expand Down Expand Up @@ -537,8 +554,9 @@ export default class TRAPIQueryHandler {
});
const qEdgesLogStr = qEdgesToLog.length > 1 ? `[${qEdgesToLog.join(', ')}]` : `${qEdgesToLog.join(', ')}`;
if (len > 0) {
const terminateLog = `Query Edge${len !== 1 ? 's' : ''} ${qEdgesLogStr} ${len !== 1 ? 'have' : 'has'
} no MetaKG edges. Your query terminates.`;
const terminateLog = `Query Edge${len !== 1 ? 's' : ''} ${qEdgesLogStr} ${
len !== 1 ? 'have' : 'has'
} no MetaKG edges. Your query terminates.`;
debug(terminateLog);
this.logs.push(new LogEntry('WARNING', null, terminateLog).getLog());
return false;
Expand Down Expand Up @@ -652,7 +670,8 @@ export default class TRAPIQueryHandler {
new LogEntry(
'INFO',
null,
`Execution Summary: (${KGNodes}) nodes / (${kgEdges}) edges / (${results}) results; (${resultQueries}/${queries}) queries${cached ? ` (${cached} cached qEdges)` : ''
`Execution Summary: (${KGNodes}) nodes / (${kgEdges}) edges / (${results}) results; (${resultQueries}/${queries}) queries${
cached ? ` (${cached} cached qEdges)` : ''
} returned results from(${sources.length}) unique API${sources.length === 1 ? 's' : ''}`,
).getLog(),
new LogEntry('INFO', null, `APIs: ${sources.join(', ')} `).getLog(),
Expand Down
11 changes: 7 additions & 4 deletions src/types.ts
View file
Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,10 @@ export interface CompactQualifiers {
}

export interface SubclassEdges {
[expandedID: string]: {
[parentID: string]: string[] /* QNode IDs */
}
}
[expandedID: string]: {
[parentID: string]: {
source: string;
qNodes: string[];
};
};
}

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