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Merge pull request #63 from biothings/monarch-migration
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Update JQ transform for new monarch API
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@tokebe
tokebe authored Feb 21, 2024
2 parents 11ba036 + e117b37 commit 4fe3dec
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Showing 6 changed files with 304 additions and 123 deletions.
49 changes: 49 additions & 0 deletions data/jq/pair/monarch.jq
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Original file line number Diff line number Diff line change
@@ -0,0 +1,49 @@
generateCurie($edge.input.id; $edge.input.curies) as $input_curie
| if $edge.response_mapping[$edge.predicate].output_name | contains("object")
then "object_namespace"
else "subject_namespace"
end
| . as $output_namespace
| { $input_curie: [$response] } | .[$input_curie][0].items = [
$response.items[]
| select(. != null)
# | select(
# .[$output_namespace] == $edge.output.id
# )
| .publications = [
if .publications != null
then .publications
else []
end
| .[]
| select(. | startswith("PMID:"))
]
| .primary_knowledge_source as $primary_knowledge_source
| .sources = (
if .primary_knowledge_source != null and .aggregator_knowledge_source != null
then
[
{
resource_role: "primary_knowledge_source",
resource_id: $primary_knowledge_source
}
]
+ (.aggregator_knowledge_source | reverse | reduce .[] as $source (
null;
if . == null
then [{
resource_role: "aggregator_knowledge_source",
resource_id: $source,
upstream_resource_ids: [$primary_knowledge_source]
}]
else . + [{
resource_role: "aggregator_knowledge_source",
resource_id: $source,
upstream_resource_ids: [.[-1].resource_id]
}]
end
))
else [{ resource_role: "primary_knowledge_source", resource_id:"infores:monarchinitiative" }]
end
)
]
18 changes: 0 additions & 18 deletions data/jq/wrap/biolink.jq
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This file was deleted.

6 changes: 2 additions & 4 deletions src/index.ts
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Original file line number Diff line number Diff line change
@@ -1,4 +1,3 @@
import BiolinkTransformer from "./transformers/biolink_transformer";
import BioThingsTransformer from "./transformers/biothings_transformer";
// import CordTransformer from "./transformers/cord_transformer";
import CTDTransformer from "./transformers/ctd_transformer";
Expand Down Expand Up @@ -46,9 +45,8 @@ export default class Transformer {
this.tf = new TRAPITransformer(this.data, this.config);
} else if (api.startsWith("SEMMED")) {
this.tf = new SemmedTransformer(this.data, this.config);
} else if (api === "BioLink API") {
// this.tf = new BiolinkTransformer(this.data, this.config);
this.tf = new JQTransformer(this.data, { ...this.config, type: "biolink" });
} else if (api === "Monarch API") {
this.tf = new JQTransformer(this.data, { ...this.config, type: "monarch" });
} else if (api === "EBI Proteins API") {
// this.tf = new EBIProteinTransformer(this.data, this.config)
this.tf = new JQTransformer(this.data, { ...this.config, type: "ebi" });
Expand Down
165 changes: 119 additions & 46 deletions src/record.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -11,14 +11,21 @@ export class RecordNode {
_qNode: QNode;
_apiLabel: string;

constructor(node: FrozenNode | VerboseFrozenNode | MinimalFrozenNode, qNode: QNode) {
constructor(
node: FrozenNode | VerboseFrozenNode | MinimalFrozenNode,
qNode: QNode,
) {
this.original = node.original;
this.normalizedInfo = node.normalizedInfo ? node.normalizedInfo : this.makeFakeInfo(node);
this.normalizedInfo = node.normalizedInfo
? node.normalizedInfo
: this.makeFakeInfo(node);
this._qNode = qNode;
this._apiLabel = node.apiLabel;
}

makeFakeInfo(node: FrozenNode | VerboseFrozenNode | MinimalFrozenNode): NodeNormalizerResultObj {
makeFakeInfo(
node: FrozenNode | VerboseFrozenNode | MinimalFrozenNode,
): NodeNormalizerResultObj {
return {
primaryID: node.curie,
equivalentIDs: node.equivalentCuries ?? [],
Expand Down Expand Up @@ -82,19 +89,30 @@ export class RecordNode {

get UMLS(): string[] {
return (
this.normalizedInfo?.equivalentIDs.reduce((arr: string[], curie: string) => {
if (curie.includes("UMLS")) arr.push(curie.replace("UMLS:", ""));
return arr;
}, []) ?? []
this.normalizedInfo?.equivalentIDs.reduce(
(arr: string[], curie: string) => {
if (curie.includes("UMLS")) arr.push(curie.replace("UMLS:", ""));
return arr;
},
[],
) ?? []
);
}

get semanticType(): string[] {
return this.normalizedInfo?.primaryTypes.map(semanticType => `biolink:${semanticType}`) ?? [];
return (
this.normalizedInfo?.primaryTypes.map(
semanticType => `biolink:${semanticType}`,
) ?? []
);
}

get semanticTypes(): string[] {
return this.normalizedInfo?.semanticTypes.map(semanticType => `biolink:${semanticType}`) ?? [];
return (
this.normalizedInfo?.semanticTypes.map(
semanticType => `biolink:${semanticType}`,
) ?? []
);
}

get label(): string {
Expand Down Expand Up @@ -157,30 +175,39 @@ export class Record {
reversedAPIEdge.input_type = frozen.association.output_type;
reversedAPIEdge.output_id = frozen.association.input_id;
reversedAPIEdge.output_type = frozen.association.input_type;
const predicate = this.qEdge.getReversedPredicate(frozen.association.predicate);
const predicate = this.qEdge.getReversedPredicate(
frozen.association.predicate,
);
reversedAPIEdge.predicate = predicate;
if (reversedAPIEdge.qualifiers) {
const reversedQualifiers = Object.fromEntries(
Object.entries(reversedAPIEdge.qualifiers).map(([qualifierType, qualifier]) => {
let newQualifierType: string = qualifierType;
let newQualifier: string | string[] = qualifier;
if (qualifierType.includes("predicate")) {
if (Array.isArray(qualifier)) {
newQualifier = qualifier.map(
(str: string) => `biolink:${this.qEdge.getReversedPredicate(str.replace("biolink:", ""))}`,
);
} else {
newQualifier = `biolink:${this.qEdge.getReversedPredicate(qualifier.replace("biolink:", ""))}`;
Object.entries(reversedAPIEdge.qualifiers).map(
([qualifierType, qualifier]) => {
let newQualifierType: string = qualifierType;
let newQualifier: string | string[] = qualifier;
if (qualifierType.includes("predicate")) {
if (Array.isArray(qualifier)) {
newQualifier = qualifier.map(
(str: string) =>
`biolink:${this.qEdge.getReversedPredicate(
str.replace("biolink:", ""),
)}`,
);
} else {
newQualifier = `biolink:${this.qEdge.getReversedPredicate(
qualifier.replace("biolink:", ""),
)}`;
}
}
}
if (qualifierType.includes("subject")) {
newQualifierType = qualifierType.replace("subject", "object");
}
if (qualifierType.includes("object")) {
newQualifierType = qualifierType.replace("object", "subject");
}
return [newQualifierType, newQualifier];
}),
if (qualifierType.includes("subject")) {
newQualifierType = qualifierType.replace("subject", "object");
}
if (qualifierType.includes("object")) {
newQualifierType = qualifierType.replace("object", "subject");
}
return [newQualifierType, newQualifier];
},
),
);

reversedAPIEdge.qualifiers = reversedQualifiers;
Expand All @@ -191,7 +218,13 @@ export class Record {
const temp = frozen.subject;
frozen.subject = frozen.object;
frozen.object = temp;
return new Record(frozen, this.config, frozen.association, this.qEdge, !this.reverseToExecution);
return new Record(
frozen,
this.config,
frozen.association,
this.qEdge,
!this.reverseToExecution,
);
}

queryDirection() {
Expand All @@ -203,7 +236,9 @@ export class Record {
}

// for user-made records lacking qEdge
makeFakeQEdge(record: FrozenRecord | VerboseFrozenRecord | MinimalFrozenRecord): QEdge {
makeFakeQEdge(
record: FrozenRecord | VerboseFrozenRecord | MinimalFrozenRecord,
): QEdge {
return {
getID(): string {
return "fakeEdge";
Expand Down Expand Up @@ -244,14 +279,18 @@ export class Record {
};
}

makeAPIEdge(record: FrozenRecord | VerboseFrozenRecord | MinimalFrozenRecord): Association {
makeAPIEdge(
record: FrozenRecord | VerboseFrozenRecord | MinimalFrozenRecord,
): Association {
return {
predicate: record.predicate?.replace("biolink:", ""),
qualifiers: record.qualifiers
? Object.fromEntries(
Object.entries(record.qualifiers).map(([qualifierType, qualifier]: [string, string]) => {
return [qualifierType.replace("biolink:", ""), qualifier];
}),
Object.entries(record.qualifiers).map(
([qualifierType, qualifier]: [string, string]) => {
return [qualifierType.replace("biolink:", ""), qualifier];
},
),
)
: undefined,
api_name: record.api,
Expand All @@ -267,8 +306,13 @@ export class Record {
return records.map((record: Record): FrozenRecord => record.freeze());
}

public static unfreezeRecords(records: FrozenRecord[], config?: any): Record[] {
return records.map((record: FrozenRecord): Record => new Record(record, config));
public static unfreezeRecords(
records: FrozenRecord[],
config?: any,
): Record[] {
return records.map(
(record: FrozenRecord): Record => new Record(record, config),
);
}

public static packRecords(records: Record[]): RecordPackage {
Expand All @@ -281,7 +325,9 @@ export class Record {

const apiEdgeHash = hash(JSON.stringify(record.association));

let apiEdgeHashIndex = apiEdgeHashes.findIndex(hash => hash === apiEdgeHash);
let apiEdgeHashIndex = apiEdgeHashes.findIndex(
hash => hash === apiEdgeHash,
);

if (apiEdgeHashIndex === -1) {
apiEdgeHashes.push(apiEdgeHash);
Expand All @@ -298,7 +344,11 @@ export class Record {
return [apiEdges, ...frozenRecords];
}

public static unpackRecords(recordPack: RecordPackage, qEdge: QEdge, config?: any): Record[] {
public static unpackRecords(
recordPack: RecordPackage,
qEdge: QEdge,
config?: any,
): Record[] {
const [apiEdges, ...frozenRecords] = recordPack;
return frozenRecords.map((record: any): Record => {
const apiEdge = apiEdges[record.apiEdge];
Expand Down Expand Up @@ -353,17 +403,24 @@ export class Record {
return attributes
? attributes.reduce((arr: EdgeAttribute[], attribute: EdgeAttribute) => {
attribute.attributes
? arr.push(attribute, ...this._getFlattenedEdgeAttributes(attribute.attributes))
? arr.push(
attribute,
...this._getFlattenedEdgeAttributes(attribute.attributes),
)
: arr.push(attribute);
return arr;
}, [])
: [];
}

get _configuredEdgeAttributesForHash(): string {
return this._getFlattenedEdgeAttributes(this.mappedResponse["edge-attributes"])
return this._getFlattenedEdgeAttributes(
this.mappedResponse["edge-attributes"],
)
.filter(attribute => {
return this.config?.EDGE_ATTRIBUTES_USED_IN_RECORD_HASH?.includes(attribute.attribute_type_id);
return this.config?.EDGE_ATTRIBUTES_USED_IN_RECORD_HASH?.includes(
attribute.attribute_type_id,
);
})
.reduce((acc, attribute) => {
return [...acc, `${attribute.attribute_type_id}:${attribute.value}`];
Expand All @@ -378,10 +435,19 @@ export class Record {
this.object.curie,
Object.entries(this.qualifiers)
.sort(([qTa, qVa], [qTb, qVb]) => qTa.localeCompare(qTb))
.reduce((str, [qualifierType, qualifierValue]) => `${str};${qualifierType}:${qualifierValue}`, ""),
.reduce(
(str, [qualifierType, qualifierValue]) =>
`${str};${qualifierType}:${JSON.stringify(qualifierValue)}`,
"",
),
this.api,
this.metaEdgeSource,
this._configuredEdgeAttributesForHash,
JSON.stringify(
this.provenanceChain.sort((sourceA, sourceB) =>
sourceA.resource_id.localeCompare(sourceB.resource_id),
),
),
].join("-");
}

Expand All @@ -399,11 +465,16 @@ export class Record {
}
return Object.fromEntries(
Object.entries(this._qualifiers).map(([qualifierType, qualifier]) => {
const newQualifierType = `biolink:${qualifierType.replace("biolink:", "")}`;
const newQualifierType = `biolink:${qualifierType.replace(
"biolink:",
"",
)}`;
let newQualifier = qualifier;
if (qualifierType.includes("predicate")) {
if (Array.isArray(qualifier)) {
newQualifier = qualifier.map(str => `biolink:${str.replace("biolink", "")}`);
newQualifier = qualifier.map(
str => `biolink:${str.replace("biolink", "")}`,
);
} else {
newQualifier = `biolink:${qualifier.replace("biolink:", "")}`;
}
Expand Down Expand Up @@ -434,7 +505,9 @@ export class Record {
returnValue = _.cloneDeep(this.mappedResponse.trapi_sources);
} else {
returnValue.push({
resource_id: this.association.apiIsPrimaryKnowledgeSource ? this.apiInforesCurie : this.metaEdgeSource,
resource_id: this.association.apiIsPrimaryKnowledgeSource
? this.apiInforesCurie
: this.metaEdgeSource,
resource_role: "primary_knowledge_source",
});
if (!this.association.apiIsPrimaryKnowledgeSource) {
Expand Down
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