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[WIP] Configurable bgraph queries #441

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[WIP] Configurable bgraph queries #441

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3 changes: 2 additions & 1 deletion client/src/types/typesLex.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,8 @@ export interface QueryFieldEntry {
order?: number, // used to sort fields
// baseType/lexType defines the type conversion required from/to base/lex types
baseType: LexConvertType,
lexType: LexConvertType
lexType: LexConvertType,
queryFunctionConfig?: any,
}
export type QueryFieldMap = Record<QueryFieldKey, QueryFieldEntry>

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130 changes: 51 additions & 79 deletions client/src/utils/BGraphQueryUtil.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -42,17 +42,6 @@ const bioPathPost = (bgraphPathQuery, clause: Filter): any => {

// EDGE QUERIES
// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types
const bioEdgeTested = (bgraphPathQuery, clause: Filter): any => {
return bgraphPathQuery.filter(document => {
if (document._type === 'edge') {
const edge = document;
return edge.tested === Boolean(clause.values[0]);
}
// Document is not an edge
return false;
});
};
// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types
const bioEdgeType = (bgraphPathQuery, clause: Filter): any => {
return bgraphPathQuery.filter(document => {
if (document._type === 'edge') {
Expand Down Expand Up @@ -80,20 +69,47 @@ const bioEdgeDOI = (bgraphPathQuery, clause: Filter): any => {
};

// NODE QUERIES
// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types
const bioNodeName = (bgraphPathQuery, clause: Filter): any => {
let names = clause.values as string[];
// Filter matching case insensitive names
names = names.map(name => name.toLowerCase());
return bgraphPathQuery.filter(document => {
if (document._type === 'node') {
const node = document;
return names.some(name => name === node.name.toLowerCase());

const propertyMatchQueryFactory = (config: any): (bgQuery: any, clause: Filter) => any => {
return (bgQuery: any, clause: Filter): any => {
let values = clause.values;

if (config.matchType === 'string' && config.toLowerCase) {
values = values.map(v => {
if (typeof v === 'string') {
return v.toLowerCase();
} else {
return v;
}
});
}
// Document is not a node
return false;
});

return bgQuery.filter(document => {
if (document._type === config.documentType) {
if (config.matchType === 'string') {
return values.some(v => {
let documentProperty = document[config.property];
if (config.toLowerCase) documentProperty = documentProperty.toLowerCase();
if (config.includes) {
return documentProperty.includes(v);
} else {
return v === documentProperty;
}
});
} else if (config.matchType === 'boolean') {
return document[config.property] === Boolean(values[0]);
} else if (config.matchType === 'number') {
return values.some(v => {
return document[config.property] === Number(v);
});
}
}
// Document is not specified document type
return false;
});
};
};

// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types
const bioNodeGroup = (bgraphPathQuery, clause: Filter): any => {
return bgraphPathQuery.filter(document => {
Expand All @@ -105,50 +121,6 @@ const bioNodeGroup = (bgraphPathQuery, clause: Filter): any => {
return false;
});
};
// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types
const bioNodeGrounded = (bgraphPathQuery, clause: Filter): any => {
return bgraphPathQuery.filter(document => {
if (document._type === 'node') {
const node = document;
return node.grounded_db === Boolean(clause.values[0]);
}
// Document type is an edge
return false;
});
};
// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types
const bioNodeGroundedOnto = (bgraphPathQuery, clause: Filter): any => {
return bgraphPathQuery.filter(document => {
if (document._type === 'node') {
const node = document;
return node.grounded_group === Boolean(clause.values[0]);
}
// Document type is an edge
return false;
});
};
// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types
const bioNodeInDegree = (bgraphPathQuery, clause: Filter): any => {
return bgraphPathQuery.filter(document => {
if (document._type === 'node') {
const node = document;
return clause.values.some(value => node.in_degree === Number(value));
}
// Document type is an edge
return false;
});
};
// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types
const bioNodeOutDegree = (bgraphPathQuery, clause: Filter): any => {
return bgraphPathQuery.filter(document => {
if (document._type === 'node') {
const node = document;
return clause.values.some(value => node.out_degree === Number(value));
}
// Document type is an edge
return false;
});
};

const docsClustersNodeTitle = (bgraphPathQuery, clause: Filter): any => {
let titles = clause.values as string[];
Expand Down Expand Up @@ -260,7 +232,7 @@ export const executeBgraphEdges = (bgraphEdgeQuery, clause: Filter): any => {
switch (clause.field) {
// EDGE CLAUSES
case QUERY_FIELDS_MAP.BIO_EDGE_PRE.field: return bgraphEdgeQuery;
case QUERY_FIELDS_MAP.BIO_EDGE_TESTED.field: return bioEdgeTested(bgraphEdgeQuery, clause);
case QUERY_FIELDS_MAP.BIO_EDGE_TESTED.field: return propertyMatchQueryFactory(QUERY_FIELDS_MAP.BIO_EDGE_TESTED.queryFunctionConfig)(bgraphEdgeQuery, clause);
case QUERY_FIELDS_MAP.BIO_EDGE_TYPE.field: return bioEdgeType(bgraphEdgeQuery, clause);
case QUERY_FIELDS_MAP.BIO_EDGE_DOI.field: return bioEdgeDOI(bgraphEdgeQuery, clause);
case QUERY_FIELDS_MAP.BIO_EDGE_POST.field: return bgraphEdgeQuery.as('edgeOnly').out().as('target').back('edgeOnly').in().as('source').merge('edgeOnly', 'source', 'target');
Expand All @@ -276,15 +248,15 @@ export const executeBgraphPathQuery = (bgraphPathQuery, clause: Filter): any =>
case QUERY_FIELDS_MAP.BIO_PATH_PRE.field: return bioPathPre(bgraphPathQuery, clause);
case QUERY_FIELDS_MAP.BIO_PATH_PRE_NODE_FILTER_LOOP.field: return bioPathPreNodeFilterLoop(bgraphPathQuery, clause);
case QUERY_FIELDS_MAP.BIO_PATH_PRE_EDGE_FILTER_LOOP.field: return bioPathPreEdgeFilterLoop(bgraphPathQuery, clause);
case QUERY_FIELDS_MAP.BIO_EDGE_TESTED.field: return bioEdgeTested(bgraphPathQuery, clause);
case QUERY_FIELDS_MAP.BIO_EDGE_TESTED.field: return propertyMatchQueryFactory(QUERY_FIELDS_MAP.BIO_EDGE_TESTED.queryFunctionConfig)(bgraphPathQuery, clause);
case QUERY_FIELDS_MAP.BIO_EDGE_TYPE.field: return bioEdgeType(bgraphPathQuery, clause);
case QUERY_FIELDS_MAP.BIO_EDGE_DOI.field: return bioEdgeDOI(bgraphPathQuery, clause);
case QUERY_FIELDS_MAP.BIO_NODE_NAME.field: return bioNodeName(bgraphPathQuery, clause);
case QUERY_FIELDS_MAP.BIO_NODE_NAME.field: return propertyMatchQueryFactory(QUERY_FIELDS_MAP.BIO_NODE_NAME.queryFunctionConfig)(bgraphPathQuery, clause);
case QUERY_FIELDS_MAP.BIO_NODE_GROUP.field: return bioNodeGroup(bgraphPathQuery, clause);
case QUERY_FIELDS_MAP.BIO_NODE_GROUNDED.field: return bioNodeGrounded(bgraphPathQuery, clause);
case QUERY_FIELDS_MAP.BIO_NODE_GROUNDED_ONTO.field: return bioNodeGroundedOnto(bgraphPathQuery, clause);
case QUERY_FIELDS_MAP.BIO_NODE_IN_DEGREE.field: return bioNodeInDegree(bgraphPathQuery, clause);
case QUERY_FIELDS_MAP.BIO_NODE_OUT_DEGREE.field: return bioNodeOutDegree(bgraphPathQuery, clause);
case QUERY_FIELDS_MAP.BIO_NODE_GROUNDED.field: return propertyMatchQueryFactory(QUERY_FIELDS_MAP.BIO_NODE_GROUNDED.queryFunctionConfig)(bgraphPathQuery, clause);
case QUERY_FIELDS_MAP.BIO_NODE_GROUNDED_ONTO.field: return propertyMatchQueryFactory(QUERY_FIELDS_MAP.BIO_NODE_GROUNDED_ONTO.queryFunctionConfig)(bgraphPathQuery, clause);
case QUERY_FIELDS_MAP.BIO_NODE_IN_DEGREE.field: return propertyMatchQueryFactory(QUERY_FIELDS_MAP.BIO_NODE_IN_DEGREE.queryFunctionConfig)(bgraphPathQuery, clause);
case QUERY_FIELDS_MAP.BIO_NODE_OUT_DEGREE.field: return propertyMatchQueryFactory(QUERY_FIELDS_MAP.BIO_NODE_OUT_DEGREE.queryFunctionConfig)(bgraphPathQuery, clause);
case QUERY_FIELDS_MAP.BIO_PATH_POST.field: return bioPathPost(bgraphPathQuery, clause);
// EPI PATH CLAUSES
case QUERY_FIELDS_MAP.EPI_PATH_PRE.field: return epiPathPre(bgraphPathQuery, clause);
Expand All @@ -300,12 +272,12 @@ export const executeBgraphNodes = (bgraphNodeQuery: any, clause: Filter): any =>
switch (clause.field) {
// NODE CLAUSES
case QUERY_FIELDS_MAP.BIO_NODE_PRE.field: return bgraphNodeQuery;
case QUERY_FIELDS_MAP.BIO_NODE_NAME.field: return bioNodeName(bgraphNodeQuery, clause);
case QUERY_FIELDS_MAP.BIO_NODE_NAME.field: return propertyMatchQueryFactory(QUERY_FIELDS_MAP.BIO_NODE_NAME.queryFunctionConfig)(bgraphNodeQuery, clause);
case QUERY_FIELDS_MAP.BIO_NODE_GROUP.field: return bioNodeGroup(bgraphNodeQuery, clause);
case QUERY_FIELDS_MAP.BIO_NODE_GROUNDED.field: return bioNodeGrounded(bgraphNodeQuery, clause);
case QUERY_FIELDS_MAP.BIO_NODE_GROUNDED_ONTO.field: return bioNodeGroundedOnto(bgraphNodeQuery, clause);
case QUERY_FIELDS_MAP.BIO_NODE_IN_DEGREE.field: return bioNodeInDegree(bgraphNodeQuery, clause);
case QUERY_FIELDS_MAP.BIO_NODE_OUT_DEGREE.field: return bioNodeOutDegree(bgraphNodeQuery, clause);
case QUERY_FIELDS_MAP.BIO_NODE_GROUNDED.field: return propertyMatchQueryFactory(QUERY_FIELDS_MAP.BIO_NODE_GROUNDED.queryFunctionConfig)(bgraphNodeQuery, clause);
case QUERY_FIELDS_MAP.BIO_NODE_GROUNDED_ONTO.field: return propertyMatchQueryFactory(QUERY_FIELDS_MAP.BIO_NODE_GROUNDED_ONTO.queryFunctionConfig)(bgraphNodeQuery, clause);
case QUERY_FIELDS_MAP.BIO_NODE_IN_DEGREE.field: return propertyMatchQueryFactory(QUERY_FIELDS_MAP.BIO_NODE_IN_DEGREE.queryFunctionConfig)(bgraphNodeQuery, clause);
case QUERY_FIELDS_MAP.BIO_NODE_OUT_DEGREE.field: return propertyMatchQueryFactory(QUERY_FIELDS_MAP.BIO_NODE_OUT_DEGREE.queryFunctionConfig)(bgraphNodeQuery, clause);
case QUERY_FIELDS_MAP.BIO_NODE_POST.field: return bgraphNodeQuery;
// DOC CLAUSES
// TODO: Currently we are using the BIO_NODE_PRE/POST for document cluster queries
Expand Down
31 changes: 31 additions & 0 deletions client/src/utils/QueryFieldsUtil.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -58,18 +58,34 @@ const QUERY_FIELDS_MAP: QueryFieldMap = {
..._searchable('Node Name', false),
baseType: 'string',
lexType: 'string',
queryFunctionConfig: {
documentType: 'node',
property: 'name',
matchType: 'string',
toLowerCase: true,
},
},
BIO_NODE_GROUNDED: {
..._field('bioNodeGrounded', 'Node Grounded'),
..._searchable('Node Grounded', false),
baseType: 'integer',
lexType: 'integer',
queryFunctionConfig: {
documentType: 'node',
property: 'grounded_db',
matchType: 'boolean',
},
},
BIO_NODE_GROUNDED_ONTO: {
..._field('bioNodeGroundedOnto', 'Node Grounded Onto'),
..._searchable('Node Grounded Onto', false),
baseType: 'integer',
lexType: 'integer',
queryFunctionConfig: {
documentType: 'node',
property: 'grounded_group',
matchType: 'boolean',
},
},
BIO_NODE_GROUP: {
..._field('bioNodeGroup', 'Node Group'),
Expand All @@ -82,12 +98,22 @@ const QUERY_FIELDS_MAP: QueryFieldMap = {
..._searchable('Node In-degree', false),
baseType: 'integer',
lexType: 'integer',
queryFunctionConfig: {
documentType: 'node',
property: 'in_degree',
matchType: 'number',
},
},
BIO_NODE_OUT_DEGREE: {
..._field('bioNodeOutDegree', 'Node Out-degree'),
..._searchable('Node Out-degree', false),
baseType: 'integer',
lexType: 'integer',
queryFunctionConfig: {
documentType: 'node',
property: 'out_degree',
matchType: 'number',
},
},
BIO_NODE_POST: {
..._field('bioNodePost', 'Node Post'),
Expand Down Expand Up @@ -119,6 +145,11 @@ const QUERY_FIELDS_MAP: QueryFieldMap = {
..._searchable('Edge Tested', false),
baseType: 'integer',
lexType: 'integer',
queryFunctionConfig: {
documentType: 'edge',
property: 'tested',
matchType: 'boolean',
},
},
BIO_EDGE_DOI: {
..._field('bioEdgeDoi', 'Edge DOI'),
Expand Down