From 10c42ab992c519aaa0529ca7453cdba54a2814e8 Mon Sep 17 00:00:00 2001 From: smessie Date: Tue, 9 Jul 2024 15:30:42 +0200 Subject: [PATCH 01/16] feat: Move time-based fragmentation to dedicated bucketizer --- package-lock.json | 17 +-- package.json | 4 +- processor.ttl | 30 ----- src/fragmentHelper.ts | 294 +----------------------------------------- src/index.ts | 292 ++++++++++++++++------------------------- 5 files changed, 122 insertions(+), 515 deletions(-) diff --git a/package-lock.json b/package-lock.json index f1ac38a..c60d9ae 100644 --- a/package-lock.json +++ b/package-lock.json @@ -10,7 +10,7 @@ "license": "MIT", "dependencies": { "@treecg/types": "^0.4.6", - "mongodb": "^6.7.0", + "mongodb": "^6.8.0", "n3": "^1.17.3", "winston": "^3.13.0" }, @@ -3010,7 +3010,7 @@ }, "node_modules/ip-address": { "version": "9.0.5", - "devOptional": true, + "dev": true, "license": "MIT", "dependencies": { "jsbn": "1.1.0", @@ -3371,7 +3371,7 @@ }, "node_modules/jsbn": { "version": "1.1.0", - "devOptional": true, + "dev": true, "license": "MIT" }, "node_modules/jsesc": { @@ -3795,8 +3795,9 @@ } }, "node_modules/mongodb": { - "version": "6.7.0", - "license": "Apache-2.0", + "version": "6.8.0", + "resolved": "https://registry.npmjs.org/mongodb/-/mongodb-6.8.0.tgz", + "integrity": "sha512-HGQ9NWDle5WvwMnrvUxsFYPd3JEbqD3RgABHBQRuoCEND0qzhsd0iH5ypHsf1eJ+sXmvmyKpP+FLOKY8Il7jMw==", "dependencies": { "@mongodb-js/saslprep": "^1.1.5", "bson": "^6.7.0", @@ -4790,7 +4791,7 @@ }, "node_modules/smart-buffer": { "version": "4.2.0", - "devOptional": true, + "dev": true, "license": "MIT", "engines": { "node": ">= 6.0.0", @@ -4799,7 +4800,7 @@ }, "node_modules/socks": { "version": "2.8.3", - "devOptional": true, + "dev": true, "license": "MIT", "dependencies": { "ip-address": "^9.0.5", @@ -4827,7 +4828,7 @@ }, "node_modules/sprintf-js": { "version": "1.1.3", - "devOptional": true, + "dev": true, "license": "BSD-3-Clause" }, "node_modules/stack-trace": { diff --git a/package.json b/package.json index 4b4807a..79c45f1 100644 --- a/package.json +++ b/package.json @@ -26,8 +26,8 @@ ], "license": "MIT", "devDependencies": { - "@rdfc/js-runner": "^0.2.1", "@jest/globals": "^29.7.0", + "@rdfc/js-runner": "^0.2.1", "@types/n3": "^1.16.4", "@types/node": "^20.14.2", "mongodb-memory-server": "^9.3.0", @@ -35,7 +35,7 @@ }, "dependencies": { "@treecg/types": "^0.4.6", - "mongodb": "^6.7.0", + "mongodb": "^6.8.0", "n3": "^1.17.3", "winston": "^3.13.0" } diff --git a/processor.ttl b/processor.ttl index 0020a6c..dae38b5 100644 --- a/processor.ttl +++ b/processor.ttl @@ -58,18 +58,6 @@ js:Ingest a js:JsProcess; a fnom:PositionParameterMapping; fnom:functionParameter "Database config"; fnom:implementationParameterPosition "2"^^xsd:int; - ], [ - a fnom:PositionParameterMapping; - fnom:functionParameter "Page Size"; - fnom:implementationParameterPosition "3"^^xsd:int; - ], [ - a fnom:PositionParameterMapping; - fnom:functionParameter "Branch Size"; - fnom:implementationParameterPosition "4"^^xsd:int; - ], [ - a fnom:PositionParameterMapping; - fnom:functionParameter "Min bucket span"; - fnom:implementationParameterPosition "5"^^xsd:int; ]; ]. @@ -93,23 +81,5 @@ js:Ingest a js:JsProcess; sh:minCount 1; sh:maxCount 1; sh:name "Database config"; - ], [ - sh:datatype xsd:integer; - sh:path js:pageSize; - sh:maxCount 1; - sh:defaultValue 100; - sh:name "Page Size"; - ], [ - sh:datatype xsd:integer; - sh:path js:branchSize; - sh:maxCount 1; - sh:defaultValue 4; - sh:name "Branch Size"; - ], [ - sh:datatype xsd:integer; - sh:path js:minBucketSpan; - sh:maxCount 1; - sh:defaultValue 300; - sh:name "Min bucket span"; ]. diff --git a/src/fragmentHelper.ts b/src/fragmentHelper.ts index 67c7668..815b146 100644 --- a/src/fragmentHelper.ts +++ b/src/fragmentHelper.ts @@ -1,9 +1,4 @@ - -import type * as RDF from '@rdfjs/types'; -import { Member, RelationType } from '@treecg/types'; -import { Collection } from "mongodb"; -import type { Logger } from 'winston'; -import { DataRecord } from '.'; +import {RelationType} from '@treecg/types'; export type TREEFragment = { id?: string, @@ -24,290 +19,3 @@ export type TREEFragment = { root: boolean, page: number }; - -export type ExtractIndices = (member: Member, mongo: Collection, timestampPath?: RDF.Term) => Promise; - -export interface Fragment { - streamId: string, - extract: ExtractIndices, -} - -// TODO: Check if scheduling updates for each new fragment using setTimeout -// is the best way to handle immutable labeling. -export async function handleTimestampPath( - id: string | null, - streamId: string, - path: string, - timestampValue: Date, - memberId: string, - indexColl: Collection, - memberColl: Collection, - maxSize: number, - k: number = 4, - minBucketSpan: number, - logger: Logger -) { - logger.debug("-----------------------------------------------------------------------------------"); - logger.debug(`[ingest] handleTimeStamp: Processing record ${memberId} with timestamp ${timestampValue.toISOString()}`); - - // Candidate fragment where we want to put this member (most granular fragment) - const candidateFragment: undefined | TREEFragment = ( - await indexColl.find({ streamId, timeStamp: { "$lte": timestampValue } }) - .sort({ timeStamp: -1, span: -1, page: -1 }).limit(1).toArray() - )[0]; - - if (candidateFragment) { - logger.debug(`[ingest] handleTimeStamp: Found this closest candidate fragment: ${candidateFragment.timeStamp?.toISOString()} (page ${candidateFragment.page})`); - - // Check if this member belongs to a new top level fragment (i.e. a new year) - if (timestampValue.getFullYear() > candidateFragment.timeStamp!.getFullYear()) { - await indexColl.insertOne(createNewYearFragment(streamId, id, memberId, timestampValue.getFullYear())); - logger.debug(`[ingest] handleTimeStamp: Created new top level fragment spanning 1 year: ${timestampValue.getFullYear()}`); - return; - } - - // Check if this fragment is still mutable - if (!candidateFragment.immutable) { - // We can still write this member to this fragment, unless it is full already - if (candidateFragment.count < maxSize) { - // There is still room in this fragment - await indexColl.updateOne( - candidateFragment, - { - $inc: { count: 1 }, - $push: { members: memberId } - } - ); - logger.debug(`[ingest] handleTimeStamp: Added new record to candidate fragment ${candidateFragment.timeStamp?.toISOString()}`); - return; - } else { - // We need to further split this fragment in k sub-fragments (recursively), - // while respecting the fragment max size - await splitFragmentRecursively( - k, - maxSize, - candidateFragment, - memberId, - streamId, - path, - memberColl, - indexColl, - minBucketSpan, - logger - ); - } - } else { - // TODO: implement optional strict mode that fails in this case - logger.warn(`[ingest] handleTimeStamp: Received out of order member (${memberId}) or current bucket has already expired (${candidateFragment.id})`); - return; - } - } else { - // Check if there is no candidate fragment because this is the first fragment ever - // or because this member is older than all existing fragments - if (await indexColl.countDocuments() > 0) { - // TODO: implement optional strict mode that fails in this case - logger.warn(`[ingest] handleTimeStamp: Received out of order member that cannot be added to the collection: ${memberId}`); - } else { - // This is the first fragment ever. Let's create a fragment spanning 1 year based on the member's timestamp - const currYear = timestampValue.getFullYear(); - await indexColl.insertOne(createNewYearFragment(streamId, id, memberId, currYear)); - logger.debug(`[ingest] handleTimeStamp: Created initial fragment spanning 1 year: ${currYear}`); - } - } -} - -function createNewYearFragment( - streamId: string, - id: string | null, - memberId: string, - year: number): TREEFragment { - const timeStamp = new Date(); - timeStamp.setUTCFullYear(year); - timeStamp.setUTCMonth(0); - timeStamp.setUTCDate(1); - timeStamp.setUTCHours(0, 0, 0, 0); - - return { - streamId, - id: id ? id : `${timeStamp.toISOString()}/31536000000/0`, - timeStamp, - relations: [], - members: [memberId], - count: 1, - span: 31536000000, - immutable: false, - root: true, - page: 0 - } -} - -async function splitFragmentRecursively( - k: number, - maxSize: number, - candidateFragment: TREEFragment, - newMember: string | null, - streamId: string, - path: string, - memberColl: Collection, - indexColl: Collection, - minBucketSpan: number, - logger: Logger -) { - // Time span for new sub-fragment(s) - const newSpan = candidateFragment.span / k; - // Gather all the members of the full fragment - const membersRefs = candidateFragment.members!; - if (newMember) { - // Include the new member (if any) - membersRefs.push(newMember); - } - const members = await memberColl.find({ id: { $in: membersRefs } }).toArray(); - // Sort members per timestamp - members.sort((a, b) => a.timestamp.getTime() - b.timestamp.getTime()); - - if (newSpan < minBucketSpan * 1000) { - // We don't want to split temporal fragments under a given time resolution. - // Instead we opt for a 1-dimensional pagination when the amount of members - // is too high for a very short time span. - - const baseBucketId = `${candidateFragment.timeStamp!.toISOString()}/${candidateFragment.span}`; - - const newFragment: TREEFragment = { - id: `${baseBucketId}/${candidateFragment.page + 1}`, - streamId, - relations: [], - members: members.slice(maxSize).map(m => m.id), - count: members.slice(maxSize).map(m => m.id).length, - timeStamp: candidateFragment.timeStamp!, - span: candidateFragment.span, - immutable: false, - root: false, - page: candidateFragment.page + 1 - }; - - const newRelation = { - type: RelationType.Relation, - bucket: `${baseBucketId}/${candidateFragment.page + 1}`, - timestampRelation: false - }; - - // Persist new paginated fragment and its relation - await Promise.all([ - indexColl.insertOne(newFragment), - indexColl.updateOne( - { id: candidateFragment.id! }, - { - $set: { - streamId, - members: members.slice(0, maxSize).map(m => m.id), - count: maxSize, - relations: [newRelation], - timeStamp: candidateFragment.timeStamp, - span: candidateFragment.span, - immutable: candidateFragment.immutable, - root: candidateFragment.root, - page: candidateFragment.page - } - }, - { upsert: true } - ) - ]); - logger.debug(`Added paginated (page ${newFragment.page}) new sub-fragment ${newFragment.timeStamp?.toISOString()}`); - - } else { - // New relations to be added - const newRelations: TREEFragment["relations"] = [] - // New sub-fragments - const subFragments: TREEFragment[] = []; - - for (let i = 0; i < k; i++) { - const newTs = new Date(candidateFragment.timeStamp!.getTime() + (i * newSpan)); - const subFragment: TREEFragment = { - id: `${newTs.toISOString()}/${newSpan}/0`, - streamId, - relations: [], - members: [], - count: 0, - timeStamp: newTs, - span: newSpan, - immutable: false, - root: false, - page: 0 - }; - - for (const member of members) { - // Check which members belong in this new sub-fragment - if (member.timestamp.getTime() >= newTs.getTime() - && member.timestamp.getTime() < (newTs.getTime() + newSpan)) { - subFragment.members?.push(member.id); - subFragment.count++; - - } - } - - // These are the new relations that are added from the originally full - // candidate fragment towards this new sub-fragment - newRelations.push(...[ - { - type: RelationType.GreaterThanOrEqualTo, - value: newTs.toISOString(), - bucket: subFragment.id!, - path, - timestampRelation: true - }, - { - type: RelationType.LessThan, - value: new Date(newTs.getTime() + newSpan).toISOString(), - bucket: subFragment.id!, - path, - timestampRelation: true - } - ]); - - // Check we if this new sub-fragment is violating the max size constraint - if (subFragment.members!.length > maxSize) { - // Further split this fragment that is currently too large - logger.debug(`Splitting one level deeper for sub-fragment ${subFragment.timeStamp?.toISOString()} (span: ${subFragment.span})`); - await splitFragmentRecursively( - k, - maxSize, - subFragment, - null, - streamId, - path, - memberColl, - indexColl, - minBucketSpan, - logger - ); - } else { - // Sub-fragment to be persisted in a bulk operation - subFragments.push(subFragment); - } - } - - // Persist new sub-fragments and their relations - await Promise.all([ - indexColl.insertMany(subFragments), - indexColl.updateOne( - { id: candidateFragment.id! }, - { - $set: { - streamId, - members: [], - count: 0, - timeStamp: candidateFragment.timeStamp, - span: candidateFragment.span, - immutable: candidateFragment.immutable, - root: candidateFragment.root, - page: candidateFragment.page - }, - $push: { relations: { $each: newRelations } } - }, - { upsert: true } - ) - ]); - logger.debug(`Added ${subFragments.length} new sub-fragments (${subFragments.map(sf => ` ${sf.id}`)})`); - } -} - diff --git a/src/index.ts b/src/index.ts index c6e47f4..477292b 100644 --- a/src/index.ts +++ b/src/index.ts @@ -1,23 +1,16 @@ import type * as RDF from "@rdfjs/types"; -import { Stream } from "@rdfc/js-runner"; -import { - LDES, - Member, - PROV, - RDF as RDFT, - RelationType, - SDS, -} from "@treecg/types"; -import { Collection, MongoClient } from "mongodb"; -import { Parser, Writer } from "n3"; -import { env } from "process"; +import {Stream} from "@rdfc/js-runner"; +import {LDES, Member, PROV, RDF as RDFT, RelationType, SDS,} from "@treecg/types"; +import {Collection, MongoClient} from "mongodb"; +import {Parser, Writer} from "n3"; +import {env} from "process"; import winston from "winston"; -import { handleTimestampPath, TREEFragment } from "./fragmentHelper"; +import {TREEFragment} from "./fragmentHelper"; const consoleTransport = new winston.transports.Console(); const logger = winston.createLogger({ format: winston.format.combine( - winston.format.colorize({ level: true }), + winston.format.colorize({level: true}), winston.format.simple(), ), transports: [consoleTransport], @@ -106,59 +99,10 @@ function maybe_parse(data: RDF.Quad[] | string): RDF.Quad[] { } } -function getRelatedBuckets( - quads: RDF.Quad[], - bucket: RDF.Term, - done: Set, -): RDF.Term[] { - const set: RDF.Term[] = []; - const get = (q: RDF.Term) => { - if (done.has(q.value)) { - return; - } - done.add(q.value); - set.push(q); - // Find forward relations - quads - .filter( - (x) => x.subject.equals(q) && x.predicate.equals(SDS.terms.relation), - ) - .map((x) => x.object) - .flatMap((bn) => - quads - .filter( - (q) => - q.subject.equals(bn) && - q.predicate.equals(SDS.terms.relationBucket), - ) - .map((x) => x.object), - ) - .forEach(get); - - // Find backwards relations - quads - .filter( - (x) => - x.object.equals(q) && x.predicate.equals(SDS.terms.relationBucket), - ) - .map((x) => x.subject) - .flatMap((bn) => - quads - .filter( - (q) => - q.object.equals(bn) && q.predicate.equals(SDS.terms.relation), - ) - .map((x) => x.subject), - ) - .forEach(get); - }; - - get(bucket); - return set; -} - -function parseBool(bo?: string): boolean { - if (!bo) { +function parseBool(bo?: string): boolean | undefined { + if (bo === undefined) { + return undefined; + } else if (!bo) { return false; } else { const bos = bo.toLowerCase(); @@ -167,13 +111,24 @@ function parseBool(bo?: string): boolean { } function gatherBuckets( - buckets: Bucket[], data: RDF.Quad[], - subject: RDF.Term, - stream: string, - found: Set, -) { - for (let bucket of getRelatedBuckets(data, subject, found)) { +): Bucket[] { + const buckets: Bucket[] = []; + + const bucketTerms: Set = new Set(); + data.filter(q => + q.predicate.equals(RDFT.terms.type) + && q.object.equals(SDS.terms.custom("Bucket")) + && q.graph.equals(SDS.terms.custom("DataDescription"))) + .map(q => q.subject).forEach(bucket => bucketTerms.add(bucket)); + + data.filter(q => + q.predicate.equals(SDS.terms.bucket) + && q.graph.equals(SDS.terms.custom("DataDescription"))) + .map(q => q.object).forEach(bucket => bucketTerms.add(bucket)); + + bucketTerms.forEach(bucket => { + const isRoot = data.find( (q) => q.subject.equals(bucket) && @@ -184,6 +139,26 @@ function gatherBuckets( q.subject.equals(bucket) && q.predicate.equals(SDS.terms.custom("immutable")), )?.object.value; + + // If the subject has a triple with the Stream, use that one. Otherwise, we need to find the stream via the record the bucket is attached to. + const stream = data.find( + (q) => + q.subject.equals(bucket) && + q.predicate.equals(SDS.terms.stream), + )?.object.value || data.find( + (q) => + q.subject.equals(data.find( + (record) => + record.predicate.equals(SDS.terms.bucket) && + record.object.equals(bucket), + )?.subject) && + q.predicate.equals(SDS.terms.stream), + )?.object.value; + if (!stream) { + logger.error(`Found SDS bucket without a stream! ${bucket.value}`); + return; + } + const b = { root: isRoot === "true", id: bucket.value, @@ -192,6 +167,7 @@ function gatherBuckets( immutable: parseBool(immutable), }; + // Find all relations of the bucket const relations = data .filter( (q) => @@ -215,11 +191,12 @@ function gatherBuckets( q.predicate.equals(SDS.terms.relationValue), )?.object.value; - b.relations.push({ type, bucket: target, path, value }); + b.relations.push({type, bucket: target, path, value}); } buckets.push(b); - } + }); + return buckets; } function gatherRecords( @@ -268,6 +245,24 @@ function gatherRecords( return out; } +async function emptyBuckets(data: RDF.Quad[], collection: Collection) { + const bucketsToEmpty = data.filter(q => + q.predicate.equals(SDS.terms.custom("empty")) && + q.object.value === "true" && + q.graph.equals(SDS.terms.custom("DataDescription"))) + .map(q => q.subject); + + for (const bucket of bucketsToEmpty) { + await collection.updateOne( + {id: bucket.value}, + { + $set: {members: []}, + }, + {upsert: true}, + ); + } +} + // This could be a memory problem in the long run // TODO: Find a way to persist written records efficiently //const addedMembers: Set = new Set(); @@ -284,13 +279,17 @@ async function addDataRecord( //addedMembers.add(value); // Check if record is already written in the collection - const present = (await collection.countDocuments({ id: value })) > 0; + const present = (await collection.countDocuments({id: value})) > 0; if (present) return; const member = filterMember(quads, record.payload, [ (q) => q.predicate.equals(SDS.terms.payload), ]); + if (!member?.length) { + return; + } + const ser = new Writer().quadsToString(member); updateRecords.push({ @@ -302,6 +301,7 @@ async function addDataRecord( const setRoots: Set = new Set(); const immutables: Set = new Set(); + async function addBucket( bucket: Bucket, collection: Collection, @@ -310,32 +310,41 @@ async function addBucket( if (bucket.root && !setRoots.has(bucket.stream)) { setRoots.add(bucket.stream); await collection.updateOne( - { streamId: bucket.stream, id: bucket.id }, + {streamId: bucket.stream, id: bucket.id}, { - $set: { root: true }, + $set: {root: true}, }, - { upsert: true }, + {upsert: true}, ); } if (bucket.immutable && !immutables.has(bucket.id)) { immutables.add(bucket.id); await collection.updateOne( - { streamId: bucket.stream, id: bucket.id }, + {streamId: bucket.stream, id: bucket.id}, + { + $set: {immutable: true}, + }, + {upsert: true}, + ); + } else if (bucket.immutable === false) { + // If it is explicitly set as false, set it in the database, so we persist the bucket. + await collection.updateOne( + {streamId: bucket.stream, id: bucket.id}, { - $set: { immutable: true }, + $set: {immutable: false}, }, - { upsert: true }, + {upsert: true}, ); } for (let newRelation of bucket.relations) { await collection.updateOne( - { streamId: bucket.stream, id: bucket.id }, + {streamId: bucket.stream, id: bucket.id}, { - $push: { relations: newRelation }, + $addToSet: {relations: newRelation}, }, - { upsert: true }, + {upsert: true}, ); } } @@ -409,9 +418,9 @@ async function setup_metadata( const ser = new Writer().quadsToString(streamMember); await metaCollection.updateOne( - { type: SDS.Stream, id: streamId.value }, - { $set: { value: ser } }, - { upsert: true }, + {type: SDS.Stream, id: streamId.value}, + {$set: {value: ser}}, + {upsert: true}, ); } }; @@ -419,7 +428,7 @@ async function setup_metadata( metadata.data(handleMetadata); if (metadata.lastElement) { - handleMetadata(metadata.lastElement); + await handleMetadata(metadata.lastElement); } } @@ -427,9 +436,6 @@ export async function ingest( data: Stream, metadata: Stream, database: DBConfig, - maxSize: number = 100, - k: number = 4, - minBucketSpan: number = 300 ) { const url = database.url || env.DB_CONN_STRING || "mongodb://localhost:27017/ldes"; const mongo = await new MongoClient(url).connect(); @@ -442,7 +448,6 @@ export async function ingest( let ingestMetadata = true; let ingestData = true; let closed = false; - let lastMemberTimestamp = null; const closeMongo = () => { if (!ingestMetadata && !ingestData && !closed) { @@ -472,53 +477,16 @@ export async function ingest( const bs = record.buckets; if (bs.length === 0) { await indexCollection.updateOne( - { root: true, streamId: record.stream, id: "" }, - { $push: { members: record.payload.value } }, - { upsert: true }, + {root: true, streamId: record.stream, id: ""}, + {$addToSet: {members: record.payload.value}}, + {upsert: true}, ); } else { for (let bucket of bs) { await indexCollection.updateOne( - { streamId: record.stream, id: bucket.value }, - { $push: { members: record.payload.value } }, - { upsert: true }, - ); - } - } - }; - - const pushTimstampMemberToDB = async (record: SDSRecord) => { - const bs = record.buckets; - const timestamp = new Date(record.timestampValue!); - - if (bs.length === 0) { - await handleTimestampPath( - null, - record.stream, - streamTimestampPaths[record.stream], - timestamp, - record.payload.value, - indexCollection, - memberCollection, - maxSize, - k, - minBucketSpan, - logger - ); - } else { - for (let bucket of bs) { - await handleTimestampPath( - bucket.value, - record.stream, - streamTimestampPaths[record.stream], - timestamp, - record.payload.value, - indexCollection, - memberCollection, - maxSize, - k, - minBucketSpan, - logger + {streamId: record.stream, id: bucket.value}, + {$addToSet: {members: record.payload.value}}, + {upsert: true}, ); } } @@ -550,56 +518,16 @@ export async function ingest( // Update INDEX collection accordingly for (const r of records) { - await (r.timestampValue ? pushTimstampMemberToDB(r) : pushMemberToDB(r)); + await pushMemberToDB(r); } - const isDefaultTimestamp = records[0].timestampValue !== undefined; - - // If the fragmentation strategy is the default timestamp-based - // we need to handle the labeling of buckets/fragments as immutable - // based on the current time - if (isDefaultTimestamp) { - // Last known member timestamp - lastMemberTimestamp = new Date(records[records.length -1].timestampValue!) - // Gather all mutable fragments that have expired - - // TODO: Check if we can directly update all expired fragments - // Not sure how to add the timestamp and the span while querying - const expiredBuckets = await indexCollection.find({ - timeStamp: { $lte: lastMemberTimestamp }, - immutable: false - }).toArray(); - - for (const buck of expiredBuckets) { - const expDate = buck.timeStamp!.getTime() + buck.span; - if (expDate < lastMemberTimestamp.getTime()) { - logger.debug(`Labeling bucket ${buck.timeStamp?.toISOString()} (span: ${buck.span}) as immutable`); - // Label these buckets as immutable - await indexCollection.updateOne(buck, { - $set: { immutable: true } - }); - } - } + const buckets: Bucket[] = gatherBuckets(data); + for (let bucket of buckets) { + await addBucket(bucket, indexCollection); } - // This next steps are only performed if the fragmentation strategy - // is already defined in the SDS metadata and the stream is not relying - // on the default timestamp-based strategy, which is handled within the - // pushTimstampMemberToDB() function. - if (!isDefaultTimestamp) { - const found: Set = new Set(); - const buckets: Bucket[] = []; - - for (const r of records) { - r.buckets.forEach((b) => - gatherBuckets(buckets, data, b, r.stream, found), - ); - } - - for (let bucket of buckets) { - await addBucket(bucket, indexCollection); - } - } + // Empty buckets that are marked so. + await emptyBuckets(data, indexCollection); }); logger.debug("[ingest] Attached data handler"); From 35a66475ba52c7ee2d73ed1d7b2c89067c1dd786 Mon Sep 17 00:00:00 2001 From: smessie Date: Wed, 10 Jul 2024 17:22:58 +0200 Subject: [PATCH 02/16] test: Update existing tests --- package-lock.json | 3412 ++++++++++++++++++++++++++-------------- test/ingest.test.ts | 16 +- test/processor.test.ts | 12 +- 3 files changed, 2267 insertions(+), 1173 deletions(-) diff --git a/package-lock.json b/package-lock.json index c60d9ae..c6fba11 100644 --- a/package-lock.json +++ b/package-lock.json @@ -23,10 +23,33 @@ "typescript": "^5.4.5" } }, + "node_modules/@75lb/deep-merge": { + "version": "1.1.1", + "resolved": "https://registry.npmjs.org/@75lb/deep-merge/-/deep-merge-1.1.1.tgz", + "integrity": "sha512-xvgv6pkMGBA6GwdyJbNAnDmfAIR/DfWhrj9jgWh3TY7gRm3KO46x/GPjRg6wJ0nOepwqrNxFfojebh0Df4h4Tw==", + "dev": true, + "dependencies": { + "lodash.assignwith": "^4.2.0", + "typical": "^7.1.1" + }, + "engines": { + "node": ">=12.17" + } + }, + "node_modules/@75lb/deep-merge/node_modules/typical": { + "version": "7.1.1", + "resolved": "https://registry.npmjs.org/typical/-/typical-7.1.1.tgz", + "integrity": "sha512-T+tKVNs6Wu7IWiAce5BgMd7OZfNYUndHwc5MknN+UHOudi7sGZzuHdCadllRuqJ3fPtgFtIH9+lt9qRv6lmpfA==", + "dev": true, + "engines": { + "node": ">=12.17" + } + }, "node_modules/@ampproject/remapping": { "version": "2.3.0", + "resolved": "https://registry.npmjs.org/@ampproject/remapping/-/remapping-2.3.0.tgz", + "integrity": "sha512-30iZtAPgz+LTIYoeivqYo853f02jBYSd5uGnGpkFV0M3xOt9aN73erkgYAmZU43x4VfqcnLxW9Kpg3R5LC4YYw==", "dev": true, - "license": "Apache-2.0", "dependencies": { "@jridgewell/gen-mapping": "^0.3.5", "@jridgewell/trace-mapping": "^0.3.24" @@ -37,8 +60,9 @@ }, "node_modules/@babel/code-frame": { "version": "7.24.7", + "resolved": "https://registry.npmjs.org/@babel/code-frame/-/code-frame-7.24.7.tgz", + "integrity": "sha512-BcYH1CVJBO9tvyIZ2jVeXgSIMvGZ2FDRvDdOIVQyuklNKSsx+eppDEBq/g47Ayw+RqNFE+URvOShmf+f/qwAlA==", "dev": true, - "license": "MIT", "dependencies": { "@babel/highlight": "^7.24.7", "picocolors": "^1.0.0" @@ -49,16 +73,18 @@ }, "node_modules/@babel/compat-data": { "version": "7.24.7", + "resolved": "https://registry.npmjs.org/@babel/compat-data/-/compat-data-7.24.7.tgz", + "integrity": "sha512-qJzAIcv03PyaWqxRgO4mSU3lihncDT296vnyuE2O8uA4w3UHWI4S3hgeZd1L8W1Bft40w9JxJ2b412iDUFFRhw==", "dev": true, - "license": "MIT", "engines": { "node": ">=6.9.0" } }, "node_modules/@babel/core": { "version": "7.24.7", + "resolved": "https://registry.npmjs.org/@babel/core/-/core-7.24.7.tgz", + "integrity": "sha512-nykK+LEK86ahTkX/3TgauT0ikKoNCfKHEaZYTUVupJdTLzGNvrblu4u6fa7DhZONAltdf8e662t/abY8idrd/g==", "dev": true, - "license": "MIT", "dependencies": { "@ampproject/remapping": "^2.2.0", "@babel/code-frame": "^7.24.7", @@ -86,16 +112,18 @@ }, "node_modules/@babel/core/node_modules/semver": { "version": 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"license": "MIT", "engines": { "node": ">=12" }, @@ -5662,8 +6761,9 @@ }, "node_modules/wrap-ansi/node_modules/strip-ansi": { "version": "7.1.0", + "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-7.1.0.tgz", + "integrity": "sha512-iq6eVVI64nQQTRYq2KtEg2d2uU7LElhTJwsH4YzIHZshxlgZms/wIc4VoDQTlG/IvVIrBKG06CrZnp0qv7hkcQ==", "dev": true, - "license": "MIT", "dependencies": { "ansi-regex": "^6.0.1" }, @@ -5674,26 +6774,17 @@ "url": "https://github.com/chalk/strip-ansi?sponsor=1" } }, - "node_modules/wrap-ansi/node_modules/strip-ansi/node_modules/ansi-regex": { - "version": "6.0.1", - "dev": true, - "license": "MIT", - "engines": { - "node": ">=12" - }, - "funding": { - "url": "https://github.com/chalk/ansi-regex?sponsor=1" - } - }, "node_modules/wrappy": { "version": "1.0.2", - "dev": true, - "license": "ISC" + "resolved": "https://registry.npmjs.org/wrappy/-/wrappy-1.0.2.tgz", + "integrity": "sha512-l4Sp/DRseor9wL6EvV2+TuQn63dMkPjZ/sp9XkghTEbV9KlPS1xUsZ3u7/IQO4wxtcFB4bgpQPRcR3QCvezPcQ==", + "dev": true }, "node_modules/write-file-atomic": { "version": "4.0.2", + "resolved": "https://registry.npmjs.org/write-file-atomic/-/write-file-atomic-4.0.2.tgz", + "integrity": "sha512-7KxauUdBmSdWnmpaGFg+ppNjKF8uNLry8LyzjauQDOVONfFLNKrKvQOxZ/VuTIcS/gge/YNahf5RIIQWTSarlg==", "dev": true, - "license": "ISC", "dependencies": { "imurmurhash": "^0.1.4", "signal-exit": "^3.0.7" @@ -5704,13 +6795,15 @@ }, "node_modules/write-file-atomic/node_modules/signal-exit": { "version": "3.0.7", - "dev": true, - "license": "ISC" + "resolved": "https://registry.npmjs.org/signal-exit/-/signal-exit-3.0.7.tgz", + "integrity": "sha512-wnD2ZE+l+SPC/uoS0vXeE9L1+0wuaMqKlfz9AMUo38JsyLSBWSFcHR1Rri62LZc12vLr1gb3jl7iwQhgwpAbGQ==", + "dev": true }, "node_modules/ws": { - "version": "8.17.0", + "version": "8.18.0", + "resolved": "https://registry.npmjs.org/ws/-/ws-8.18.0.tgz", + "integrity": "sha512-8VbfWfHLbbwu3+N6OKsOMpBdT4kXPDDB9cJk2bJ6mh9ucxdlnNvH1e+roYkKmN9Nxw2yjz7VzeO9oOz2zJ04Pw==", "dev": true, - "license": "MIT", "engines": { "node": ">=10.0.0" }, @@ -5729,13 +6822,15 @@ }, "node_modules/yallist": { "version": "3.1.1", - "dev": true, - "license": "ISC" + "resolved": "https://registry.npmjs.org/yallist/-/yallist-3.1.1.tgz", + "integrity": "sha512-a4UGQaWPH59mOXUYnAG2ewncQS4i4F43Tv3JoAM+s2VDAmS9NsK8GpDMLrCHPksFT7h3K6TOoUNn2pb7RoXx4g==", + "dev": true }, "node_modules/yaml": { "version": "2.4.5", + "resolved": "https://registry.npmjs.org/yaml/-/yaml-2.4.5.tgz", + "integrity": "sha512-aBx2bnqDzVOyNKfsysjA2ms5ZlnjSAW2eG3/L5G/CSujfjLJTJsEw1bGw8kCf04KodQWk1pxlGnZ56CRxiawmg==", "dev": true, - "license": "ISC", "bin": { "yaml": "bin.mjs" }, @@ -5745,8 +6840,9 @@ }, "node_modules/yauzl": { "version": "3.1.3", + "resolved": "https://registry.npmjs.org/yauzl/-/yauzl-3.1.3.tgz", + "integrity": "sha512-JCCdmlJJWv7L0q/KylOekyRaUrdEoUxWkWVcgorosTROCFWiS9p2NNPE9Yb91ak7b1N5SxAZEliWpspbZccivw==", "dev": true, - "license": "MIT", "dependencies": { "buffer-crc32": "~0.2.3", "pend": "~1.2.0" @@ -5757,16 +6853,18 @@ }, "node_modules/yn": { "version": "3.1.1", + "resolved": "https://registry.npmjs.org/yn/-/yn-3.1.1.tgz", + "integrity": "sha512-Ux4ygGWsu2c7isFWe8Yu1YluJmqVhxqK2cLXNQA5AcC3QfbGNpM7fu0Y8b/z16pXLnFxZYvWhd3fhBY9DLmC6Q==", "dev": true, - "license": "MIT", "engines": { "node": ">=6" } }, "node_modules/yocto-queue": { - "version": "1.0.0", + "version": "1.1.1", + "resolved": "https://registry.npmjs.org/yocto-queue/-/yocto-queue-1.1.1.tgz", + "integrity": "sha512-b4JR1PFR10y1mKjhHY9LaGo6tmrgjit7hxVIeAmyMw3jegXR4dhYqLaQF5zMXZxY7tLpMyJeLjr1C4rLmkVe8g==", "dev": true, - "license": "MIT", "engines": { "node": ">=12.20" }, diff --git a/test/ingest.test.ts b/test/ingest.test.ts index 44ca20f..b1c6250 100644 --- a/test/ingest.test.ts +++ b/test/ingest.test.ts @@ -7,6 +7,7 @@ import { RelationType, SDS } from "@treecg/types"; import { TREEFragment } from "../src/fragmentHelper"; describe("Functional tests for the ingest function", () => { + /* const PREFIXES = ` @prefix rdfs: . @prefix p-plan: . @@ -25,7 +26,7 @@ describe("Functional tests for the ingest function", () => { ${PREFIXES} ex:somePlan a p-plan:Plan; rdfs:comment "An epic plan to publish an LDES". - + ex:streamVar0 a p-plan:Variable; p-plan:isVariableOfPlan ex:somePlan. @@ -65,7 +66,7 @@ describe("Functional tests for the ingest function", () => { p-plan:correspondsToStep ex:step1; prov:used ex:rmlStream ]; - sds:carries [ a sds:Member ]; + sds:carries [ a sds:Member ]; sds:dataset [ a dcat:Dataset; dcat:title "Epic dataset"; @@ -130,7 +131,7 @@ describe("Functional tests for the ingest function", () => { // Max number of members allowed per fragment const m = 10; - // Number of sub-fragments per level in the default B+Tree structure + // Number of sub-fragments per level in the default B+Tree structure const k = 4; // Total number of members to be pushed const n = 100 @@ -206,7 +207,7 @@ describe("Functional tests for the ingest function", () => { // Max number of members allowed per fragment const m = 100; - // Number of sub-fragments per level in the default B+Tree structure + // Number of sub-fragments per level in the default B+Tree structure const k = 3; // Total number of members to be pushed const n = 1000; @@ -282,7 +283,7 @@ describe("Functional tests for the ingest function", () => { // Max number of members allowed per fragment const m = 10; - // Number of sub-fragments per level in the default B+Tree structure + // Number of sub-fragments per level in the default B+Tree structure const k = 4; // Total number of members to be pushed const n = 100 @@ -364,7 +365,7 @@ describe("Functional tests for the ingest function", () => { // Max number of members allowed per fragment const m = 10; - // Number of sub-fragments per level in the default B+Tree structure + // Number of sub-fragments per level in the default B+Tree structure const k = 4; // Total number of members to be pushed const n = 500; @@ -435,6 +436,7 @@ describe("Functional tests for the ingest function", () => { } } }); + */ }); function* dataGenerator(n: number, inc: number, startDate?: Date): Generator { @@ -463,4 +465,4 @@ function* dataGenerator(n: number, inc: number, startDate?: Date): Generator { js:metadata "meta"; js:data "data"; js:index "index"; - ]; - js:pageSize 500; - js:branchSize 3; - js:minBucketSpan 600. + ]. `; const baseIRI = process.cwd() + "/config.ttl"; console.log(baseIRI); @@ -51,9 +48,9 @@ describe("SDS storage writer tests", () => { const argss = extractSteps(proc, quads, config); expect(argss.length).toBe(1); - expect(argss[0].length).toBe(6); + expect(argss[0].length).toBe(3); - const [[i, mi, db, pageSize, branchSize, minBucketSpan]] = argss; + const [[i, mi, db]] = argss; testReader(i); testReader(mi); expect(db).toBeDefined(); @@ -61,9 +58,6 @@ describe("SDS storage writer tests", () => { expect(db.index).toBe("index"); expect(db.metadata).toBe("meta"); expect(db.data).toBe("data"); - expect(pageSize).toBe(500); - expect(branchSize).toBe(3); - expect(minBucketSpan).toBe(600); await checkProc(proc.file, proc.func); }); From b3c5fb2e1e160d9ce297323d48cbb4460508ac91 Mon Sep 17 00:00:00 2001 From: smessie Date: Wed, 10 Jul 2024 17:27:39 +0200 Subject: [PATCH 03/16] docs: Update readme --- README.md | 10 ++-------- 1 file changed, 2 insertions(+), 8 deletions(-) diff --git a/README.md b/README.md index c96550e..ed72cb9 100644 --- a/README.md +++ b/README.md @@ -4,7 +4,7 @@ Given an [SDS stream](https://w3id.org/sds/specification) and its correspondent stream of members, this processor will write everything into a supported data storage system. So far, it only supports MongoDB instances. -SDS stream updates are stored into MongoDB collections for the LDES server to find this information when serving requests. If a `ldes:timestampPath` property is given as part of the dataset metadata, the storage writer will automatically start up a timestamp fragmentation, based on a B+ Tree strategy. +SDS stream updates are stored into MongoDB collections for the LDES server to find this information when serving requests. An example of a SDS data stream with a predefined fragmentation strategy is shown next: @@ -54,9 +54,7 @@ This processor can be used within data processing pipelines to write a SDS strea js:metadata "METADATA"; js:data "DATA"; js:index "INDEX"; - ]; - js:pageSize 500; - js:branchSize 4. + ]. ``` ### As a library @@ -68,8 +66,6 @@ async function ingest( data: Stream, metadata: Stream, database: DBConfig, - maxsize: number = 100, - k: number = 4 ) { /* snip */ } ``` @@ -78,8 +74,6 @@ arguments: - `data`: a stream reader that carries data (as `string` or `Quad[]`). - `metadata`: a stream reader that carries SDS metadata (as `string` or `Quad[]`). - `database`: connection parameters for a reachable MongoDB instance. -- `maxsize`: max number of members per fragment. -- `k`: max number of child nodes in the default time-based B+ Tree fragmentation. ## Authors and License From e39e852397e11b5762c0a10cc5de5a07d668468e Mon Sep 17 00:00:00 2001 From: smessie Date: Wed, 10 Jul 2024 17:27:57 +0200 Subject: [PATCH 04/16] 0.3.0-alpha.1 --- package-lock.json | 4 ++-- package.json | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/package-lock.json b/package-lock.json index c6fba11..ece33dc 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,12 +1,12 @@ { "name": "@rdfc/sds-storage-writer-ts", - "version": "0.2.7", + "version": "0.3.0-alpha.1", "lockfileVersion": 3, "requires": true, "packages": { "": { "name": "@rdfc/sds-storage-writer-ts", - "version": "0.2.7", + "version": "0.3.0-alpha.1", "license": "MIT", "dependencies": { "@treecg/types": "^0.4.6", diff --git a/package.json b/package.json index 79c45f1..c38acd3 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "@rdfc/sds-storage-writer-ts", - "version": "0.2.7", + "version": "0.3.0-alpha.1", "description": "An RDF-Connect processor to write SDS streams into a given storage system", "main": "lib/index.js", "scripts": { From 774b9cbe370720a11364957dd74b80b9cab45a9a Mon Sep 17 00:00:00 2001 From: smessie Date: Mon, 15 Jul 2024 17:14:51 +0200 Subject: [PATCH 05/16] chore: Bulk write operations to MongoDB --- src/index.ts | 114 ++++++++++++++++++++++++--------------------------- 1 file changed, 54 insertions(+), 60 deletions(-) diff --git a/src/index.ts b/src/index.ts index 477292b..11bb378 100644 --- a/src/index.ts +++ b/src/index.ts @@ -1,7 +1,7 @@ import type * as RDF from "@rdfjs/types"; import {Stream} from "@rdfc/js-runner"; import {LDES, Member, PROV, RDF as RDFT, RelationType, SDS,} from "@treecg/types"; -import {Collection, MongoClient} from "mongodb"; +import {AnyBulkWriteOperation, Collection, MongoClient} from "mongodb"; import {Parser, Writer} from "n3"; import {env} from "process"; import winston from "winston"; @@ -245,22 +245,22 @@ function gatherRecords( return out; } -async function emptyBuckets(data: RDF.Quad[], collection: Collection) { +function emptyBuckets(data: RDF.Quad[], operations: AnyBulkWriteOperation[]) { const bucketsToEmpty = data.filter(q => q.predicate.equals(SDS.terms.custom("empty")) && q.object.value === "true" && q.graph.equals(SDS.terms.custom("DataDescription"))) .map(q => q.subject); - for (const bucket of bucketsToEmpty) { - await collection.updateOne( - {id: bucket.value}, - { + operations.push({ + updateMany: { + filter: {id: {$in: bucketsToEmpty.map(b => b.value)}}, + update: { $set: {members: []}, }, - {upsert: true}, - ); - } + upsert: true, + } + }); } // This could be a memory problem in the long run @@ -278,10 +278,6 @@ async function addDataRecord( //if (addedMembers.has(value)) return; //addedMembers.add(value); - // Check if record is already written in the collection - const present = (await collection.countDocuments({id: value})) > 0; - if (present) return; - const member = filterMember(quads, record.payload, [ (q) => q.predicate.equals(SDS.terms.payload), ]); @@ -290,6 +286,11 @@ async function addDataRecord( return; } + // Check if record is already written in the collection + const present = (await collection.countDocuments({id: value}, {limit: 1})) > 0; + if (present) return; + + const ser = new Writer().quadsToString(member); updateRecords.push({ @@ -302,51 +303,35 @@ async function addDataRecord( const setRoots: Set = new Set(); const immutables: Set = new Set(); -async function addBucket( +function addBucket( bucket: Bucket, - collection: Collection, + operations: AnyBulkWriteOperation[], ) { + const set: any = {}; // Handle root setting if (bucket.root && !setRoots.has(bucket.stream)) { setRoots.add(bucket.stream); - await collection.updateOne( - {streamId: bucket.stream, id: bucket.id}, - { - $set: {root: true}, - }, - {upsert: true}, - ); + set.root = true; } if (bucket.immutable && !immutables.has(bucket.id)) { immutables.add(bucket.id); - await collection.updateOne( - {streamId: bucket.stream, id: bucket.id}, - { - $set: {immutable: true}, - }, - {upsert: true}, - ); + set.immutable = true; } else if (bucket.immutable === false) { // If it is explicitly set as false, set it in the database, so we persist the bucket. - await collection.updateOne( - {streamId: bucket.stream, id: bucket.id}, - { - $set: {immutable: false}, - }, - {upsert: true}, - ); + set.immutable = false; } - for (let newRelation of bucket.relations) { - await collection.updateOne( - {streamId: bucket.stream, id: bucket.id}, - { - $addToSet: {relations: newRelation}, + operations.push({ + updateOne: { + filter: {streamId: bucket.stream, id: bucket.id}, + update: { + $set: set, + $addToSet: {relations: {$each: bucket.relations}}, }, - {upsert: true}, - ); - } + upsert: true, + } + }); } async function setup_metadata( @@ -473,22 +458,28 @@ export async function ingest( const memberCollection = db.collection(database.data); const indexCollection = db.collection(database.index); - const pushMemberToDB = async (record: SDSRecord) => { + const pushMemberToDB = (record: SDSRecord, operations: AnyBulkWriteOperation[]) => { const bs = record.buckets; if (bs.length === 0) { - await indexCollection.updateOne( - {root: true, streamId: record.stream, id: ""}, - {$addToSet: {members: record.payload.value}}, - {upsert: true}, - ); + operations.push({ + updateOne: { + filter: {root: true, streamId: record.stream, id: ""}, + update: { + $addToSet: {members: record.payload.value}, + }, + upsert: true, + } + }); } else { - for (let bucket of bs) { - await indexCollection.updateOne( - {streamId: record.stream, id: bucket.value}, - {$addToSet: {members: record.payload.value}}, - {upsert: true}, - ); - } + operations.push({ + updateMany: { + filter: {streamId: record.stream, id: {$in: bs.map(b => b.value)}}, + update: { + $addToSet: {members: record.payload.value}, + }, + upsert: true, + } + }); } }; @@ -517,17 +508,20 @@ export async function ingest( } // Update INDEX collection accordingly + const indexOperations: AnyBulkWriteOperation[] = []; for (const r of records) { - await pushMemberToDB(r); + pushMemberToDB(r, indexOperations); } const buckets: Bucket[] = gatherBuckets(data); for (let bucket of buckets) { - await addBucket(bucket, indexCollection); + addBucket(bucket, indexOperations); } // Empty buckets that are marked so. - await emptyBuckets(data, indexCollection); + emptyBuckets(data, indexOperations); + + await indexCollection.bulkWrite(indexOperations); }); logger.debug("[ingest] Attached data handler"); From 1db14edcdd31465c2b3a02a513191116d4d96171 Mon Sep 17 00:00:00 2001 From: smessie Date: Tue, 16 Jul 2024 10:24:26 +0200 Subject: [PATCH 06/16] 0.3.0-alpha.2 --- package-lock.json | 4 ++-- package.json | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/package-lock.json b/package-lock.json index ece33dc..954923e 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,12 +1,12 @@ { "name": "@rdfc/sds-storage-writer-ts", - "version": "0.3.0-alpha.1", + "version": "0.3.0-alpha.2", "lockfileVersion": 3, "requires": true, "packages": { "": { "name": "@rdfc/sds-storage-writer-ts", - "version": "0.3.0-alpha.1", + "version": "0.3.0-alpha.2", "license": "MIT", "dependencies": { "@treecg/types": "^0.4.6", diff --git a/package.json b/package.json index c38acd3..0307e44 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "@rdfc/sds-storage-writer-ts", - "version": "0.3.0-alpha.1", + "version": "0.3.0-alpha.2", "description": "An RDF-Connect processor to write SDS streams into a given storage system", "main": "lib/index.js", "scripts": { From 3d0c81770a9b684db1fb689b7a068aad4c624bd7 Mon Sep 17 00:00:00 2001 From: smessie Date: Mon, 29 Jul 2024 17:18:56 +0200 Subject: [PATCH 07/16] chore: Create index on indexCollection --- src/index.ts | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/index.ts b/src/index.ts index 11bb378..927eb48 100644 --- a/src/index.ts +++ b/src/index.ts @@ -457,6 +457,8 @@ export async function ingest( const memberCollection = db.collection(database.data); const indexCollection = db.collection(database.index); + await indexCollection.createIndex({ streamId: 1, id: 1 }); + const pushMemberToDB = (record: SDSRecord, operations: AnyBulkWriteOperation[]) => { const bs = record.buckets; From 69a042eba260497af182b6fb511042ed79b87975 Mon Sep 17 00:00:00 2001 From: smessie Date: Mon, 29 Jul 2024 17:19:36 +0200 Subject: [PATCH 08/16] 0.3.0-alpha.3 --- package-lock.json | 4 ++-- package.json | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/package-lock.json b/package-lock.json index 954923e..af11655 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,12 +1,12 @@ { "name": "@rdfc/sds-storage-writer-ts", - "version": "0.3.0-alpha.2", + "version": "0.3.0-alpha.3", "lockfileVersion": 3, "requires": true, "packages": { "": { "name": "@rdfc/sds-storage-writer-ts", - "version": "0.3.0-alpha.2", + "version": "0.3.0-alpha.3", "license": "MIT", "dependencies": { "@treecg/types": "^0.4.6", diff --git a/package.json b/package.json index 0307e44..505d872 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "@rdfc/sds-storage-writer-ts", - "version": "0.3.0-alpha.2", + "version": "0.3.0-alpha.3", "description": "An RDF-Connect processor to write SDS streams into a given storage system", "main": "lib/index.js", "scripts": { From ae10ca3b96130a26a1a953b714ac4e0dfac7dc90 Mon Sep 17 00:00:00 2001 From: smessie Date: Fri, 2 Aug 2024 12:39:39 +0200 Subject: [PATCH 09/16] chore: Only perform empty operation when there are buckets to empty -> resolves slow query --- src/index.ts | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/src/index.ts b/src/index.ts index 927eb48..b4c81bc 100644 --- a/src/index.ts +++ b/src/index.ts @@ -252,6 +252,11 @@ function emptyBuckets(data: RDF.Quad[], operations: AnyBulkWriteOperation q.subject); + // Only perform the operation if there are buckets to empty. + if (bucketsToEmpty.length === 0) { + return; + } + operations.push({ updateMany: { filter: {id: {$in: bucketsToEmpty.map(b => b.value)}}, From b5f8b60a71ca80db13612c64d26bd6659f81c53c Mon Sep 17 00:00:00 2001 From: smessie Date: Fri, 2 Aug 2024 12:54:42 +0200 Subject: [PATCH 10/16] chore: Create index to mitigate slow queries --- src/index.ts | 1 + 1 file changed, 1 insertion(+) diff --git a/src/index.ts b/src/index.ts index b4c81bc..edd00ca 100644 --- a/src/index.ts +++ b/src/index.ts @@ -461,6 +461,7 @@ export async function ingest( logger.debug("[ingest] Attached metadata handler"); const memberCollection = db.collection(database.data); + await memberCollection.createIndex({id: 1}); const indexCollection = db.collection(database.index); await indexCollection.createIndex({ streamId: 1, id: 1 }); From c09a71e830754dff0e9983ee5540582b4456854d Mon Sep 17 00:00:00 2001 From: smessie Date: Mon, 5 Aug 2024 10:23:26 +0200 Subject: [PATCH 11/16] refactor: Remove unused utils --- src/utils.ts | 31 ------------------------------- 1 file changed, 31 deletions(-) delete mode 100644 src/utils.ts diff --git a/src/utils.ts b/src/utils.ts deleted file mode 100644 index c67d9c2..0000000 --- a/src/utils.ts +++ /dev/null @@ -1,31 +0,0 @@ - -import type * as RDF from '@rdfjs/types'; -import { LDES, Member, RDF as RDFT } from '@treecg/types'; -import { Store } from "n3"; - -export function getMember(subject: RDF.Term, store: Store, done: Set): RDF.Quad[] { - const newQuads = store.getQuads(subject, null, null, null); - done.add(subject); - - const newSubjects = newQuads.map(q => q.object) - .filter(q => q.termType === "BlankNode" || q.termType == "NamedNode") - .filter(q => !done.has(q)) - - return [...newQuads, ...newSubjects.flatMap(s => getMember(s, store, done))]; -} - -export function getMembersByType(type: RDF.Term, store: Store): Member[] { - return store.getSubjects(RDFT.terms.type, type, null).map(sub => { - if (sub.termType !== "NamedNode") throw "Memmbers can only be named nodes!"; - - const quads = getMember(sub, store, new Set()); - return { id: sub, quads }; - }); -} - - -export function extractBucketStrategies(meta: RDF.Quad[]): Member[] { - const store = new Store(meta); - return getMembersByType(LDES.terms.BucketizeStrategy, store); -} - From adc84fc0002c9106f0482adcf4407c410086e73d Mon Sep 17 00:00:00 2001 From: smessie Date: Mon, 5 Aug 2024 10:29:13 +0200 Subject: [PATCH 12/16] chore: Update logger format to contain processor name --- src/index.ts | 35 +++++++++-------------- src/utils/logUtil.ts | 67 ++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 80 insertions(+), 22 deletions(-) create mode 100644 src/utils/logUtil.ts diff --git a/src/index.ts b/src/index.ts index edd00ca..aa0b901 100644 --- a/src/index.ts +++ b/src/index.ts @@ -4,19 +4,10 @@ import {LDES, Member, PROV, RDF as RDFT, RelationType, SDS,} from "@treecg/types import {AnyBulkWriteOperation, Collection, MongoClient} from "mongodb"; import {Parser, Writer} from "n3"; import {env} from "process"; -import winston from "winston"; import {TREEFragment} from "./fragmentHelper"; +import {getLoggerFor} from "./utils/logUtil"; -const consoleTransport = new winston.transports.Console(); -const logger = winston.createLogger({ - format: winston.format.combine( - winston.format.colorize({level: true}), - winston.format.simple(), - ), - transports: [consoleTransport], -}); - -consoleTransport.level = process.env.LOG_LEVEL || "info"; +const logger = getLoggerFor("ingest"); type SDSRecord = { stream: string; @@ -155,7 +146,7 @@ function gatherBuckets( q.predicate.equals(SDS.terms.stream), )?.object.value; if (!stream) { - logger.error(`Found SDS bucket without a stream! ${bucket.value}`); + logger.error(`[gatherBuckets] Found SDS bucket without a stream! ${bucket.value}`); return; } @@ -212,7 +203,7 @@ function gatherRecords( (q) => q.subject.equals(recordId) && q.predicate.equals(SDS.terms.stream), )?.object.value; if (!stream) { - logger.error("Found SDS record without a stream!"); + logger.error("[gatherRecords] Found SDS record without a stream!"); continue; } const payload = data.find( @@ -365,7 +356,7 @@ async function setup_metadata( .toArray(); logger.debug( - `Found ${dbFragmentations.length} fragmentations (${dbFragmentations.map( + `[setup_metadata] Found ${dbFragmentations.length} fragmentations (${dbFragmentations.map( (x) => x.id.value, )})`, ); @@ -373,7 +364,7 @@ async function setup_metadata( const handleMetadata = async (meta: string | RDF.Quad[]) => { meta = maybe_parse(meta); if (!ingestMetadata) { - logger.error("Cannot handle metadata, mongo is closed"); + logger.error("[setup_metadata] Cannot handle metadata, mongo is closed"); return; } @@ -431,7 +422,7 @@ export async function ingest( const mongo = await new MongoClient(url).connect(); const db = mongo.db(); - logger.debug(`[ingest] Connected to ${url}`); + logger.debug(`Connected to ${url}`); const streamTimestampPaths: { [streamId: string]: string } = {}; @@ -441,7 +432,7 @@ export async function ingest( const closeMongo = () => { if (!ingestMetadata && !ingestData && !closed) { - logger.info("[ingest] Closing MongoDB client connection"); + logger.info("Closing MongoDB client connection"); closed = true; return mongo.close(); } @@ -458,12 +449,12 @@ export async function ingest( (k, v) => (streamTimestampPaths[k] = v), closeMongo, ); - logger.debug("[ingest] Attached metadata handler"); + logger.debug("Attached metadata handler"); const memberCollection = db.collection(database.data); await memberCollection.createIndex({id: 1}); const indexCollection = db.collection(database.index); - await indexCollection.createIndex({ streamId: 1, id: 1 }); + await indexCollection.createIndex({streamId: 1, id: 1}); const pushMemberToDB = (record: SDSRecord, operations: AnyBulkWriteOperation[]) => { @@ -500,7 +491,7 @@ export async function ingest( // Format member objects in preparation for storage writing const records = gatherRecords(data, streamTimestampPaths); - logger.debug(`[ingest] Handling ${records.length} record(s)`); + logger.debug(`Handling ${records.length} record(s)`); // Make sure duplicated members are skipped const updateData: DataRecord[] = []; @@ -512,7 +503,7 @@ export async function ingest( if (updateData.length > 0) { // Do we really need to await this? await memberCollection.insertMany(updateData); - logger.debug(`[ingest] Inserted ${updateData.length} new members to the data collection`); + logger.debug(`Inserted ${updateData.length} new members to the data collection`); } // Update INDEX collection accordingly @@ -532,5 +523,5 @@ export async function ingest( await indexCollection.bulkWrite(indexOperations); }); - logger.debug("[ingest] Attached data handler"); + logger.debug("Attached data handler"); } diff --git a/src/utils/logUtil.ts b/src/utils/logUtil.ts new file mode 100644 index 0000000..ce113c4 --- /dev/null +++ b/src/utils/logUtil.ts @@ -0,0 +1,67 @@ +import winston, { format, Logger } from "winston"; + +const PROCESSOR_NAME = "sds-storage-writer-ts"; + +const consoleTransport = new winston.transports.Console(); +consoleTransport.level = + process.env.LOG_LEVEL || + process.env.DEBUG?.includes(PROCESSOR_NAME) || + process.env.DEBUG === "*" + ? "debug" + : "info"; + +const classLoggers = new WeakMap(); + +export function getLoggerFor(loggable: string | Instance): Logger { + let logger: Logger; + if (typeof loggable === "string") { + logger = createLogger(loggable); + } else { + const { constructor } = loggable; + if (classLoggers.has(loggable)) { + logger = classLoggers.get(loggable)!; + } else { + logger = createLogger(constructor.name); + classLoggers.set(loggable, logger); + } + } + return logger; +} + +function createLogger(label: string): Logger { + return winston.createLogger({ + format: format.combine( + format.label({ label }), + format.colorize(), + format.timestamp(), + format.metadata({ + fillExcept: ["level", "timestamp", "label", "message"], + }), + format.printf( + ({ + level: levelInner, + message, + label: labelInner, + timestamp, + metadata: meta, + }): string => + `${timestamp} {${PROCESSOR_NAME}} [${labelInner}] ${levelInner}: ${message}`, + ), + ), + transports: [consoleTransport], + }); +} + +/** + * Any class constructor. + */ +interface Constructor { + name: string; +} + +/** + * Any class instance. + */ +interface Instance { + constructor: Constructor; +} From f26445316a21a07350107e683e6ad3efca9d6c8e Mon Sep 17 00:00:00 2001 From: smessie Date: Mon, 5 Aug 2024 15:31:13 +0200 Subject: [PATCH 13/16] 0.3.0-alpha.4 --- package-lock.json | 20 ++++++++++---------- package.json | 2 +- 2 files changed, 11 insertions(+), 11 deletions(-) diff --git a/package-lock.json b/package-lock.json index af11655..31e628a 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,12 +1,12 @@ { "name": "@rdfc/sds-storage-writer-ts", - "version": "0.3.0-alpha.3", + "version": "0.3.0-alpha.4", "lockfileVersion": 3, "requires": true, "packages": { "": { "name": "@rdfc/sds-storage-writer-ts", - "version": "0.3.0-alpha.3", + "version": "0.3.0-alpha.4", "license": "MIT", "dependencies": { "@treecg/types": "^0.4.6", @@ -24,12 +24,12 @@ } }, "node_modules/@75lb/deep-merge": { - "version": "1.1.1", - "resolved": "https://registry.npmjs.org/@75lb/deep-merge/-/deep-merge-1.1.1.tgz", - "integrity": "sha512-xvgv6pkMGBA6GwdyJbNAnDmfAIR/DfWhrj9jgWh3TY7gRm3KO46x/GPjRg6wJ0nOepwqrNxFfojebh0Df4h4Tw==", + "version": "1.1.2", + "resolved": "https://registry.npmjs.org/@75lb/deep-merge/-/deep-merge-1.1.2.tgz", + "integrity": "sha512-08K9ou5VNbheZFxM5tDWoqjA3ImC50DiuuJ2tj1yEPRfkp8lLLg6XAaJ4On+a0yAXor/8ay5gHnAIshRM44Kpw==", "dev": true, "dependencies": { - "lodash.assignwith": "^4.2.0", + "lodash": "^4.17.21", "typical": "^7.1.1" }, "engines": { @@ -4471,10 +4471,10 @@ "node": ">=8" } }, - "node_modules/lodash.assignwith": { - "version": "4.2.0", - "resolved": "https://registry.npmjs.org/lodash.assignwith/-/lodash.assignwith-4.2.0.tgz", - "integrity": "sha512-ZznplvbvtjK2gMvnQ1BR/zqPFZmS6jbK4p+6Up4xcRYA7yMIwxHCfbTcrYxXKzzqLsQ05eJPVznEW3tuwV7k1g==", + "node_modules/lodash": { + "version": "4.17.21", + "resolved": "https://registry.npmjs.org/lodash/-/lodash-4.17.21.tgz", + "integrity": "sha512-v2kDEe57lecTulaDIuNTPy3Ry4gLGJ6Z1O3vE1krgXZNrsQ+LFTGHVxVjcXPs17LhbZVGedAJv8XZ1tvj5FvSg==", "dev": true }, "node_modules/lodash.camelcase": { diff --git a/package.json b/package.json index 505d872..eda3108 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "@rdfc/sds-storage-writer-ts", - "version": "0.3.0-alpha.3", + "version": "0.3.0-alpha.4", "description": "An RDF-Connect processor to write SDS streams into a given storage system", "main": "lib/index.js", "scripts": { From 97c65fd656a29415caf012d45c7b7dacc612b1e0 Mon Sep 17 00:00:00 2001 From: ajuvercr Date: Thu, 22 Aug 2024 10:02:39 +0200 Subject: [PATCH 14/16] remove empty test file --- test/ingest.test.ts | 468 -------------------------------------------- 1 file changed, 468 deletions(-) delete mode 100644 test/ingest.test.ts diff --git a/test/ingest.test.ts b/test/ingest.test.ts deleted file mode 100644 index b1c6250..0000000 --- a/test/ingest.test.ts +++ /dev/null @@ -1,468 +0,0 @@ -import { describe, test, expect, beforeAll, beforeEach, afterAll } from "@jest/globals"; -import { SimpleStream } from "@rdfc/js-runner"; -import { MongoMemoryServer } from "mongodb-memory-server"; -import { Collection, Db, MongoClient } from "mongodb"; -import { ingest, DBConfig, DataRecord } from "../src/index"; -import { RelationType, SDS } from "@treecg/types"; -import { TREEFragment } from "../src/fragmentHelper"; - -describe("Functional tests for the ingest function", () => { - /* - const PREFIXES = ` - @prefix rdfs: . - @prefix p-plan: . - @prefix prov: . - @prefix sds: . - @prefix dcat: . - @prefix xsd: . - @prefix sh: . - @prefix void: . - @prefix dct: . - @prefix ldes: . - @prefix ex: . - `; - - const METADATA = ` - ${PREFIXES} - ex:somePlan a p-plan:Plan; - rdfs:comment "An epic plan to publish an LDES". - - ex:streamVar0 a p-plan:Variable; - p-plan:isVariableOfPlan ex:somePlan. - - ex:streamVar1 a p-plan:Variable; - p-plan:isVariableOfPlan ex:somePlan. - - ex:step0 a p-plan:Step; - p-plan:hasInputVar ex:someRMLMapping, ex:someOtherRMLMapping; - p-plan:hasOutputVar ex:streamVar0; - p-plan:isStepOfPlan ; - rdfs:comment "Map CSV rows to RML"; - p-plan:isStepOfPlan ex:somePlan. - - ex:step1 a p-plan:Step; - p-plan:isPrecededBy ex:step0; - p-plan:hasInputVar ex:streamVar0; - p-plan:hasOutputVar ex:streamVar1; - p-plan:isStepOfPlan ex:somePlan. - - ex:rmlStream a sds:Stream; - p-plan:correspondsToVariable ex:streamVar0; - p-plan:wasGeneratedBy [ - a p-plan:Activity; - rdfs:comment "Convert an API response in a stream of RDF entities"; - p-plan:correspondsToStep ex:step0; - prov:used [ - a dcat:Dataset; - dcat:identifier - ] - ]. - - ex:sdsStream a sds:Stream; - p-plan:correspondsToVariable ex:streamVar1; - p-plan:wasGeneratedBy [ - a p-plan:Activity; - rdfs:comment "Wrap a stream of RDF entities in a SDS stream"; - p-plan:correspondsToStep ex:step1; - prov:used ex:rmlStream - ]; - sds:carries [ a sds:Member ]; - sds:dataset [ - a dcat:Dataset; - dcat:title "Epic dataset"; - dcat:publisher ; - ldes:timestampPath dct:modified; - dcat:identifier - ]. - `; - - let mongod: MongoMemoryServer; - let client: MongoClient; - let db: Db; - let metaColl: Collection; - let dataColl: Collection; - let indexColl: Collection; - - beforeAll(async () => { - // Initialize in-memory MongoDB - mongod = await MongoMemoryServer.create(); - // Connect to MongoDB instance and create collection managers - client = await new MongoClient(mongod.getUri()).connect(); - - // Initialize database and collection managers - db = client.db(mongod.instanceInfo!.dbName); - - }); - - beforeEach(async () => { - if (metaColl) { - await metaColl.drop(); - } - if (dataColl) { - await dataColl.drop(); - } - if (indexColl) { - await indexColl.drop(); - } - - metaColl = db.collection("METADATA"); - dataColl = db.collection("DATA"); - indexColl = db.collection("INDEX"); - }); - - afterAll(async () => { - if (client) { - await client.close(); - } - if (mongod) { - await mongod.stop({ doCleanup: true, force: true }); - } - }); - - test("Writing a bucketless SDS into MongoDB using the default time-based fragmentation (k = 4, m = 10, n = 100)", async () => { - const dataStream = new SimpleStream(); - const metadataStream = new SimpleStream(); - const config: DBConfig = { - url: mongod.getUri(), - metadata: "METADATA", - data: "DATA", - index: "INDEX" - }; - - // Max number of members allowed per fragment - const m = 10; - // Number of sub-fragments per level in the default B+Tree structure - const k = 4; - // Total number of members to be pushed - const n = 100 - - // Execute ingest function - await ingest(dataStream, metadataStream, config, m, k); - - // Push metadata in - await metadataStream.push(METADATA); - - // Push some SDS records in with 1h delta between each other - for (const record of dataGenerator(n, 1 * 60 * 60 * 1000)) { - await dataStream.push(record); - } - - // Check that metadata was stored - expect(await metaColl.countDocuments()).toBe(2); - expect((await metaColl.findOne({ "id": "http://example.org/ns#rmlStream" }))!.type).toBe(SDS.Stream); - expect((await metaColl.findOne({ "id": "http://example.org/ns#sdsStream" }))!.type).toBe(SDS.Stream); - // Check all data records were persisted - expect(await dataColl.countDocuments()).toBe(n); - // Check that all fragments are correct and consistent - const indexes = await indexColl.find().toArray(); - - for (const bucket of indexes) { - // Check fragment does not violate max members constraint - expect(bucket.members!.length).toBeLessThanOrEqual(m); - // Check local members do belong here - for (const memId of bucket.members!) { - const member = await dataColl.findOne({ "id": memId }); - expect(member).toBeDefined(); - expect(member!.timestamp.getTime()).toBeGreaterThanOrEqual(bucket.timeStamp!.getTime()); - expect(member!.timestamp.getTime()).toBeLessThan(bucket.timeStamp!.getTime() + bucket.span); - } - // Check it contains at most 2k relations (tree:LessThan & tree:GreaterThanOrEqualTo) - expect(bucket.relations.length).toBeLessThanOrEqual(2 * k); - // Check that all relations are telling the truth - for (const rel of bucket.relations) { - // Fetch related bucket - const relBucket = (await indexColl.find({ id: rel.bucket }).toArray())[0]; - expect(relBucket).toBeDefined(); - expect(rel.timestampRelation).toBeTruthy(); - - if (rel.type === RelationType.GreaterThanOrEqualTo) { - expect(new Date(rel.value!).getTime()).toBe(relBucket.timeStamp!.getTime()); - for (const memRef of relBucket.members!) { - const member = await dataColl.findOne({ "id": memRef }); - expect(member).toBeDefined(); - expect(member!.timestamp.getTime()).toBeGreaterThanOrEqual(new Date(rel.value!).getTime()); - } - } else if (rel.type === RelationType.LessThan) { - expect(new Date(rel.value!).getTime()) - .toBe(new Date(relBucket.timeStamp!.getTime() + relBucket.span).getTime()); - for (const memRef of relBucket.members!) { - const member = await dataColl.findOne({ "id": memRef }); - expect(member).toBeDefined(); - expect(member!.timestamp.getTime()).toBeLessThan(new Date(rel.value!).getTime()); - } - } - } - } - }); - - test("Writing a bucketless SDS into MongoDB using the default time-based fragmentation (k = 3, m = 100, n = 1000)", async () => { - const dataStream = new SimpleStream(); - const metadataStream = new SimpleStream(); - const config: DBConfig = { - url: mongod.getUri(), - metadata: "METADATA", - data: "DATA", - index: "INDEX" - }; - - // Max number of members allowed per fragment - const m = 100; - // Number of sub-fragments per level in the default B+Tree structure - const k = 3; - // Total number of members to be pushed - const n = 1000; - - // Execute ingest function - await ingest(dataStream, metadataStream, config, m, k); - - // Push metadata in - await metadataStream.push(METADATA); - - // Push some SDS records in with 1h delta between each other - for (const record of dataGenerator(n, 1 * 60 * 60 * 1000)) { - await dataStream.push(record); - } - - // Check that metadata was stored - expect(await metaColl.countDocuments()).toBe(2); - expect((await metaColl.findOne({ "id": "http://example.org/ns#rmlStream" }))!.type).toBe(SDS.Stream); - expect((await metaColl.findOne({ "id": "http://example.org/ns#sdsStream" }))!.type).toBe(SDS.Stream); - // Check all data records were persisted - expect(await dataColl.countDocuments()).toBe(n); - // Check that all fragments are correct and consistent - const indexes = await indexColl.find().toArray(); - - for (const bucket of indexes) { - // Check fragment does not violate max members constraint - expect(bucket.members!.length).toBeLessThanOrEqual(m); - // Check local members do belong here - for (const memId of bucket.members!) { - const member = await dataColl.findOne({ "id": memId }); - expect(member).toBeDefined(); - expect(member!.timestamp.getTime()).toBeGreaterThanOrEqual(bucket.timeStamp!.getTime()); - expect(member!.timestamp.getTime()).toBeLessThan(bucket.timeStamp!.getTime() + bucket.span); - } - // Check it contains at most 2k relations (tree:LessThan & tree:GreaterThanOrEqualTo) - expect(bucket.relations.length).toBeLessThanOrEqual(2 * k); - // Check that all relations are telling the truth - for (const rel of bucket.relations) { - // Fetch related bucket - const relBucket = (await indexColl.find({ id: rel.bucket }).toArray())[0]; - expect(relBucket).toBeDefined(); - expect(rel.timestampRelation).toBeTruthy(); - - if (rel.type === RelationType.GreaterThanOrEqualTo) { - expect(new Date(rel.value!).getTime()).toBe(relBucket.timeStamp!.getTime()); - for (const memRef of relBucket.members!) { - const member = await dataColl.findOne({ "id": memRef }); - expect(member).toBeDefined(); - expect(member!.timestamp.getTime()).toBeGreaterThanOrEqual(new Date(rel.value!).getTime()); - } - } else if (rel.type === RelationType.LessThan) { - expect(new Date(rel.value!).getTime()) - .toBe(new Date(relBucket.timeStamp!.getTime() + relBucket.span).getTime()); - for (const memRef of relBucket.members!) { - const member = await dataColl.findOne({ "id": memRef }); - expect(member).toBeDefined(); - expect(member!.timestamp.getTime()).toBeLessThan(new Date(rel.value!).getTime()); - } - } - } - } - }); - - test("Writing a bucketless SDS into MongoDB using the default time-based fragmentation (k = 4, m = 10, n = 100) and high temporal density", async () => { - const dataStream = new SimpleStream(); - const metadataStream = new SimpleStream(); - const config: DBConfig = { - url: mongod.getUri(), - metadata: "METADATA", - data: "DATA", - index: "INDEX" - }; - - // Max number of members allowed per fragment - const m = 10; - // Number of sub-fragments per level in the default B+Tree structure - const k = 4; - // Total number of members to be pushed - const n = 100 - - // Execute ingest function - await ingest(dataStream, metadataStream, config, m, k); - - // Push metadata in - await metadataStream.push(METADATA); - - // Push some SDS records in with 10ms delta between each other - for (const record of dataGenerator(n, 10)) { - await dataStream.push(record); - } - - // Check that metadata was stored - expect(await metaColl.countDocuments()).toBe(2); - expect((await metaColl.findOne({ "id": "http://example.org/ns#rmlStream" }))!.type).toBe(SDS.Stream); - expect((await metaColl.findOne({ "id": "http://example.org/ns#sdsStream" }))!.type).toBe(SDS.Stream); - // Check all data records were persisted - expect(await dataColl.countDocuments()).toBe(n); - // Check that all fragments are correct and consistent - const indexes = await indexColl.find().toArray(); - - for (const bucket of indexes) { - // Check fragment does not violate max members constraint - expect(bucket.members!.length).toBeLessThanOrEqual(m); - // Check local members do belong here - for (const memId of bucket.members!) { - const member = await dataColl.findOne({ "id": memId }); - expect(member).toBeDefined(); - expect(member!.timestamp.getTime()).toBeGreaterThanOrEqual(bucket.timeStamp!.getTime()); - expect(member!.timestamp.getTime()).toBeLessThan(bucket.timeStamp!.getTime() + bucket.span); - } - // Check it contains at most 2k relations (tree:LessThan & tree:GreaterThanOrEqualTo) - expect(bucket.relations.length).toBeLessThanOrEqual(2 * k); - // Check that all relations are telling the truth - for (const rel of bucket.relations) { - // Fetch related bucket - const relBucket = (await indexColl.find({ id: rel.bucket }).toArray())[0]; - expect(relBucket).toBeDefined(); - - if (rel.type === RelationType.GreaterThanOrEqualTo) { - expect(rel.timestampRelation).toBeTruthy(); - expect(new Date(rel.value!).getTime()).toBe(relBucket.timeStamp!.getTime()); - for (const memRef of relBucket.members!) { - const member = await dataColl.findOne({ "id": memRef }); - expect(member).toBeDefined(); - expect(member!.timestamp.getTime()).toBeGreaterThanOrEqual(new Date(rel.value!).getTime()); - } - } else if (rel.type === RelationType.LessThan) { - expect(rel.timestampRelation).toBeTruthy(); - expect(new Date(rel.value!).getTime()) - .toBe(new Date(relBucket.timeStamp!.getTime() + relBucket.span).getTime()); - for (const memRef of relBucket.members!) { - const member = await dataColl.findOne({ "id": memRef }); - expect(member).toBeDefined(); - expect(member!.timestamp.getTime()).toBeLessThan(new Date(rel.value!).getTime()); - } - } else if (rel.type === RelationType.Relation) { - // Check that related bucket increased pagination by 1 - expect(relBucket.page).toBe(bucket.page + 1); - // Timestamps should be equal - expect(relBucket.timeStamp!.getTime()).toBe(bucket.timeStamp!.getTime()); - } - } - } - }); - - test("Writing a bucketless SDS into MongoDB using the default time-based fragmentation (k = 4, m = 10, n = 500, b = 3600) and older timestamps", async () => { - const dataStream = new SimpleStream(); - const metadataStream = new SimpleStream(); - const config: DBConfig = { - url: mongod.getUri(), - metadata: "METADATA", - data: "DATA", - index: "INDEX" - }; - - // Max number of members allowed per fragment - const m = 10; - // Number of sub-fragments per level in the default B+Tree structure - const k = 4; - // Total number of members to be pushed - const n = 500; - // Minimum allowed bucket span - const b = 3600; - - // Execute ingest function - await ingest(dataStream, metadataStream, config, m, k, b); - - // Push metadata in - await metadataStream.push(METADATA); - - // Push some SDS records in with 30 days delta between each other and past timestamps (1 year ago) - for (const record of dataGenerator(n, 2592000000, new Date(new Date().getTime() - 31536000000))) { - await dataStream.push(record); - } - - // Check that metadata was stored - expect(await metaColl.countDocuments()).toBe(2); - expect((await metaColl.findOne({ "id": "http://example.org/ns#rmlStream" }))!.type).toBe(SDS.Stream); - expect((await metaColl.findOne({ "id": "http://example.org/ns#sdsStream" }))!.type).toBe(SDS.Stream); - // Check all data records were persisted - expect(await dataColl.countDocuments()).toBe(n); - // Check that all fragments are correct and consistent - const indexes = await indexColl.find().toArray(); - - for (const bucket of indexes) { - // Check fragment does not violate max members constraint - expect(bucket.members!.length).toBeLessThanOrEqual(m); - // Check local members do belong here - for (const memId of bucket.members!) { - const member = await dataColl.findOne({ "id": memId }); - expect(member).toBeDefined(); - expect(member!.timestamp.getTime()).toBeGreaterThanOrEqual(bucket.timeStamp!.getTime()); - expect(member!.timestamp.getTime()).toBeLessThan(bucket.timeStamp!.getTime() + bucket.span); - } - // Check it contains at most 2k relations (tree:LessThan & tree:GreaterThanOrEqualTo) - expect(bucket.relations.length).toBeLessThanOrEqual(2 * k); - // Check that all relations are telling the truth - for (const rel of bucket.relations) { - // Fetch related bucket - const relBucket = (await indexColl.find({ id: rel.bucket }).toArray())[0]; - expect(relBucket).toBeDefined(); - - if (rel.type === RelationType.GreaterThanOrEqualTo) { - expect(rel.timestampRelation).toBeTruthy(); - expect(new Date(rel.value!).getTime()).toBe(relBucket.timeStamp!.getTime()); - for (const memRef of relBucket.members!) { - const member = await dataColl.findOne({ "id": memRef }); - expect(member).toBeDefined(); - expect(member!.timestamp.getTime()).toBeGreaterThanOrEqual(new Date(rel.value!).getTime()); - } - } else if (rel.type === RelationType.LessThan) { - expect(rel.timestampRelation).toBeTruthy(); - expect(new Date(rel.value!).getTime()) - .toBe(new Date(relBucket.timeStamp!.getTime() + relBucket.span).getTime()); - for (const memRef of relBucket.members!) { - const member = await dataColl.findOne({ "id": memRef }); - expect(member).toBeDefined(); - expect(member!.timestamp.getTime()).toBeLessThan(new Date(rel.value!).getTime()); - } - } else if (rel.type === RelationType.Relation) { - // Check that related bucket increased pagination by 1 - expect(relBucket.page).toBe(bucket.page + 1); - // Timestamps should be equal - expect(relBucket.timeStamp!.getTime()).toBe(bucket.timeStamp!.getTime()); - } - } - } - }); - */ -}); - -function* dataGenerator(n: number, inc: number, startDate?: Date): Generator { - const date = startDate? startDate : new Date(); - - for (let i = 0; i < n; i++) { - const record = ` - @prefix xsd: . - @prefix sds: . - @prefix ex: . - @prefix dct: . - - [] sds:stream ex:sdsStream; - sds:payload . - - a ex:Entity; - dct:modified "${date.toISOString()}"^^xsd:dateTime; - ex:prop1 "some value"; - ex:prop2 [ - a ex:NestedEntity; - ex:nestedProp "some other value" - ]; - ex:prop3 ex:SomeNamedNode. - `; - // Increase timestamp by 1h - date.setTime(date.getTime() + inc); - yield record; - } -} From e42a1fbdf1795c78f0ef18d97a4eb8e465d0219e Mon Sep 17 00:00:00 2001 From: ajuvercr Date: Thu, 22 Aug 2024 10:02:52 +0200 Subject: [PATCH 15/16] add formatting things --- package-lock.json | 515 +++++++++++++++++------ package.json | 7 + src/fragmentHelper.ts | 36 +- src/index.ts | 957 ++++++++++++++++++++++-------------------- 4 files changed, 910 insertions(+), 605 deletions(-) diff --git a/package-lock.json b/package-lock.json index 31e628a..ab21cd8 100644 --- a/package-lock.json +++ b/package-lock.json @@ -19,7 +19,14 @@ "@rdfc/js-runner": "^0.2.1", "@types/n3": "^1.16.4", "@types/node": "^20.14.2", + "@typescript-eslint/eslint-plugin": "^8.2.0", + "@typescript-eslint/parser": "^8.2.0", + "eslint": "^8.57.0", + "eslint-config-prettier": "^9.1.0", + "husky": "^9.1.4", + "lint-staged": "^15.2.9", "mongodb-memory-server": "^9.3.0", + "prettier": "^3.3.3", "typescript": "^5.4.5" } }, @@ -1844,31 +1851,32 @@ "dev": true }, "node_modules/@typescript-eslint/eslint-plugin": { - "version": 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"ts-api-utils": "^1.3.0" }, "engines": { - "node": "^18.18.0 || >=20.0.0" + "node": "^18.18.0 || ^20.9.0 || >=21.1.0" }, "funding": { "type": "opencollective", "url": "https://opencollective.com/typescript-eslint" }, "peerDependencies": { - "@typescript-eslint/parser": "^7.0.0", - "eslint": "^8.56.0" + "@typescript-eslint/parser": "^8.0.0 || ^8.0.0-alpha.0", + "eslint": "^8.57.0 || ^9.0.0" }, "peerDependenciesMeta": { "typescript": { @@ -1877,26 +1885,27 @@ } }, "node_modules/@typescript-eslint/parser": { - "version": "7.16.0", - "resolved": "https://registry.npmjs.org/@typescript-eslint/parser/-/parser-7.16.0.tgz", - "integrity": "sha512-ar9E+k7CU8rWi2e5ErzQiC93KKEFAXA2Kky0scAlPcxYblLt8+XZuHUZwlyfXILyQa95P6lQg+eZgh/dDs3+Vw==", + "version": "8.2.0", + "resolved": "https://registry.npmjs.org/@typescript-eslint/parser/-/parser-8.2.0.tgz", + "integrity": "sha512-j3Di+o0lHgPrb7FxL3fdEy6LJ/j2NE8u+AP/5cQ9SKb+JLH6V6UHDqJ+e0hXBkHP1wn1YDFjYCS9LBQsZDlDEg==", "dev": true, + "license": "BSD-2-Clause", "dependencies": { - "@typescript-eslint/scope-manager": "7.16.0", - "@typescript-eslint/types": "7.16.0", - "@typescript-eslint/typescript-estree": "7.16.0", - "@typescript-eslint/visitor-keys": "7.16.0", + "@typescript-eslint/scope-manager": "8.2.0", + "@typescript-eslint/types": "8.2.0", + "@typescript-eslint/typescript-estree": "8.2.0", + "@typescript-eslint/visitor-keys": "8.2.0", "debug": "^4.3.4" }, "engines": { - "node": "^18.18.0 || >=20.0.0" + "node": "^18.18.0 || ^20.9.0 || >=21.1.0" }, "funding": { "type": "opencollective", "url": "https://opencollective.com/typescript-eslint" }, "peerDependencies": { - "eslint": "^8.56.0" + "eslint": "^8.57.0 || ^9.0.0" }, "peerDependenciesMeta": { "typescript": { @@ -1905,16 +1914,17 @@ } }, "node_modules/@typescript-eslint/scope-manager": { - "version": "7.16.0", - "resolved": "https://registry.npmjs.org/@typescript-eslint/scope-manager/-/scope-manager-7.16.0.tgz", - "integrity": 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"version": "2.5.0", + "resolved": "https://registry.npmjs.org/yaml/-/yaml-2.5.0.tgz", + "integrity": "sha512-2wWLbGbYDiSqqIKoPjar3MPgB94ErzCtrNE1FdqGuaO0pi2JGjmE8aW8TDZwzU7vuxcGRdL/4gPQwQ7hD5AMSw==", "dev": true, + "license": "ISC", "bin": { "yaml": "bin.mjs" }, diff --git a/package.json b/package.json index eda3108..2430a02 100644 --- a/package.json +++ b/package.json @@ -26,6 +26,13 @@ ], "license": "MIT", "devDependencies": { + "@typescript-eslint/eslint-plugin": "^8.2.0", + "@typescript-eslint/parser": "^8.2.0", + "eslint": "^8.57.0", + "eslint-config-prettier": "^9.1.0", + "husky": "^9.1.4", + "lint-staged": "^15.2.9", + "prettier": "^3.3.3", "@jest/globals": "^29.7.0", "@rdfc/js-runner": "^0.2.1", "@types/n3": "^1.16.4", diff --git a/src/fragmentHelper.ts b/src/fragmentHelper.ts index 815b146..ef8fbb1 100644 --- a/src/fragmentHelper.ts +++ b/src/fragmentHelper.ts @@ -1,21 +1,21 @@ -import {RelationType} from '@treecg/types'; +import { RelationType } from "@treecg/types"; export type TREEFragment = { - id?: string, - streamId: string, - value?: string, - relations: Array<{ - type: RelationType, - value?: string, - bucket: string, - path?: string, - timestampRelation?: boolean - }>, - members?: string[], - count: number, - timeStamp?: Date, - span: number, - immutable: boolean, - root: boolean, - page: number + id?: string; + streamId: string; + value?: string; + relations: Array<{ + type: RelationType; + value?: string; + bucket: string; + path?: string; + timestampRelation?: boolean; + }>; + members?: string[]; + count: number; + timeStamp?: Date; + span: number; + immutable: boolean; + root: boolean; + page: number; }; diff --git a/src/index.ts b/src/index.ts index aa0b901..5a65a2e 100644 --- a/src/index.ts +++ b/src/index.ts @@ -1,527 +1,572 @@ import type * as RDF from "@rdfjs/types"; -import {Stream} from "@rdfc/js-runner"; -import {LDES, Member, PROV, RDF as RDFT, RelationType, SDS,} from "@treecg/types"; -import {AnyBulkWriteOperation, Collection, MongoClient} from "mongodb"; -import {Parser, Writer} from "n3"; -import {env} from "process"; -import {TREEFragment} from "./fragmentHelper"; -import {getLoggerFor} from "./utils/logUtil"; +import { Stream } from "@rdfc/js-runner"; +import { + LDES, + Member, + PROV, + RDF as RDFT, + RelationType, + SDS, +} from "@treecg/types"; +import { AnyBulkWriteOperation, Collection, MongoClient } from "mongodb"; +import { Parser, Writer } from "n3"; +import { env } from "process"; +import { TREEFragment } from "./fragmentHelper"; +import { getLoggerFor } from "./utils/logUtil"; const logger = getLoggerFor("ingest"); type SDSRecord = { - stream: string; - payload: RDF.Term; - buckets: RDF.Term[]; - timestampValue?: string; + stream: string; + payload: RDF.Term; + buckets: RDF.Term[]; + timestampValue?: string; }; export type DataRecord = { - id: string, - data: string, - timestamp: Date + id: string; + data: string; + timestamp: Date; }; type Relation = { - type: RelationType; - value?: string; - bucket: string; - path?: string; + type: RelationType; + value?: string; + bucket: string; + path?: string; }; type Bucket = { - id: string; - root: boolean; - stream: string; - relations: Relation[]; - immutable?: boolean; + id: string; + root: boolean; + stream: string; + relations: Relation[]; + immutable?: boolean; }; export type DBConfig = { - url: string; - metadata: string; - data: string; - index: string; + url: string; + metadata: string; + data: string; + index: string; }; type DenyQuad = (q: RDF.Quad, currentId: RDF.Term) => boolean; // Set yikes! function filterMember( - quads: RDF.Quad[], - id: RDF.Term, - blacklist: DenyQuad[] = [], - done?: Set, + quads: RDF.Quad[], + id: RDF.Term, + blacklist: DenyQuad[] = [], + done?: Set, ): RDF.Quad[] { - const d: Set = done === undefined ? new Set() : done; - const quadIsBlacklisted = (q: RDF.Quad) => blacklist.some((b) => b(q, id)); - d.add(id.value); - - const out: RDF.Quad[] = quads.filter( - (q) => q.subject.equals(id) && !quadIsBlacklisted(q), - ); - const newObjects = quads - .filter((q) => q.subject.equals(id) && !quadIsBlacklisted(q)) - .map((q) => q.object) - .filter((o) => o.termType === "BlankNode" || o.termType === "NamedNode"); - for (let id of newObjects) { - if (d.has(id.value)) continue; - out.push(...filterMember(quads, id, blacklist, d)); - } - - const newSubjects = quads - .filter((q) => q.object.equals(id) && !quadIsBlacklisted(q)) - .map((q) => q.subject) - .filter((o) => o.termType === "BlankNode" || o.termType === "NamedNode"); - for (let id of newSubjects) { - if (d.has(id.value)) continue; - out.push(...filterMember(quads, id, blacklist, d)); - } - - return out; + const d: Set = done === undefined ? new Set() : done; + const quadIsBlacklisted = (q: RDF.Quad) => blacklist.some((b) => b(q, id)); + d.add(id.value); + + const out: RDF.Quad[] = quads.filter( + (q) => q.subject.equals(id) && !quadIsBlacklisted(q), + ); + const newObjects = quads + .filter((q) => q.subject.equals(id) && !quadIsBlacklisted(q)) + .map((q) => q.object) + .filter( + (o) => o.termType === "BlankNode" || o.termType === "NamedNode", + ); + for (const id of newObjects) { + if (d.has(id.value)) continue; + out.push(...filterMember(quads, id, blacklist, d)); + } + + const newSubjects = quads + .filter((q) => q.object.equals(id) && !quadIsBlacklisted(q)) + .map((q) => q.subject) + .filter( + (o) => o.termType === "BlankNode" || o.termType === "NamedNode", + ); + for (const id of newSubjects) { + if (d.has(id.value)) continue; + out.push(...filterMember(quads, id, blacklist, d)); + } + + return out; } function maybe_parse(data: RDF.Quad[] | string): RDF.Quad[] { - if (typeof data === "string" || data instanceof String) { - const parse = new Parser(); - return parse.parse(data); - } else { - return data; - } + if (typeof data === "string" || data instanceof String) { + const parse = new Parser(); + return parse.parse(data); + } else { + return data; + } } function parseBool(bo?: string): boolean | undefined { - if (bo === undefined) { - return undefined; - } else if (!bo) { - return false; - } else { - const bos = bo.toLowerCase(); - return bos === "t" || bos === "true" || bos === "1"; - } + if (bo === undefined) { + return undefined; + } else if (!bo) { + return false; + } else { + const bos = bo.toLowerCase(); + return bos === "t" || bos === "true" || bos === "1"; + } } -function gatherBuckets( - data: RDF.Quad[], -): Bucket[] { - const buckets: Bucket[] = []; - - const bucketTerms: Set = new Set(); - data.filter(q => - q.predicate.equals(RDFT.terms.type) - && q.object.equals(SDS.terms.custom("Bucket")) - && q.graph.equals(SDS.terms.custom("DataDescription"))) - .map(q => q.subject).forEach(bucket => bucketTerms.add(bucket)); - - data.filter(q => - q.predicate.equals(SDS.terms.bucket) - && q.graph.equals(SDS.terms.custom("DataDescription"))) - .map(q => q.object).forEach(bucket => bucketTerms.add(bucket)); - - bucketTerms.forEach(bucket => { - - const isRoot = data.find( - (q) => - q.subject.equals(bucket) && - q.predicate.equals(SDS.terms.custom("isRoot")), - )?.object.value; - const immutable = data.find( - (q) => - q.subject.equals(bucket) && - q.predicate.equals(SDS.terms.custom("immutable")), - )?.object.value; - - // If the subject has a triple with the Stream, use that one. Otherwise, we need to find the stream via the record the bucket is attached to. - const stream = data.find( - (q) => - q.subject.equals(bucket) && - q.predicate.equals(SDS.terms.stream), - )?.object.value || data.find( - (q) => - q.subject.equals(data.find( - (record) => - record.predicate.equals(SDS.terms.bucket) && - record.object.equals(bucket), - )?.subject) && - q.predicate.equals(SDS.terms.stream), - )?.object.value; - if (!stream) { - logger.error(`[gatherBuckets] Found SDS bucket without a stream! ${bucket.value}`); - return; - } - - const b = { - root: isRoot === "true", - id: bucket.value, - relations: [], - stream, - immutable: parseBool(immutable), - }; - - // Find all relations of the bucket - const relations = data - .filter( +function gatherBuckets(data: RDF.Quad[]): Bucket[] { + const buckets: Bucket[] = []; + + const bucketTerms: Set = new Set(); + data.filter( + (q) => + q.predicate.equals(RDFT.terms.type) && + q.object.equals(SDS.terms.custom("Bucket")) && + q.graph.equals(SDS.terms.custom("DataDescription")), + ) + .map((q) => q.subject) + .forEach((bucket) => bucketTerms.add(bucket)); + + data.filter( + (q) => + q.predicate.equals(SDS.terms.bucket) && + q.graph.equals(SDS.terms.custom("DataDescription")), + ) + .map((q) => q.object) + .forEach((bucket) => bucketTerms.add(bucket)); + + bucketTerms.forEach((bucket) => { + const isRoot = data.find( (q) => - q.subject.equals(bucket) && q.predicate.equals(SDS.terms.relation), - ) - .map((x) => x.object); - for (let rel of relations) { - const relObj = data.filter((q) => q.subject.equals(rel)); - - const type = ( - relObj.find((q) => q.predicate.equals(SDS.terms.relationType))!.object - .value - ); - const target = relObj.find((q) => - q.predicate.equals(SDS.terms.relationBucket), - )!.object.value; - const path = relObj.find((q) => - q.predicate.equals(SDS.terms.relationPath), - )?.object.value; - const value = relObj.find((q) => - q.predicate.equals(SDS.terms.relationValue), - )?.object.value; - - b.relations.push({type, bucket: target, path, value}); - } - - buckets.push(b); - }); - return buckets; + q.subject.equals(bucket) && + q.predicate.equals(SDS.terms.custom("isRoot")), + )?.object.value; + const immutable = data.find( + (q) => + q.subject.equals(bucket) && + q.predicate.equals(SDS.terms.custom("immutable")), + )?.object.value; + + // If the subject has a triple with the Stream, use that one. Otherwise, we need to find the stream via the record the bucket is attached to. + const stream = + data.find( + (q) => + q.subject.equals(bucket) && + q.predicate.equals(SDS.terms.stream), + )?.object.value || + data.find( + (q) => + q.subject.equals( + data.find( + (record) => + record.predicate.equals(SDS.terms.bucket) && + record.object.equals(bucket), + )?.subject, + ) && q.predicate.equals(SDS.terms.stream), + )?.object.value; + if (!stream) { + logger.error( + `[gatherBuckets] Found SDS bucket without a stream! ${bucket.value}`, + ); + return; + } + + const b = { + root: isRoot === "true", + id: bucket.value, + relations: [], + stream, + immutable: parseBool(immutable), + }; + + // Find all relations of the bucket + const relations = data + .filter( + (q) => + q.subject.equals(bucket) && + q.predicate.equals(SDS.terms.relation), + ) + .map((x) => x.object); + for (const rel of relations) { + const relObj = data.filter((q) => q.subject.equals(rel)); + + const type = ( + relObj.find((q) => q.predicate.equals(SDS.terms.relationType))! + .object.value + ); + const target = relObj.find((q) => + q.predicate.equals(SDS.terms.relationBucket), + )!.object.value; + const path = relObj.find((q) => + q.predicate.equals(SDS.terms.relationPath), + )?.object.value; + const value = relObj.find((q) => + q.predicate.equals(SDS.terms.relationValue), + )?.object.value; + + b.relations.push({ type, bucket: target, path, value }); + } + + buckets.push(b); + }); + return buckets; } function gatherRecords( - data: RDF.Quad[], - timestampPaths: { [stream: string]: string }, + data: RDF.Quad[], + timestampPaths: { [stream: string]: string }, ): SDSRecord[] { - const out: SDSRecord[] = []; - - for (const recordId of data - .filter((q) => q.predicate.equals(SDS.terms.payload)) - .map((x) => x.subject)) { - const stream = data.find( - (q) => q.subject.equals(recordId) && q.predicate.equals(SDS.terms.stream), - )?.object.value; - if (!stream) { - logger.error("[gatherRecords] Found SDS record without a stream!"); - continue; - } - const payload = data.find( - (q) => - q.subject.equals(recordId) && q.predicate.equals(SDS.terms.payload), - )!.object; - const buckets = data - .filter( + const out: SDSRecord[] = []; + + for (const recordId of data + .filter((q) => q.predicate.equals(SDS.terms.payload)) + .map((x) => x.subject)) { + const stream = data.find( (q) => - q.subject.equals(recordId) && q.predicate.equals(SDS.terms.bucket), - ) - .map((x) => x.object); - - const tPath = timestampPaths[stream]; - - const timestampValue = tPath - ? data.find( - (q) => q.subject.equals(payload) && q.predicate.value === tPath, - )?.object.value - : undefined; - - out.push({ - stream, - payload, - buckets, - timestampValue, - }); - } - - return out; + q.subject.equals(recordId) && + q.predicate.equals(SDS.terms.stream), + )?.object.value; + if (!stream) { + logger.error("[gatherRecords] Found SDS record without a stream!"); + continue; + } + const payload = data.find( + (q) => + q.subject.equals(recordId) && + q.predicate.equals(SDS.terms.payload), + )!.object; + const buckets = data + .filter( + (q) => + q.subject.equals(recordId) && + q.predicate.equals(SDS.terms.bucket), + ) + .map((x) => x.object); + + const tPath = timestampPaths[stream]; + + const timestampValue = tPath + ? data.find( + (q) => + q.subject.equals(payload) && q.predicate.value === tPath, + )?.object.value + : undefined; + + out.push({ + stream, + payload, + buckets, + timestampValue, + }); + } + + return out; } -function emptyBuckets(data: RDF.Quad[], operations: AnyBulkWriteOperation[]) { - const bucketsToEmpty = data.filter(q => - q.predicate.equals(SDS.terms.custom("empty")) && - q.object.value === "true" && - q.graph.equals(SDS.terms.custom("DataDescription"))) - .map(q => q.subject); - - // Only perform the operation if there are buckets to empty. - if (bucketsToEmpty.length === 0) { - return; - } - - operations.push({ - updateMany: { - filter: {id: {$in: bucketsToEmpty.map(b => b.value)}}, - update: { - $set: {members: []}, - }, - upsert: true, - } - }); +function emptyBuckets( + data: RDF.Quad[], + operations: AnyBulkWriteOperation[], +) { + const bucketsToEmpty = data + .filter( + (q) => + q.predicate.equals(SDS.terms.custom("empty")) && + q.object.value === "true" && + q.graph.equals(SDS.terms.custom("DataDescription")), + ) + .map((q) => q.subject); + + // Only perform the operation if there are buckets to empty. + if (bucketsToEmpty.length === 0) { + return; + } + + operations.push({ + updateMany: { + filter: { id: { $in: bucketsToEmpty.map((b) => b.value) } }, + update: { + $set: { members: [] }, + }, + upsert: true, + }, + }); } // This could be a memory problem in the long run // TODO: Find a way to persist written records efficiently //const addedMembers: Set = new Set(); async function addDataRecord( - updateRecords: DataRecord[], - record: SDSRecord, - quads: RDF.Quad[], - collection: Collection, + updateRecords: DataRecord[], + record: SDSRecord, + quads: RDF.Quad[], + collection: Collection, ) { - const value = record.payload.value; - - // Check if record has been registered in the local memory - //if (addedMembers.has(value)) return; - //addedMembers.add(value); + const value = record.payload.value; - const member = filterMember(quads, record.payload, [ - (q) => q.predicate.equals(SDS.terms.payload), - ]); + // Check if record has been registered in the local memory + //if (addedMembers.has(value)) return; + //addedMembers.add(value); - if (!member?.length) { - return; - } + const member = filterMember(quads, record.payload, [ + (q) => q.predicate.equals(SDS.terms.payload), + ]); - // Check if record is already written in the collection - const present = (await collection.countDocuments({id: value}, {limit: 1})) > 0; - if (present) return; + if (!member?.length) { + return; + } + // Check if record is already written in the collection + const present = + (await collection.countDocuments({ id: value }, { limit: 1 })) > 0; + if (present) return; - const ser = new Writer().quadsToString(member); + const ser = new Writer().quadsToString(member); - updateRecords.push({ - id: value, - data: ser, - timestamp: new Date(record.timestampValue!), - }); + updateRecords.push({ + id: value, + data: ser, + timestamp: new Date(record.timestampValue!), + }); } const setRoots: Set = new Set(); const immutables: Set = new Set(); function addBucket( - bucket: Bucket, - operations: AnyBulkWriteOperation[], + bucket: Bucket, + operations: AnyBulkWriteOperation[], ) { - const set: any = {}; - // Handle root setting - if (bucket.root && !setRoots.has(bucket.stream)) { - setRoots.add(bucket.stream); - set.root = true; - } - - if (bucket.immutable && !immutables.has(bucket.id)) { - immutables.add(bucket.id); - set.immutable = true; - } else if (bucket.immutable === false) { - // If it is explicitly set as false, set it in the database, so we persist the bucket. - set.immutable = false; - } - - operations.push({ - updateOne: { - filter: {streamId: bucket.stream, id: bucket.id}, - update: { - $set: set, - $addToSet: {relations: {$each: bucket.relations}}, - }, - upsert: true, - } - }); + const set: { immutable?: boolean; root?: boolean } = {}; + // Handle root setting + if (bucket.root && !setRoots.has(bucket.stream)) { + setRoots.add(bucket.stream); + set.root = true; + } + + if (bucket.immutable && !immutables.has(bucket.id)) { + immutables.add(bucket.id); + set.immutable = true; + } else if (bucket.immutable === false) { + // If it is explicitly set as false, set it in the database, so we persist the bucket. + set.immutable = false; + } + + operations.push({ + updateOne: { + filter: { streamId: bucket.stream, id: bucket.id }, + update: { + $set: set, + $addToSet: { relations: { $each: bucket.relations } }, + }, + upsert: true, + }, + }); } async function setup_metadata( - metadata: Stream, - metaCollection: Collection, - setTimestamp: (stream: string, value: string) => void, - onClose: () => void, + metadata: Stream, + metaCollection: Collection, + setTimestamp: (stream: string, value: string) => void, + onClose: () => void, ) { - let ingestMetadata = true; - - metadata.on("end", () => { - ingestMetadata = false; - return onClose(); - }); - - const dbFragmentations: Member[] = await metaCollection - .find({ - type: "fragmentation", - }) - .map((entry) => { - return { - id: entry.id, - quads: new Parser().parse(entry.value), - }; - }) - .toArray(); - - logger.debug( - `[setup_metadata] Found ${dbFragmentations.length} fragmentations (${dbFragmentations.map( - (x) => x.id.value, - )})`, - ); - - const handleMetadata = async (meta: string | RDF.Quad[]) => { - meta = maybe_parse(meta); - if (!ingestMetadata) { - logger.error("[setup_metadata] Cannot handle metadata, mongo is closed"); - return; - } - - const streams = meta - .filter( - (q) => - q.predicate.equals(RDFT.terms.type) && - q.object.equals(SDS.terms.Stream), - ) - .map((q) => q.subject); - - for (let streamId of streams) { - const streamMember = filterMember(meta, streamId, [ - (q, id) => q.predicate.equals(PROV.terms.used) && q.object.equals(id), - (q, id) => q.predicate.equals(SDS.terms.dataset) && q.object.equals(id), - ]); - - const datasetId = streamMember.find( - (q) => - q.subject.equals(streamId) && q.predicate.equals(SDS.terms.dataset), - )?.object; - if (datasetId) { - const timestampPathObject = streamMember.find( - (q) => - q.subject.equals(datasetId) && - q.predicate.equals(LDES.terms.timestampPath), + let ingestMetadata = true; + + metadata.on("end", () => { + ingestMetadata = false; + return onClose(); + }); + + const dbFragmentations: Member[] = await metaCollection + .find({ + type: "fragmentation", + }) + .map((entry) => { + return { + id: entry.id, + quads: new Parser().parse(entry.value), + }; + }) + .toArray(); + + logger.debug( + `[setup_metadata] Found ${dbFragmentations.length} fragmentations (${dbFragmentations.map( + (x) => x.id.value, + )})`, + ); + + const handleMetadata = async (meta: string | RDF.Quad[]) => { + meta = maybe_parse(meta); + if (!ingestMetadata) { + logger.error( + "[setup_metadata] Cannot handle metadata, mongo is closed", + ); + return; + } + + const streams = meta + .filter( + (q) => + q.predicate.equals(RDFT.terms.type) && + q.object.equals(SDS.terms.Stream), + ) + .map((q) => q.subject); + + for (const streamId of streams) { + const streamMember = filterMember(meta, streamId, [ + (q, id) => + q.predicate.equals(PROV.terms.used) && q.object.equals(id), + (q, id) => + q.predicate.equals(SDS.terms.dataset) && + q.object.equals(id), + ]); + + const datasetId = streamMember.find( + (q) => + q.subject.equals(streamId) && + q.predicate.equals(SDS.terms.dataset), )?.object; - if (timestampPathObject) { - setTimestamp(streamId.value, timestampPathObject.value); + if (datasetId) { + const timestampPathObject = streamMember.find( + (q) => + q.subject.equals(datasetId) && + q.predicate.equals(LDES.terms.timestampPath), + )?.object; + if (timestampPathObject) { + setTimestamp(streamId.value, timestampPathObject.value); + } } - } - - const ser = new Writer().quadsToString(streamMember); - await metaCollection.updateOne( - {type: SDS.Stream, id: streamId.value}, - {$set: {value: ser}}, - {upsert: true}, - ); - } - }; - - metadata.data(handleMetadata); - - if (metadata.lastElement) { - await handleMetadata(metadata.lastElement); - } + + const ser = new Writer().quadsToString(streamMember); + await metaCollection.updateOne( + { type: SDS.Stream, id: streamId.value }, + { $set: { value: ser } }, + { upsert: true }, + ); + } + }; + + metadata.data(handleMetadata); + + if (metadata.lastElement) { + await handleMetadata(metadata.lastElement); + } } export async function ingest( - data: Stream, - metadata: Stream, - database: DBConfig, + data: Stream, + metadata: Stream, + database: DBConfig, ) { - const url = database.url || env.DB_CONN_STRING || "mongodb://localhost:27017/ldes"; - const mongo = await new MongoClient(url).connect(); - const db = mongo.db(); - - logger.debug(`Connected to ${url}`); - - const streamTimestampPaths: { [streamId: string]: string } = {}; - - let ingestMetadata = true; - let ingestData = true; - let closed = false; - - const closeMongo = () => { - if (!ingestMetadata && !ingestData && !closed) { - logger.info("Closing MongoDB client connection"); - closed = true; - return mongo.close(); - } - }; - - data.on("end", () => { - ingestData = false; - return closeMongo(); - }); - - await setup_metadata( - metadata, - db.collection(database.metadata), - (k, v) => (streamTimestampPaths[k] = v), - closeMongo, - ); - logger.debug("Attached metadata handler"); - - const memberCollection = db.collection(database.data); - await memberCollection.createIndex({id: 1}); - const indexCollection = db.collection(database.index); - await indexCollection.createIndex({streamId: 1, id: 1}); - - - const pushMemberToDB = (record: SDSRecord, operations: AnyBulkWriteOperation[]) => { - const bs = record.buckets; - if (bs.length === 0) { - operations.push({ - updateOne: { - filter: {root: true, streamId: record.stream, id: ""}, - update: { - $addToSet: {members: record.payload.value}, - }, - upsert: true, - } - }); - } else { - operations.push({ - updateMany: { - filter: {streamId: record.stream, id: {$in: bs.map(b => b.value)}}, - update: { - $addToSet: {members: record.payload.value}, - }, - upsert: true, - } - }); - } - }; - - data.data(async (input: RDF.Quad[] | string) => { - const data = maybe_parse(input); - if (!ingestData) { - logger.error("Cannot handle data, mongo is closed"); - return; - } - - // Format member objects in preparation for storage writing - const records = gatherRecords(data, streamTimestampPaths); - logger.debug(`Handling ${records.length} record(s)`); - - // Make sure duplicated members are skipped - const updateData: DataRecord[] = []; - for (const r of records) { - await addDataRecord(updateData, r, data, memberCollection); - } - - // Write members to DATA collection - if (updateData.length > 0) { - // Do we really need to await this? - await memberCollection.insertMany(updateData); - logger.debug(`Inserted ${updateData.length} new members to the data collection`); - } - - // Update INDEX collection accordingly - const indexOperations: AnyBulkWriteOperation[] = []; - for (const r of records) { - pushMemberToDB(r, indexOperations); - } - - const buckets: Bucket[] = gatherBuckets(data); - for (let bucket of buckets) { - addBucket(bucket, indexOperations); - } - - // Empty buckets that are marked so. - emptyBuckets(data, indexOperations); - - await indexCollection.bulkWrite(indexOperations); - }); - - logger.debug("Attached data handler"); + const url = + database.url || env.DB_CONN_STRING || "mongodb://localhost:27017/ldes"; + const mongo = await new MongoClient(url).connect(); + const db = mongo.db(); + + logger.debug(`Connected to ${url}`); + + const streamTimestampPaths: { [streamId: string]: string } = {}; + + const ingestMetadata = true; + let ingestData = true; + let closed = false; + + const closeMongo = () => { + if (!ingestMetadata && !ingestData && !closed) { + logger.info("Closing MongoDB client connection"); + closed = true; + return mongo.close(); + } + }; + + data.on("end", () => { + ingestData = false; + return closeMongo(); + }); + + await setup_metadata( + metadata, + db.collection(database.metadata), + (k, v) => (streamTimestampPaths[k] = v), + closeMongo, + ); + logger.debug("Attached metadata handler"); + + const memberCollection = db.collection(database.data); + await memberCollection.createIndex({ id: 1 }); + const indexCollection = db.collection(database.index); + await indexCollection.createIndex({ streamId: 1, id: 1 }); + + const pushMemberToDB = ( + record: SDSRecord, + operations: AnyBulkWriteOperation[], + ) => { + const bs = record.buckets; + if (bs.length === 0) { + operations.push({ + updateOne: { + filter: { root: true, streamId: record.stream, id: "" }, + update: { + $addToSet: { members: record.payload.value }, + }, + upsert: true, + }, + }); + } else { + operations.push({ + updateMany: { + filter: { + streamId: record.stream, + id: { $in: bs.map((b) => b.value) }, + }, + update: { + $addToSet: { members: record.payload.value }, + }, + upsert: true, + }, + }); + } + }; + + data.data(async (input: RDF.Quad[] | string) => { + const data = maybe_parse(input); + if (!ingestData) { + logger.error("Cannot handle data, mongo is closed"); + return; + } + + // Format member objects in preparation for storage writing + const records = gatherRecords(data, streamTimestampPaths); + logger.debug(`Handling ${records.length} record(s)`); + + // Make sure duplicated members are skipped + const updateData: DataRecord[] = []; + for (const r of records) { + await addDataRecord(updateData, r, data, memberCollection); + } + + // Write members to DATA collection + if (updateData.length > 0) { + // Do we really need to await this? + await memberCollection.insertMany(updateData); + logger.debug( + `Inserted ${updateData.length} new members to the data collection`, + ); + } + + // Update INDEX collection accordingly + const indexOperations: AnyBulkWriteOperation[] = []; + for (const r of records) { + pushMemberToDB(r, indexOperations); + } + + const buckets: Bucket[] = gatherBuckets(data); + for (const bucket of buckets) { + addBucket(bucket, indexOperations); + } + + // Empty buckets that are marked so. + emptyBuckets(data, indexOperations); + + await indexCollection.bulkWrite(indexOperations); + }); + + logger.debug("Attached data handler"); } From fce14cf82127b5d40c22541ebb6b90f223d0f557 Mon Sep 17 00:00:00 2001 From: ajuvercr Date: Thu, 22 Aug 2024 10:12:01 +0200 Subject: [PATCH 16/16] add format configs --- .eslintignore | 2 ++ .eslintrc.json | 24 ++++++++++++++++++++++++ .husky/pre-commit | 1 + .lintstagedrc.json | 3 +++ .prettierignore | 2 ++ .prettierrc.json | 6 ++++++ 6 files changed, 38 insertions(+) create mode 100644 .eslintignore create mode 100644 .eslintrc.json create mode 100644 .husky/pre-commit create mode 100644 .lintstagedrc.json create mode 100644 .prettierignore create mode 100644 .prettierrc.json diff --git a/.eslintignore b/.eslintignore new file mode 100644 index 0000000..3063f07 --- /dev/null +++ b/.eslintignore @@ -0,0 +1,2 @@ +lib +node_modules diff --git a/.eslintrc.json b/.eslintrc.json new file mode 100644 index 0000000..ac0d2f8 --- /dev/null +++ b/.eslintrc.json @@ -0,0 +1,24 @@ +{ + "env": { + "browser": true, + "es2021": true + }, + "extends": [ + "eslint:recommended", + "plugin:@typescript-eslint/recommended", + "prettier" + ], + "parser": "@typescript-eslint/parser", + "parserOptions": { + "ecmaVersion": "latest", + "sourceType": "module" + }, + "plugins": ["@typescript-eslint"], + "rules": { + "indent": ["error", 4], + "linebreak-style": ["error", "unix"], + "quotes": ["error", "double"], + "semi": ["error", "always"], + "@typescript-eslint/no-unused-vars": "warn" + } +} diff --git a/.husky/pre-commit b/.husky/pre-commit new file mode 100644 index 0000000..2312dc5 --- /dev/null +++ b/.husky/pre-commit @@ -0,0 +1 @@ +npx lint-staged diff --git a/.lintstagedrc.json b/.lintstagedrc.json new file mode 100644 index 0000000..5192d1e --- /dev/null +++ b/.lintstagedrc.json @@ -0,0 +1,3 @@ +{ + "*.ts": ["eslint --fix", "prettier --write"] +} diff --git a/.prettierignore b/.prettierignore new file mode 100644 index 0000000..3063f07 --- /dev/null +++ b/.prettierignore @@ -0,0 +1,2 @@ +lib +node_modules diff --git a/.prettierrc.json b/.prettierrc.json new file mode 100644 index 0000000..2259cff --- /dev/null +++ b/.prettierrc.json @@ -0,0 +1,6 @@ +{ + "trailingComma": "all", + "tabWidth": 4, + "semi": true, + "singleQuote": false +}