build(deps): update barnard59 packages

.changeset/flat-lamps-join.md

@@ -0,0 +1,12 @@
+---
+"@cube-creator/cli": patch
+---
+
+Update barnard59 packages:
+- barnard59 1.1.0 => 5.0.1
+- barnard59-base 1.1.0 => 2.4.2
+- barnard59-formats 1.1.0 => 2.1.1
+- barnard59-graph-store 1.0.0 => 5.1.2
+- barnard59-http 1.1.1 => 2.0.0
+- barnard59-rdf 1.0.0 => 3.4.0
+- barnard59-validate-shacl 0.3.0 => barnard59-shacl 1.4.5

.changeset/tall-walls-sneeze.md

@@ -0,0 +1,5 @@
+---
+"@cube-creator/cli": patch
+---
+
+Use package barnard59-cube

apis/core/lib/handlers/csv-source.ts

@@ -4,9 +4,10 @@
 import { Enrichment } from '@hydrofoil/labyrinth/lib/middleware/preprocessResource'
 import { cc } from '@cube-creator/core/namespace'
 import { fromPointer as mediaObjectFromPointer } from '@cube-creator/model/MediaObject'
-import { AnyPointer, GraphPointer } from 'clownface'
+import clownface, { AnyPointer, GraphPointer } from 'clownface'
 import { schema } from '@tpluscode/rdf-ns-builders'
 import { ResourceIdentifier } from '@tpluscode/rdfine/RdfResource'
+import type { DatasetCore, NamedNode } from '@rdfjs/types'
 import { shaclValidate } from '../middleware/shacl'
 import { createCSVSource } from '../domain/csv-source/upload'
 import { deleteSource } from '../domain/csv-source/delete'
@@ -66,8 +67,8 @@
     return next()
   }
 
-  const csvSource = await req.hydra.resource.clownface()
-  const directDownload = getPresignedLink(csvSource)
+  const csvSource: { term: NamedNode; dataset: DatasetCore } = await req.hydra.resource.clownface()
+  const directDownload = getPresignedLink(clownface(csvSource))
   if (!directDownload) {
     return next(new Error('s3 key not found'))
   }

apis/core/lib/handlers/cube-projects.ts

@@ -7,6 +7,8 @@
 import * as ns from '@tpluscode/rdf-ns-builders'
 import cors from 'cors'
 import { isMultipart } from '@cube-creator/express/multipart'
+import type { DatasetCore, NamedNode } from '@rdfjs/types'
+import clownface from 'clownface'
 import { shaclValidate } from '../middleware/shacl'
 import { createProject } from '../domain/cube-projects/create'
 import { updateProject } from '../domain/cube-projects/update'
@@ -28,8 +30,9 @@
       throw new Error('User is not defined')
     }
 
+    const pointer: { term: NamedNode; dataset: DatasetCore } = await req.hydra.resource.clownface()
     const { project: { pointer: project }, job } = await createProject({
-      projectsCollection: await req.hydra.resource.clownface(),
+      projectsCollection: clownface(pointer),
       resource: await req.resource(),
       user,
       store: req.resourceStore(),

apis/core/lib/handlers/cube-projects/import.ts

@@ -6,6 +6,7 @@
 import $rdf from 'rdf-ext'
 import { parsers } from '@rdfjs-elements/formats-pretty'
 import toStream from 'string-to-stream'
+import type { DatasetCore, NamedNode } from '@rdfjs/types'
 import { shaclValidate } from '../../middleware/shacl'
 import { importProject } from '../../domain/cube-projects/import'
 import { streamClient } from '../../query-client'
@@ -24,8 +25,9 @@
       throw new Error('User is not defined')
     }
 
+    const pointer: { term: NamedNode; dataset: DatasetCore } = await req.hydra.resource.clownface()
     const { project, importedDataset } = await importProject({
-      projectsCollection: await req.hydra.resource.clownface(),
+      projectsCollection: clownface(pointer),
       resource: await req.parseFromMultipart(),
       files: req.multipartFileQuadsStreams(),
       store: req.resourceStore(),

apis/core/lib/handlers/dataset.ts

@@ -1,5 +1,6 @@
 import { PassThrough } from 'stream'
-import type { Term } from '@rdfjs/types'
+import toStream from 'rdf-dataset-ext/toStream.js'
+import type { DatasetCore, NamedNode, Term } from '@rdfjs/types'
 import asyncMiddleware from 'middleware-async'
 import clownface from 'clownface'
 import parsePreferHeader from 'parse-prefer-header'
@@ -20,8 +21,9 @@
 export const put = protectedResource(
   shaclValidate,
   asyncMiddleware(async (req, res) => {
+    const pointer: { term: NamedNode; dataset: DatasetCore } = await req.hydra.resource.clownface()
     const dataset = await update({
-      dataset: await req.hydra.resource.clownface(),
+      dataset: clownface(pointer),
       resource: await req.resource(),
       store: req.resourceStore(),
     })
@@ -35,7 +37,8 @@
 export const get = protectedResource(asyncMiddleware(async (req, res) => {
   const { includeInLists } = parsePreferHeader(req.header('Prefer'))
 
-  const dataset = await req.hydra.resource.clownface()
+  const ptr: { term: NamedNode; dataset: DatasetCore } = await req.hydra.resource.clownface()
+  const dataset = clownface(ptr)
   const shapeStreams = [...await loadCubeShapes(req.hydra.resource.term, !includeInLists, clients)]
   const outStream = new PassThrough({
     objectMode: true,
@@ -48,7 +51,7 @@
   const linkedResources = await loadLinkedResources(dataset, types.out(query.include).toArray(), req.labyrinth.sparql)
   const observationsTemplateStream = await observationTemplate(dataset.term)
 
-  merge([dataset.dataset.toStream(), ...shapeStreams, linkedResources.toStream(), observationsTemplateStream], { objectMode: true })
+  merge([toStream(dataset.dataset), ...shapeStreams, linkedResources.toStream(), observationsTemplateStream], { objectMode: true })
     .pipe(outStream)
 
   return res.quadStream(outStream)

apis/core/lib/handlers/observations.ts

@@ -11,6 +11,7 @@
 import * as ns from '@cube-creator/core/namespace'
 import { cc, hydraBox } from '@cube-creator/core/namespace'
 import { hydra } from '@tpluscode/rdf-ns-builders'
+import type { DatasetCore, Term } from '@rdfjs/types'
 import { warning } from '../log'
 import { getObservations } from '../domain/observations'
 
@@ -50,8 +51,8 @@
       }
     }
 
-    const templatePointer = req.hydra.operation.out(hydraBox.variables).toArray()[0]
-    const template = RdfResourceImpl.factory.createEntity<IriTemplate>(templatePointer, [IriTemplateMixin])
+    const templatePointer: { term: Term; dataset: DatasetCore } = req.hydra.operation.out(hydraBox.variables).toArray()[0]
+    const template = RdfResourceImpl.factory.createEntity<IriTemplate>(clownface(templatePointer), [IriTemplateMixin])
     const collection = await getObservations({
       sourceGraph,
       pageSize,

apis/core/lib/handlers/table/create.ts

@@ -5,14 +5,16 @@
 import clownface from 'clownface'
 import $rdf from 'rdf-ext'
 import { rdf } from '@tpluscode/rdf-ns-builders'
+import type { DatasetCore, NamedNode } from '@rdfjs/types'
 import { createTable } from '../../domain/table/create'
 import { shaclValidate } from '../../middleware/shacl'
 
 export const post = protectedResource(
   shaclValidate,
   asyncMiddleware(async (req, res) => {
+    const cfLike: { term: NamedNode; dataset: DatasetCore } = await req.hydra.resource.clownface()
     const table = await createTable({
-      tableCollection: await req.hydra.resource.clownface(),
+      tableCollection: clownface(cfLike),
       resource: await req.resource(),
       store: req.resourceStore(),
     })

apis/core/lib/middleware/operations.ts

@@ -1,11 +1,11 @@
 import { RequestHandler } from 'express'
-import clownface, { GraphPointer } from 'clownface'
+import clownface from 'clownface'
 import asyncMiddleware from 'middleware-async'
 import { hydra, rdf } from '@tpluscode/rdf-ns-builders'
 import TermSet from '@rdfjs/term-set'
 import { log } from '../log'
 
-function logRemovedOperation(operation: GraphPointer) {
+function logRemovedOperation(operation: any) {
   const method = operation.out(hydra.method).value
   const types = operation.out(rdf.type).values
   const clas = operation.in(hydra.supportedOperation).values

apis/core/package.json

@@ -59,6 +59,7 @@
     "once": "^1.4.0",
     "parse-prefer-header": "^1.0.0",
     "rdf-cube-view-query": "^1.8.2",
+    "rdf-dataset-ext": "^1.1.0",
     "rdf-ext": "^1.3.0",
     "rdf-literal": "^1.3.0",
     "set-link": "^1.0.0",

cli.Dockerfile

@@ -17,6 +17,9 @@ RUN yarn install --frozen-lockfile
 COPY . .
 RUN rm -rf ./ui
 RUN rm -rf ./apis
+RUN rm -rf ./cli/test
+RUN rm -rf ./packages/model/test
+RUN rm -rf ./packages/testing
 RUN rm -rf ./packages/express
 RUN rm -rf ./packages/express-rdf-request
 RUN rm -rf ./packages/shacl-middleware

cli/lib/bufferDebug.ts

@@ -27,7 +27,7 @@ function bufferInfo(pipeline: Pipeline) {
       const { key, value } = bufferStatePair({
         index,
         mode: 'write',
-        state: step.stream._writableState,
+        state: (step.stream as any)._writableState,
         step,
       })
 

cli/lib/commands/runner.ts

@@ -102,11 +102,12 @@ export function create<TOptions extends RunOptions>({ pipelineSources, prepare,
 
     await prepare?.(command, variables)
 
-    const { default: Runner } = await importDynamic('barnard59/runner.js')
+    const { default: Runner } = await importDynamic<typeof import('barnard59/runner.js')>('barnard59/runner.js')
+    const env = await importDynamic<typeof import('barnard59-env')>('barnard59-env')
     const run = await Runner(clownface({
       dataset,
       term: pipelines.Entrypoint,
-    }), {
+    }), env.default, {
       basePath: path.resolve(basePath, 'pipelines'),
       outputStream: process.stdout,
       variables,

cli/lib/counters.ts

@@ -1,5 +1,5 @@
 import type { Quad } from '@rdfjs/types'
-import type { Context } from 'barnard59-core/lib/Pipeline'
+import type { Context } from 'barnard59-core'
 import { PassThrough } from 'readable-stream'
 import through2 from 'through2'
 import { csvw } from '@tpluscode/rdf-ns-builders/strict'

cli/lib/csv.ts

@@ -4,7 +4,7 @@
 import { readable } from 'duplex-to'
 import { CsvSource } from '@cube-creator/model'
 import fetch from 'node-fetch'
-import type { Context } from 'barnard59-core/lib/Pipeline'
+import type { Context } from 'barnard59-core'
 
 export function openFromCsvw(this: Context) {
   const csvStream = new PassThrough()

cli/lib/cube.ts

@@ -2,7 +2,7 @@ import type { DatasetCore, Quad, Term } from '@rdfjs/types'
 import $rdf from 'rdf-ext'
 import { cc } from '@cube-creator/core/namespace'
 import clownface, { GraphPointer } from 'clownface'
-import type { Context } from 'barnard59-core/lib/Pipeline'
+import type { Context } from 'barnard59-core'
 import { obj } from 'through2'
 import { CONSTRUCT, sparql } from '@tpluscode/sparql-builder'
 import { schema, sh } from '@tpluscode/rdf-ns-builders/strict'

cli/lib/import/cube.ts

@@ -1,5 +1,5 @@
 import type { NamedNode } from '@rdfjs/types'
-import type { Context } from 'barnard59-core/lib/Pipeline'
+import type { Context } from 'barnard59-core'
 import StreamClient from 'sparql-http-client'
 import { CONSTRUCT } from '@tpluscode/sparql-builder'
 import * as ns from '@cube-creator/core/namespace'

cli/lib/import/cubeMetadata.ts

@@ -2,7 +2,7 @@ import type { DatasetCore, NamedNode, Quad, Term } from '@rdfjs/types'
 import { cc } from '@cube-creator/core/namespace'
 import DatasetExt from 'rdf-ext/lib/Dataset'
 import { dcterms, schema } from '@tpluscode/rdf-ns-builders'
-import type { Context } from 'barnard59-core/lib/Pipeline'
+import type { Context } from 'barnard59-core'
 import StreamClient from 'sparql-http-client'
 import $rdf from 'rdf-ext'
 import { sparql, CONSTRUCT } from '@tpluscode/sparql-builder'

cli/lib/import/dimensions.ts

@@ -1,5 +1,5 @@
 import type { DatasetCore, NamedNode, Term } from '@rdfjs/types'
-import type { Context } from 'barnard59-core/lib/Pipeline'
+import type { Context } from 'barnard59-core'
 import ParsingClient from 'sparql-http-client/ParsingClient'
 import clownface, { AnyContext, AnyPointer, GraphPointer } from 'clownface'
 import $rdf from 'rdf-ext'

cli/lib/job.ts

@@ -10,7 +10,7 @@ import $rdf from 'rdf-ext'
 import { cc } from '@cube-creator/core/namespace'
 import TermMap from '@rdfjs/term-map'
 import { GraphPointer } from 'clownface'
-import { ValidationError } from 'barnard59-validate-shacl/lib/errors'
+import { ValidationError } from 'barnard59-shacl/lib/errors'
 import DatasetExt from 'rdf-ext/lib/Dataset'
 import { createPlaygroundUrl } from '@zazuko/shacl-playground'
 import { shorten } from '@zazuko/s'

cli/lib/loadCube.ts

@@ -1,6 +1,6 @@
 import { Stream, PassThrough } from 'stream'
 import { spawnSync } from 'child_process'
-import type * as Pipeline from 'barnard59-core/lib/Pipeline'
+import type { Context } from 'barnard59-core'
 import { CONSTRUCT, sparql } from '@tpluscode/sparql-builder'
 import { csvw } from '@tpluscode/rdf-ns-builders'
 import { cc, cube } from '@cube-creator/core/namespace'
@@ -20,7 +20,7 @@ interface Params {
  * Opens a SPARQL stream reading the cube, excluding the Cube Constraint subgraph,
  * which will be processed alongside the rest of cube metadata
  */
-export async function loadCube(this: Pipeline.Context, { jobUri, endpoint, user, password }: Params): Promise<Stream> {
+export async function loadCube(this: Context, { jobUri, endpoint, user, password }: Params): Promise<Stream> {
   const { project } = await loadProject(jobUri, this)
 
   const patterns = sparql`

cli/lib/log.ts

@@ -1,5 +1,5 @@
 import winston from 'winston'
-import { OnViolation } from 'barnard59-validate-shacl'
+import { OnViolation } from 'barnard59-shacl/validate'
 import { fromPointer } from '@rdfine/shacl/lib/ValidationReport'
 
 export const logger = winston.createLogger({
@@ -12,7 +12,7 @@ export const logger = winston.createLogger({
   ],
 })
 
-export function prettyPrintReport({ context, report }: OnViolation) {
+export const prettyPrintReport: OnViolation = ({ context, report }) => {
   const jsonld = fromPointer(report.pointer).toJSON()
   context.logger.error(JSON.stringify(jsonld, null, 2))
 

cli/lib/metadata.ts

@@ -5,7 +5,7 @@ import { dcat, dcterms, rdf, schema, sh, _void, foaf } from '@tpluscode/rdf-ns-b
 import { cc, cube } from '@cube-creator/core/namespace'
 import { Dataset, Project, PublishJob } from '@cube-creator/model'
 import { HydraClient } from 'alcaeus/alcaeus'
-import type { Context } from 'barnard59-core/lib/Pipeline'
+import type { Context } from 'barnard59-core'
 import { Published } from '@cube-creator/model/Cube'
 import { CONSTRUCT, sparql } from '@tpluscode/sparql-builder'
 import StreamClient from 'sparql-http-client/StreamClient'

cli/lib/module.ts

@@ -1,5 +1,5 @@
 interface DynamicImport {
-  (m: string): Promise<any>
+  <T = any>(m: string): Promise<T>
 }
 
 // eslint-disable-next-line no-new-func

cli/lib/output-filter.ts

@@ -1,7 +1,7 @@
 import type { BlankNode, Quad, Term } from '@rdfjs/types'
 import { csvw, rdf } from '@tpluscode/rdf-ns-builders'
 import { cc } from '@cube-creator/core/namespace'
-import type { Context } from 'barnard59-core/lib/Pipeline'
+import type { Context } from 'barnard59-core'
 import { customAlphabet } from 'nanoid'
 import dict from 'nanoid-dictionary'
 import $rdf from 'rdf-ext'

cli/lib/output-mapper.ts

@@ -2,7 +2,7 @@ import type { DatasetCore, Quad, Term } from '@rdfjs/types'
 import $rdf from 'rdf-ext'
 import { ImportJob, TransformJob } from '@cube-creator/model'
 import { HydraClient } from 'alcaeus/alcaeus'
-import type { Context } from 'barnard59-core/lib/Pipeline'
+import type { Context } from 'barnard59-core'
 import { Dictionary } from '@rdfine/prov'
 import { prov, schema, qudt } from '@tpluscode/rdf-ns-builders/strict'
 import { cc, cube } from '@cube-creator/core/namespace'

cli/lib/pipeline.ts

@@ -1,8 +1,9 @@
-import type * as Pipeline from 'barnard59-core/lib/Pipeline'
+import type Pipeline from 'barnard59-core/lib/Pipeline'
+import type { Context } from 'barnard59-core'
 
-export const asStep = (pipeline: Pipeline.default) => pipeline
+export const asStep = (pipeline: Pipeline) => pipeline
 
-export function selectTransformation(this: Pipeline.Context, arg: {observationTable: Pipeline.default; otherTable: Pipeline.default}) {
+export function selectTransformation(this: Context, arg: {observationTable: Pipeline; otherTable: Pipeline}) {
   if (this.variables.get('transformed').isObservationTable === true) {
     this.logger.info('Input is cube table')
     return arg.observationTable

cli/lib/project.ts

@@ -1,5 +1,5 @@
 import { PublishJob, Project } from '@cube-creator/model'
-import type { Context } from 'barnard59-core/lib/Pipeline'
+import type { Context } from 'barnard59-core'
 import { tracer } from './otel/tracer'
 
 export async function loadProject(jobUri: string, { variables, logger }: Context) {

cli/lib/publish/versions.ts

@@ -1,4 +1,4 @@
-import type { Context } from 'barnard59-core/lib/Pipeline'
+import type { Context } from 'barnard59-core'
 import $rdf from 'rdf-ext'
 import through2 from 'through2'
 import clownface from 'clownface'

cli/lib/validation.ts

@@ -1,6 +1,6 @@
 import type { NamedNode, Quad } from '@rdfjs/types'
 import { turtle } from '@tpluscode/rdf-string'
-import type { Context } from 'barnard59-core/lib/Pipeline'
+import type { Context } from 'barnard59-core'
 import { validateQuad } from 'rdf-validate-datatype'
 
 export function validate(this: Context, quad: Quad): Quad {