fix: blank node clashing

zazuko · Jan 26, 2024 · 6bac13e · 6bac13e
1 parent 979056f
commit 6bac13e
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Showing 20 changed files with 762 additions and 328 deletions.
diff --git a/.changeset/nervous-moles-buy.md b/.changeset/nervous-moles-buy.md
@@ -0,0 +1,6 @@
+---
+"@view-builder/publish-views": patch
+"@view-builder/core": patch
+---
+
+Clashing blank nodes would cause invalid views being published
diff --git a/apps/www/package.json b/apps/www/package.json
@@ -45,7 +45,6 @@
     "lit": "^2.3.0",
     "n3": "^1.16.2",
     "nanoid": "^4.0.0",
-    "rdf-ext": "^2.0.1",
     "rdf-literal": "^1.3.0",
     "rdf-validate-shacl": "^0.4.4",
     "sparql-http-client": "^2.4.1",

diff --git a/packages/core/package.json b/packages/core/package.json
@@ -3,9 +3,9 @@
   "version": "0.0.0",
   "type": "module",
   "dependencies": {
-    "@rdfine/env": "^1.0.4",
-    "@rdfine/hydra": "^0.10.3",
-    "@rdfine/shacl": "^0.10.3",
+    "@rdfine/env": "^1.1.0",
+    "@rdfine/hydra": "^0.10.4",
+    "@rdfine/shacl": "^0.10.4",
     "@rdfjs/namespace": "^2.0.0",
     "@zazuko/vocabulary-extras": "^2.0.1"
   }

diff --git a/packages/publish-views/index.js b/packages/publish-views/index.js
@@ -1,7 +1,5 @@
 import Runner from 'barnard59/runner.js'
-import fromFile from 'rdf-utils-fs/fromFile.js'
-import $rdf from 'rdf-ext'
-import clownface from 'clownface'
+import $rdf from 'barnard59-env'
 import path from 'path'
 import { fileURLToPath } from 'url'
 import { PassThrough } from 'stream'
@@ -19,7 +17,7 @@ export function toNtriples({
   loadViewsStepsPath = loadViewsFromStoreStepPath,
 }) {
   return startRun({
-    term: 'ToFile',
+    term: 'urn:pipeline:ToFile',
     steps: [ntriplesStepsPath, fileStepsPath, loadViewsStepsPath],
     variables: {
       outFile,
@@ -30,19 +28,19 @@ export function toNtriples({
 
 export async function toStore(variables = {}) {
   return startRun({
-    term: 'ToStore',
+    term: 'urn:pipeline:ToStore',
     steps: [storeStepsPath, loadViewsFromStoreStepPath],
     variables,
   })
 }
 
 async function startRun({ term, steps, variables }) {
-  const dataset = await $rdf.dataset().import(fromFile(path.resolve(__dirname, pipelinePath)))
-  await Promise.all(steps.map(src => dataset.import(fromFile(path.resolve(__dirname, src)))))
-  const pipeline = clownface({ dataset }).namedNode(term)
+  const dataset = await $rdf.dataset().import($rdf.fromFile(path.resolve(__dirname, pipelinePath)))
+  await Promise.all(steps.map(src => dataset.import($rdf.fromFile(path.resolve(__dirname, src)))))
+  const pipeline = $rdf.clownface({ dataset }).namedNode(term)
 
   const outputStream = new PassThrough()
-  const run = await Runner(pipeline, {
+  const run = await Runner(pipeline, $rdf, {
     basePath: __dirname,
     variables: new Map(Object.entries(variables)),
     outputStream,

diff --git a/packages/publish-views/lib/ValidationError.js b/packages/publish-views/lib/ValidationError.js
@@ -1,11 +1,9 @@
-import { rdf, sh } from '@tpluscode/rdf-ns-builders'
-import $rdf from 'rdf-ext'
-import clownface from 'clownface'
+import $rdf from 'barnard59-env'
 
 export class ValidationError extends Error {
   constructor(reports) {
     const total = reports.reduce((sum, { pointer }) => {
-      const violations = pointer.any().has(sh.resultSeverity).terms.length
+      const violations = pointer.any().has($rdf.ns.sh.resultSeverity).terms.length
       return sum + violations
     }, 0)
 
@@ -17,8 +15,8 @@ export class ValidationError extends Error {
     })
     Object.defineProperty(this, 'reports', {
       enumerable: false,
-      value: clownface({ dataset: this.dataset })
-        .has(rdf.type, sh.ValidationReport),
+      value: $rdf.clownface({ dataset: this.dataset })
+        .has($rdf.ns.rdf.type, $rdf.ns.sh.ValidationReport),
     })
   }
 }

diff --git a/packages/publish-views/lib/loadViews.js b/packages/publish-views/lib/loadViews.js
@@ -1,11 +1,8 @@
 import { CONSTRUCT, SELECT } from '@tpluscode/sparql-builder'
 import * as ns from '@view-builder/core/ns.js'
 import through2 from 'through2'
-import $rdf from 'rdf-ext'
-import clownface from 'clownface'
-import { schema } from '@tpluscode/rdf-ns-builders'
+import $rdf from 'barnard59-env'
 import * as shapeTo from '@hydrofoil/shape-to-query'
-import toStream from 'rdf-dataset-ext/toStream.js'
 import { viewShape } from './shapes.js'
 import { getViewBuilderClient, getMetadataClient } from './sparql.js'
 
@@ -17,8 +14,8 @@ export default async function loadViewsToPublish() {
     .WHERE`
       ?viewBuilderView 
         a ${ns.view.View} ;
-        ${schema.sameAs} ?publishedView ; 
-        ${schema.isBasedOn} ?metaObject ;
+        ${$rdf.ns.schema.sameAs} ?publishedView ; 
+        ${$rdf.ns.schema.isBasedOn} ?metaObject ;
         ${ns.viewBuilder.publish} true ;
     `
     .execute(client.query)
@@ -34,7 +31,7 @@ export default async function loadViewsToPublish() {
 
     const dataset = $rdf.dataset()
     await Promise.all([dataset.import(viewQuads), dataset.import(metaQuads)])
-    this.push(clownface({ dataset, term: viewBuilderView }))
+    this.push($rdf.clownface({ dataset, term: viewBuilderView }))
 
     next()
   }))
@@ -45,11 +42,12 @@ async function loadViewMeta(publishedView, metaObject, client) {
 
   const subjectVariable = 'view'
   const query = shapeTo.constructQuery(shape, { focusNode: metaObject, subjectVariable })
-  const dataset = await query.execute(client.query, {
+  const quads = await query.execute(client.query, {
     operation: 'postDirect',
   })
 
-  return toStream(dataset).pipe(through2.obj(viewIdTransform(metaObject, publishedView)))
+  return $rdf.dataset(quads).toStream()
+    .pipe(through2.obj(viewIdTransform(metaObject, publishedView)))
 }
 
 function viewIdTransform(from, to) {

diff --git a/packages/publish-views/lib/shapes.js b/packages/publish-views/lib/shapes.js
@@ -1,7 +1,5 @@
 import onetime from 'onetime'
-import { fromFile } from 'rdf-utils-fs'
-import $rdf from 'rdf-ext'
-import clownface from 'clownface'
+import $rdf from 'barnard59-env'
 import { schema, sh } from '@tpluscode/rdf-ns-builders'
 import { createRequire } from 'module'
 import concat from 'barnard59-base/concat.js'
@@ -11,15 +9,15 @@ const metadataShapesPath = require.resolve('../shapes.ttl')
 const viewShapesPath = require.resolve('@view-builder/core/shape/ViewValidationShape.ttl')
 
 export const viewShape = onetime(async () => {
-  const dataset = await $rdf.dataset().import(fromFile(metadataShapesPath))
+  const dataset = await $rdf.dataset().import($rdf.fromFile(metadataShapesPath))
 
-  return clownface({ dataset })
+  return $rdf.clownface({ dataset })
     .has(sh.targetClass, schema.Dataset)
 })
 
 export function validationShapes() {
-  const metadataShapes = fromFile(metadataShapesPath)
-  const viewShapes = fromFile(viewShapesPath)
+  const metadataShapes = $rdf.fromFile(metadataShapesPath)
+  const viewShapes = $rdf.fromFile(viewShapesPath)
 
   return concat.object(metadataShapes, viewShapes)
 }
diff --git a/packages/publish-views/package.json b/packages/publish-views/package.json
@@ -4,33 +4,28 @@
   "type": "module",
   "main": "index.js",
   "scripts": {
-    "run:pipeline": "npx --node-options '--loader node-loader-raw --inspect' barnard59 run --pipeline",
+    "run:pipeline": "node --loader node-loader-raw --inspect ../../node_modules/barnard59/bin/barnard59.js run --pipeline",
     "postinstall": "mkdir -p .pipeline output",
-    "prestart:file": "cat pipeline/main.ttl pipeline/to-ntriples.ttl pipeline/to-file.ttl pipeline/steps/*.ttl > .pipeline/to-file.ttl",
-    "start:file": "dotenv -e ../../.env.local -e .env.local -- yarn run:pipeline ToFile --variable-all .pipeline/to-file.ttl",
-    "prestart:store": "mkdir .pipeline; cat pipeline/main.ttl pipeline/to-ntriples.ttl pipeline/to-store.ttl > .pipeline/to-store.ttl",
-    "start:store": "dotenv -e ../../.env.local -e .env.local -- yarn run:pipeline ToStore --variable-all .pipeline/to-store.ttl",
+    "start:file": "dotenv -e ../../.env -e ../../.env.local -e .env.local -- yarn run:pipeline urn:pipeline:ToFile --variable-all pipeline/to-file.ttl",
+    "start:store": "dotenv -e ../../.env.local -e .env.local -- yarn run:pipeline urn:pipeline:ToStore --variable-all pipeline/to-store.ttl",
     "pretest": "yarn postinstall; yarn start:file",
     "test": "shacl-cli validate --shapes test/shape*.ttl --shapes ../../packages/core/shape/ViewValidationShape.ttl --data output/views.nt"
   },
   "dependencies": {
     "@hydrofoil/shape-to-query": "^0.8.1",
-    "@tpluscode/rdf-ns-builders": "^4.1.0",
+    "@tpluscode/rdf-ns-builders": "^4.1.1",
     "@tpluscode/sparql-builder": "^1.1.0",
     "@view-builder/core": "^0.0.0",
     "@view-builder/view-util": "^0.0.1",
-    "barnard59": "^3.0.2",
-    "barnard59-base": "^1.2.2",
-    "barnard59-formats": "^1.4.2",
-    "barnard59-graph-store": "^1.1.1",
-    "barnard59-rdf": "^1.4.5",
-    "barnard59-validate-shacl": "^0.3.8",
-    "clownface": "^2",
+    "barnard59": "^4.5.3",
+    "barnard59-base": "^2.4.0",
+    "barnard59-env": "^1.2.3",
+    "barnard59-formats": "^2.1.0",
+    "barnard59-graph-store": "^5.1.1",
+    "barnard59-rdf": "^3.4.0",
+    "barnard59-shacl": "^1.4.1",
     "node-loader-raw": "^0.0.0",
     "onetime": "^6.0.0",
-    "rdf-dataset-ext": "^1.0.1",
-    "rdf-ext": "^2.1.0",
-    "rdf-utils-fs": "^2.2.0",
     "rimraf": "^3.0.2",
     "sparql-http-client": "^2.4.1",
     "through2": "^4.0.2"

diff --git a/packages/publish-views/pipeline/main.ttl b/packages/publish-views/pipeline/main.ttl
@@ -1,7 +1,7 @@
 @prefix : <https://pipeline.described.at/> .
 @prefix code: <https://code.described.at/> .
 
-<Main>
+<urn:pipeline:Main>
   a :Pipeline, :ReadableObjectMode ;
   :variables
     [
@@ -16,12 +16,17 @@
     [
       :stepList
         (
-          <#loadViews> <#prepareView> <#pointerToDataset> <#validate> <#checkShaclReports> <#flatten>
+          <urn:step:loadViews>
+          _:prepareView
+          _:pointerToDataset
+          _:validate
+          _:checkShaclReports
+          _:flatten
         )
     ] ;
 .
 
-<#prepareView>
+_:prepareView
   a :Step ;
   code:implementedBy
     [
@@ -37,7 +42,7 @@
     ) ;
 .
 
-<#pointerToDataset>
+_:pointerToDataset
   a :Step ;
   code:implementedBy
     [
@@ -50,22 +55,22 @@
     ) ;
 .
 
-<#validate>
+_:validate
   a :Step ;
   code:implementedBy
     [
-      code:link <node:barnard59-validate-shacl/validate.js#shacl> ;
+      code:link <node:barnard59-shacl/validate.js#shacl> ;
       a code:EcmaScriptModule ;
     ] ;
   code:arguments
-    [ code:name "shape" ; code:value <#Shapes> ] ,
+    [ code:name "shape" ; code:value _:Shapes ] ,
     [
       code:name "onViolation" ;
       code:value [ a code:EcmaScriptModule ; code:link <file:../lib/shacl.js#collectShaclReports> ] ;
     ];
 .
 
-<#checkShaclReports>
+_:checkShaclReports
    a :Step ;
   code:implementedBy
     [
@@ -74,7 +79,7 @@
     ] ;
 .
 
-<#Shapes>
+_:Shapes
   a :Pipeline, :ReadableObjectMode ;
   :steps
     [
@@ -91,7 +96,7 @@
     ]
 .
 
-<#flatten>
+_:flatten
   a :Step ;
   code:implementedBy
     [

diff --git a/packages/publish-views/pipeline/steps/loadViews.ttl b/packages/publish-views/pipeline/steps/loadViews.ttl
@@ -1,7 +1,7 @@
 PREFIX code: <https://code.described.at/>
 prefix : <https://pipeline.described.at/>
 
-<#loadViews>
+<urn:step:loadViews>
   a :Step ;
   code:implementedBy
     [

diff --git a/packages/publish-views/pipeline/to-file.ttl b/packages/publish-views/pipeline/to-file.ttl
@@ -1,13 +1,17 @@
 @prefix : <https://pipeline.described.at/> .
 @prefix code: <https://code.described.at/> .
 
-<ToFile>
+[ code:imports <./main.ttl> ] .
+[ code:imports <./to-ntriples.ttl> ] .
+[ code:imports <./steps/loadViews.ttl> ] .
+
+<urn:pipeline:ToFile>
   a :Pipeline ;
   :steps
     [
       :stepList
         (
-          <Main> <#serialize> _:save
+          <urn:pipeline:Main> <urn:step:serialize> _:save
         )
     ] ;
   :variables

diff --git a/packages/publish-views/pipeline/to-ntriples.ttl b/packages/publish-views/pipeline/to-ntriples.ttl
@@ -1,18 +1,18 @@
 @prefix : <https://pipeline.described.at/> .
 @prefix code: <https://code.described.at/> .
 
-<ToNtriples>
+<urn:pipeline:ToNtriples>
   a :Pipeline, :Readable ;
   :steps
     [
       :stepList
         (
-          <Main> <#serialize>
+          <urn:pipeline:Main> <urn:step:serialize>
         )
     ] ;
 .
 
-<#serialize>
+<urn:step:serialize>
   a :Step ;
   code:implementedBy
     [

diff --git a/packages/publish-views/pipeline/to-store.ttl b/packages/publish-views/pipeline/to-store.ttl
@@ -1,13 +1,16 @@
 @prefix : <https://pipeline.described.at/> .
 @prefix code: <https://code.described.at/> .
 
-<ToStore>
+[ code:imports <./main.ttl> ] .
+[ code:imports <./steps/loadViews.ttl> ] .
+
+<urn:pipeline:ToStore>
   a :Pipeline ;
   :steps
     [
       :stepList
         (
-          <Main> _:setGraph _:upload
+          <urn:pipeline:Main> _:setGraph _:upload
         )
     ] ;
 .

diff --git a/packages/publish-views/test/index.test.js b/packages/publish-views/test/index.test.js
@@ -7,7 +7,7 @@ import { cube, view, viewBuilder } from '@view-builder/core/ns.js'
 import { _void, dcat, foaf, rdfs, schema } from '@tpluscode/rdf-ns-builders'
 import { MetaLookup } from '@view-builder/view-util/lib/metaLookup.js'
 import sinon from 'sinon'
-import $rdf from 'rdf-ext'
+import $rdf from 'barnard59-env'
 import { toNtriples } from '../index.js'
 import { ValidationError } from '../lib/ValidationError.js'
 
@@ -42,6 +42,7 @@ describe('@view-builder/publish-views', () => {
               ${view.from} [
                 ${view.path} ${foaf.name} ;
                 ${view.source} [
+                  a ${view.CubeSource} ;
                   ${view.cube} <http://foo.cube> ;
                 ] ;
               ] ;
@@ -74,6 +75,7 @@ describe('@view-builder/publish-views', () => {
               ${view.from} [
                 ${view.path} ${schema.knows} ;
                 ${view.source} [
+                  a ${view.CubeSource} ;
                   ${view.cube} <http://foo.cube> ;
                 ] ;
               ] ;