Merge branch 'prov4itdata/publish' into 'development'

Release v1.0.0

See merge request prov4itdata-dapsi/mono-repo!3

.gitignore

@@ -0,0 +1,21 @@
+**/node_modules
+.rdf-test-suite-cache
+.idea
+lerna-debug.log
+yarn-error.log
+**/lib/**/*.js
+**/lib/**/*.js.map
+**/lib/**/*.d.ts
+**/test/**/*.js
+**/test/**/*.js.map
+**/test/**/*.d.ts
+**/bin/**/*.js
+**/bin/**/*.js.map
+**/bin/**/*.d.ts
+**/index.js
+**/index.js.map
+**/index.d.ts
+coverage
+documentation
+earl.ttl
+.eslintcache

CHANGELOG.md

@@ -0,0 +1,13 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
+and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
+
+## [1.0.0]
+
+- Comunica PROV4ITDaTa Init Actor
+- Added Comunica Federated RDF Resolve Quad Pattern Actor
+- Added Comunica Annotate Provenance RDF Metadata Extract Actor
+- Added Comunica Context Entries

README.md

@@ -1,2 +1,22 @@
-# Mono Repo
+<p align="center">
+  <a href="https://comunica.dev/">
+    <img alt="Comunica" src="https://comunica.dev/img/comunica_red.svg" width="200">
+  </a>
+</p>
 
+<p align="center">
+  <strong>Comunica: PROV4ITDaTa project</strong>
+</p>
+
+
+This is a monorepo that contains a custom Comunica engine with custom actors, 
+tailored to needs of the PROV4ITDaTa project.</br>
+Concretely, this monorepo provides the following packages:
+- [`@prov4itdata/actor-init-sparql`](https://www.npmjs.com/package/@prov4itdata/actor-init-sparql): a custom configuration of the Comunica engine. 
+- [`@prov4itdata/actor-rdf-resolve-quad-pattern-federated`](https://www.npmjs.com/package/@prov4itdata/actor-rdf-resolve-quad-pattern-federated): a slightly updated version of [`@comunica/actor-rdf-resolve-quad-pattern-federated`](https://github.com/comunica/comunica/tree/master/packages/actor-rdf-resolve-quad-pattern-federated) that allows to collect the provenance data from the federated sources.
+- [`@prov4itdata/actor-rdf-metadata-extract-annotate-provenance`](https://www.npmjs.com/package/@prov4itdata/actor-rdf-metadata-extract-annotate-provenance): a new actor that captures source-level provenance.
+- [`@prov4itdata/context-entries`](https://www.npmjs.com/package/@prov4itdata/context-entries): this package is a plain copy of the not-yet-published https://github.com/comunica/comunica/tree/master/packages/context-entries
+
+## License
+This code is copyrighted by [Ghent University – imec](http://idlab.ugent.be/)
+and released under the [MIT license](http://opensource.org/licenses/MIT).

lerna.json

@@ -0,0 +1,21 @@
+{
+  "lerna": "2.4.0",
+  "command": {
+    "publish": {
+      "ignoreChanges": [
+        "*.md"
+      ],
+      "message": "Bump to release version %s",
+      "allowBranch": "master",
+      "npmClient": "npm"
+    }
+  },
+  "packages": [
+    "packages/*"
+  ],
+  "useWorkspaces": true,
+  "version": "1.1.0",
+  "loglevel": "success",
+  "registry": "https://registry.npmjs.org/",
+  "npmClient": "yarn"
+}

package.json

@@ -0,0 +1,104 @@
+{
+  "private": true,
+  "workspaces": [
+    "packages/*"
+  ],
+  "engines": {
+    "node": ">=8.0"
+  },
+  "devDependencies": {
+    "@comunica/bus-query-operation": "^1.19.0",
+    "@comunica/bus-rdf-dereference": "^1.19.0",
+    "@comunica/bus-rdf-membership-filter": "^1.0.0",
+    "@comunica/bus-rdf-metadata-extract": "^1.19.0",
+    "@comunica/core": "^1.19.0",
+    "@rdfjs/data-model": "^1.1.1",
+    "@strictsoftware/typedoc-plugin-monorepo": "^0.4.0",
+    "@types/bloem": "^0.2.0",
+    "@types/jest": "^26.0.0",
+    "@types/murmurhash": "^0.0.1",
+    "@types/node": "^13.1.7",
+    "@typescript-eslint/eslint-plugin": "^4.1.1",
+    "@typescript-eslint/parser": "^4.1.1",
+    "arrayify-stream": "^1.0.0",
+    "asynciterator": "^3.0.2",
+    "babel-loader": "^8.1.0",
+    "coveralls": "^3.0.0",
+    "cross-fetch": "^3.0.5",
+    "eslint": "^7.9.0",
+    "eslint-config-es": "3.23.2",
+    "eslint-import-resolver-typescript": "^2.3.0",
+    "eslint-plugin-import": "^2.22.0",
+    "eslint-plugin-jest": "^24.0.2",
+    "eslint-plugin-tsdoc": "^0.2.7",
+    "eslint-plugin-unused-imports": "^1.0.0",
+    "immutable": "^3.8.2",
+    "jest": "^26.0.0",
+    "jest-rdf": "^1.3.0",
+    "lerna": "^4.0.0",
+    "lodash.assign": "^4.2.0",
+    "manual-git-changelog": "^1.0.0",
+    "pre-commit": "^1.2.2",
+    "rdf-quad": "^1.3.0",
+    "sparqlalgebrajs": "^2.0.0",
+    "stream-to-string": "^1.1.0",
+    "streamify-array": "^1.0.0",
+    "streamify-string": "^1.0.1",
+    "ts-jest": "^26.0.0",
+    "typedoc": "^0.20.0",
+    "typescript": "^3.9.0",
+    "uglifyjs-webpack-plugin": "^2.1.1",
+    "webpack": "^4.28.3",
+    "webpack-cli": "^4.0.0"
+  },
+  "pre-commit": [
+    "build",
+    "lint",
+    "test"
+  ],
+  "jest": {
+    "transform": {
+      "^.+\\.ts$": "ts-jest"
+    },
+    "testRegex": "(/test/.*|(\\.|/)(test|spec))\\.ts$",
+    "moduleFileExtensions": [
+      "ts",
+      "js"
+    ],
+    "setupFilesAfterEnv": [
+      "./setup-jest.js"
+    ],
+    "collectCoverage": true,
+    "coveragePathIgnorePatterns": [
+      "/node_modules/",
+      "/mocks/",
+      "index.js"
+    ],
+    "testEnvironment": "node",
+    "coverageThreshold": {
+      "global": {
+        "branches": 100,
+        "functions": 100,
+        "lines": 100,
+        "statements": 100
+      }
+    }
+  },
+  "scripts": {
+    "test-changed": "lerna run test --since HEAD",
+    "build-changed": "lerna run build --since HEAD",
+    "test": "jest",
+    "coveralls": "jest --coverage && cat ./coverage/lcov.info | coveralls",
+    "test-ci": "jest --ci --maxWorkers=4 --coverage",
+    "coveralls-ci": "cat ./coverage/lcov.info | coveralls",
+    "lint": "eslint . --ext .ts --cache",
+    "clean": "rm -rf ./node_modules && rm -rf ./packages/*/node_modules",
+    "build": "tsc",
+    "build-watch": "tsc --watch",
+    "publish": "yarn run build && lerna publish",
+    "publish-bare": "lerna exec -- npm publish --silent",
+    "doc": "typedoc --name 'Comunica AMF' --disableOutputCheck --external-modulemap '.*packages/([^/]+)/.*' --mode modules --out documentation",
+    "postinstall": "yarn run build && lerna run prepare",
+    "version": "manual-git-changelog onversion"
+  }
+}

packages/actor-init-sparql-prov4itdata/.gitignore

@@ -0,0 +1,5 @@
+comunica-browser.js*
+engine-default.js
+index-browser.d.ts
+index-browser.js
+index-browser.js.map

packages/actor-init-sparql-prov4itdata/CHANGELOG.md

@@ -0,0 +1,10 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
+and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
+
+## [1.0.0]
+
+- Intial release

packages/actor-init-sparql-prov4itdata/README.md

@@ -0,0 +1,54 @@
+# Comunica PROV4ITDaTa Init Actor
+
+A custom Comunica query engine, configured to be used by the PROV4ITDaTa project.
+
+<!-- This module is part of the [Comunica framework](https://comunica.dev/). -->
+
+## Install
+
+```bash
+$ yarn add @prov4itdata/actor-init-sparql
+```
+
+or
+
+```bash
+$ npm install -g @prov4itdata/actor-init-sparql
+```
+
+### Usage within application
+
+This engine can be used in JavaScript/TypeScript applications as follows:
+
+```javascript
+const newEngine = require('@comunica/actor-init-sparql-amf').newEngine;
+const myEngine = newEngine();
+
+const result = await myEngine.query(`
+  SELECT * WHERE {
+      ?s ?p ?o
+  }`, {
+  sources: ['http://localhost:3000/dataset'],
+});
+
+// Consume results as a stream (best performance)
+result.bindingsStream.on('data', (binding) => {
+    console.log(binding.get('?s').value);
+    console.log(binding.get('?s').termType);
+
+    console.log(binding.get('?p').value);
+
+    console.log(binding.get('?o').value);
+});
+
+// Consume results as an array (easier)
+const bindings = await result.bindings();
+console.log(bindings[0].get('?s').value);
+console.log(bindings[0].get('?s').termType);
+
+// Log metadata containing source-level provenance information
+const metadata = await result.metadata();
+console.log(metadata)
+```
+
+_[**Read more** about querying an application](https://comunica.dev/docs/query/getting_started/query_app/)._

packages/actor-init-sparql-prov4itdata/bin/http.ts

@@ -0,0 +1,7 @@
+#!/usr/bin/env node
+import { HttpServiceSparqlEndpoint } from '@comunica/actor-init-sparql';
+
+const defaultConfigPath = `${__dirname}/../config/config-default.json`;
+
+HttpServiceSparqlEndpoint.runArgsInProcess(process.argv.slice(2), process.stdout, process.stderr, `${__dirname}/../`, process.env, defaultConfigPath, code => process.exit(code))
+  .catch(error => process.stderr.write(`${error.message}/n`));

packages/actor-init-sparql-prov4itdata/bin/query-dynamic.ts

@@ -0,0 +1,3 @@
+#!/usr/bin/env node
+import { runArgsInProcess } from '@comunica/runner-cli';
+runArgsInProcess(`${__dirname}/../`, `${__dirname}/../config/config-default.json`);

packages/actor-init-sparql-prov4itdata/bin/query.ts

@@ -0,0 +1,3 @@
+#!/usr/bin/env node
+import { runArgsInProcessStatic } from '@comunica/runner-cli';
+runArgsInProcessStatic(require('../engine-default.js'));

packages/actor-init-sparql-prov4itdata/config/config-default.json

@@ -0,0 +1,38 @@
+{
+  "@context": [
+    "https://linkedsoftwaredependencies.org/bundles/npm/componentsjs/^4.0.0/components/context.jsonld",
+    "https://linkedsoftwaredependencies.org/bundles/npm/@comunica/actor-init-sparql/^1.0.0/components/context.jsonld",
+    "https://linkedsoftwaredependencies.org/bundles/npm/@comunica/runner/^1.0.0/components/context.jsonld",
+    {
+      "caisa": "npmd:@prov4itdata/actor-init-sparql/",
+      "files-caisa": "caisa:^1.0.0/",
+      "config-setsa": "files-caisa:config/sets/"
+    }
+  ],
+
+  "@id": "urn:comunica:my",
+  "@type": "Runner",
+  "import": [
+
+    "files-caisa:config/sets/http-solid.json",
+
+    "files-cais:config/sets/http-memento.json",
+    "files-cais:config/sets/join.json",
+    "files-cais:config/sets/rdf-dereference.json",
+    "files-cais:config/sets/rdf-parsers.json",
+    "files-cais:config/sets/rdf-serializers.json",
+    "files-caisa:config/sets/resolve-federated.json",
+    "files-cais:config/sets/resolve-hypermedia.json",
+    "files-cais:config/sets/resolve-rdfjs.json",
+    "files-cais:config/sets/resolve-sparql.json",
+    "files-cais:config/sets/sparql-init.json",
+    "files-cais:config/sets/graphql-parsers.json",
+    "files-cais:config/sets/sparql-optimize.json",
+    "files-cais:config/sets/sparql-parsers.json",
+    "files-cais:config/sets/sparql-queryoperators.json",
+    "files-cais:config/sets/sparql-queryoperators-path.json",
+    "files-cais:config/sets/sparql-serializers.json",
+
+    "files-caisa:config/sets/rdf-metadata-extract-annotate-provenance.json"
+ ]
+}

packages/actor-init-sparql-prov4itdata/config/sets/http-solid.json

@@ -0,0 +1,38 @@
+{
+  "@context": [
+    "https://linkedsoftwaredependencies.org/bundles/npm/@comunica/actor-init-sparql/^1.0.0/components/context.jsonld",
+    "https://linkedsoftwaredependencies.org/bundles/npm/@comunica/runner/^1.0.0/components/context.jsonld",
+
+    "https://linkedsoftwaredependencies.org/bundles/npm/@comunica/actor-http-solid-auth-fetch/^1.0.0/components/context.jsonld",
+    "https://linkedsoftwaredependencies.org/bundles/npm/@comunica/actor-http-proxy/^1.0.0/components/context.jsonld",
+
+    "https://linkedsoftwaredependencies.org/bundles/npm/@comunica/bus-http/^1.0.0/components/context.jsonld",
+    "https://linkedsoftwaredependencies.org/bundles/npm/@comunica/mediator-number/^1.0.0/components/context.jsonld"
+  ],
+  "@graph": [
+    {
+      "@id": "urn:comunica:my",
+      "actors": [
+        {
+          "@id": "config-sets:http.json#myHttpProxy",
+          "@type": "ActorHttpProxy",
+          "cahp:Actor/Http/Proxy/mediatorHttp": {
+            "@id": "config-sets:http.json#mediatorHttp"
+          },
+          "beforeActor": "config-sets:http.json#myHttpFetcher"
+        },
+        {
+          "@id": "config-sets:http.json#myHttpFetcher",
+          "@type": "ActorHttpSolidAuthFetch"
+        }
+      ]
+    },
+    {
+      "@id": "config-sets:http.json#mediatorHttp",
+      "@type": "MediatorNumberMin",
+      "field": "time",
+      "ignoreErrors": true,
+      "cc:Mediator/bus": { "@id": "cbh:Bus/Http" }
+    }
+  ]
+}

packages/actor-init-sparql-prov4itdata/config/sets/rdf-metadata-extract-annotate-provenance.json

@@ -0,0 +1,25 @@
+{
+  "@context": [
+    "https://linkedsoftwaredependencies.org/bundles/npm/@comunica/actor-init-sparql/^1.0.0/components/context.jsonld",
+    "https://linkedsoftwaredependencies.org/bundles/npm/@comunica/runner/^1.0.0/components/context.jsonld",
+
+    "https://linkedsoftwaredependencies.org/bundles/npm/@prov4itdata/actor-rdf-metadata-extract-annotate-provenance/^1.0.0/components/context.jsonld",
+
+    "https://linkedsoftwaredependencies.org/bundles/npm/@comunica/bus-rdf-dereference/^1.0.0/components/context.jsonld",
+
+    "https://linkedsoftwaredependencies.org/bundles/npm/@comunica/mediator-number/^1.0.0/components/context.jsonld",
+    "https://linkedsoftwaredependencies.org/bundles/npm/@comunica/mediator-race/^1.0.0/components/context.jsonld",
+    {
+      "caisa": "npmd:@prov4itdata/actor-init-sparql/",
+      "files-caisa": "caisa:^1.0.0/",
+      "config-setsa": "files-caisa:config/sets/"
+    }
+  ],
+  "@id": "urn:comunica:my",
+  "actors": [
+    {
+      "@id": "config-setsa:rdf-metadata-extract-annotate-provenance.json#myRdfMetadataExtractAnnotateProvenance",
+      "@type": "ActorRdfMetadataExtractAnnotateProvenance"
+    }
+  ]
+}