updated _everything_

.gitignore

@@ -1,2 +1,4 @@
 function.xml
 catalog*.xml
+node_modules/
+*.iml

CHANGELOG.fnoi.md

@@ -0,0 +1,19 @@
+# Function Ontology - Implementation Vocabulary Changelog
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## Unreleased
+
+## 0.1.1 - 2020-12-23
+
+### Changed
+
+- Updated and clarified definitions
+
+## 0.1.0
+
+### Added
+
+- Creation

CHANGELOG.fnom.md

@@ -0,0 +1,21 @@
+# Function Ontology - Implementation Vocabulary Changelog
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## Unreleased
+
+## 0.2.1 - 2020-12-23
+
+### Changed
+
+- Updated and clarified definitions
+
+## 0.2.0
+
+## 0.1.0
+
+### Added
+
+- Creation

CHANGELOG.md

@@ -6,10 +6,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## Roadmap
 
-- [ ] TODO auto-fill same-semantics metadata
+- [ ] TODO auto-fill same-semantics metadata as recommended by https://w3id.org/widoco/bestPractices
 
 ## Unreleased
 
+## [1.0.0] - 2020-12-23
+
 ### Added
 
 - Changelog
@@ -52,6 +54,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Added
 - creation.
 
+[1.0.0]: https://github.com/IDLabResearch/function-ontology/compare/v0.6.0...v1.0.0
 [0.6.0]: https://github.com/IDLabResearch/function-ontology/compare/v0.5.1...v0.6.0
 [0.5.1]: https://github.com/IDLabResearch/function-ontology/compare/v0.5.0...v0.5.1
 [0.5.0]: https://github.com/IDLabResearch/function-ontology/compare/0.4.1...v0.5.0

README.MD

@@ -5,3 +5,16 @@
 See https://w3id.org/function/spec for the full specification
 
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.595382.svg)](https://doi.org/10.5281/zenodo.595382)
+
+## Releasing a new version
+
+Make sure you have the WiDoCo 1.4.x jar downloaded in the root of this repo, and you have JAVA and Node.js installed.
+Then, execute
+
+```shell
+npm install
+cd ./dist
+node build.js
+```
+
+The folders in `dist` should mimic the same structure and contents under https://w3id.org/function.

dist/build.js

@@ -0,0 +1,67 @@
+const util = require('util');
+const fs = require('fs/promises');
+const exec = util.promisify(require('child_process').exec);
+
+const $rdf = require('rdflib');
+const Namespace = $rdf.Namespace;
+
+const DC = Namespace("http://purl.org/dc/elements/1.1/");
+const OWL = Namespace("http://www.w3.org/2002/07/owl#");
+const RDF = Namespace("http://www.w3.org/1999/02/22-rdf-syntax-ns#");
+const VANN = Namespace("http://purl.org/vocab/vann/");
+const VOAF = Namespace("http://purl.org/vocommons/voaf#");
+
+const map = [
+  {
+    ttlFile: "../fno.ttl",
+    outputFolder: "./ontology",
+    uri: "https://w3id.org/function/ontology#",
+  }, {
+    ttlFile: "../fnoi.ttl",
+    outputFolder: "./vocabulary/implementation",
+    uri: "https://w3id.org/function/vocabulary/implementation#",
+  }, {
+    ttlFile: "../fnom.ttl",
+    outputFolder: "./vocabulary/mapping",
+    uri: "https://w3id.org/function/vocabulary/mapping#",
+  },
+]
+
+processMap(map);
+
+async function processMap(map) {
+  for (const elem of map) {
+    const store = await getStore(elem.ttlFile);
+    await runWidoco(elem.ttlFile, elem.outputFolder, store);
+  }
+}
+
+async function runWidoco(ontFile, outFolder, store) {
+  const preStuff = 'java -jar ../widoco-1.4.14-jar-with-dependencies.jar';
+  const postStuff = '-getOntologyMetadata -oops -rewriteAll -htaccess -webVowl -analytics UA-87734787-2 -excludeIntroduction';
+  const voc = store.any(null, RDF('type'), VOAF('Vocabulary'));
+  const version = store.any(voc, OWL('versionInfo')).value;
+  const uri = store.any(voc, VANN('preferredNamespaceUri')).value;
+  const prefix = store.any(voc, VANN('preferredNamespacePrefix')).value;
+  const commandVersion = `${preStuff} -ontFile ${ontFile} -outFolder ${outFolder}/${version} ${postStuff}`;
+  const {stdout, stderr} = await exec(commandVersion);
+  console.log(stdout);
+  console.warn(stderr);
+  const command = `${preStuff} -ontFile ${ontFile} -outFolder ${outFolder} ${postStuff}`;
+  await exec(command);
+  const appendData = `<p>The namespace is <b>${uri}</b>, the preferred prefix is <b>${prefix}</b></p>`;
+  await fs.appendFile(`${outFolder}/${version}/sections/abstract-en.html`, appendData);
+  await fs.appendFile(`${outFolder}/sections/abstract-en.html`, appendData);
+  const descriptionPlaceholder = `This is a placeholder text for the description of your ontology. The description should include an explanation and a diagram explaining how the classes are related, examples of usage, etc.`;
+  let description = await fs.readFile(`${outFolder}/sections/description-en.html`, 'utf8');
+  description = description.replace(descriptionPlaceholder, "Further description and explanation of these classes and properties are given in the Function Ontology Specification at https://w3id.org/function/spec");
+  await fs.writeFile(`${outFolder}/${version}/sections/description-en.html`, description);
+  await fs.writeFile(`${outFolder}/sections/description-en.html`, description);
+}
+
+async function getStore(ontFile) {
+  const store = $rdf.graph();
+  const body = await fs.readFile(ontFile, 'utf8');
+  $rdf.parse(body, store, "http://example.com/#", 'text/turtle');
+  return store;
+}

dist/ontology/.htaccess

@@ -0,0 +1,47 @@
+# Turn off MultiViews
+Options -MultiViews
+
+# Directive to ensure *.rdf files served as appropriate content type,
+# if not present in main apache config
+AddType application/rdf+xml .rdf
+AddType application/rdf+xml .owl
+AddType text/turtle .ttl
+AddType application/n-triples .n3
+AddType application/ld+json .json
+# Rewrite engine setup
+RewriteEngine On
+#Change the path to the folder here
+RewriteBase /./ontology 
+
+# Rewrite rule to serve HTML content from the vocabulary URI if requested
+RewriteCond %{HTTP_ACCEPT} !application/rdf\+xml.*(text/html|application/xhtml\+xml)
+RewriteCond %{HTTP_ACCEPT} text/html [OR]
+RewriteCond %{HTTP_ACCEPT} application/xhtml\+xml [OR]
+RewriteCond %{HTTP_USER_AGENT} ^Mozilla/.*
+RewriteRule ^$ index-en.html [R=303,L]
+
+# Rewrite rule to serve JSON-LD content from the vocabulary URI if requested
+RewriteCond %{HTTP_ACCEPT} application/ld\+json
+RewriteRule ^$ ontology.json [R=303,L]
+
+# Rewrite rule to serve RDF/XML content from the vocabulary URI if requested
+RewriteCond %{HTTP_ACCEPT} \*/\* [OR]
+RewriteCond %{HTTP_ACCEPT} application/rdf\+xml
+RewriteRule ^$ ontology.xml [R=303,L]
+
+# Rewrite rule to serve N-Triples content from the vocabulary URI if requested
+RewriteCond %{HTTP_ACCEPT} application/n-triples
+RewriteRule ^$ ontology.nt [R=303,L]
+
+# Rewrite rule to serve TTL content from the vocabulary URI if requested
+RewriteCond %{HTTP_ACCEPT} text/turtle [OR]
+RewriteCond %{HTTP_ACCEPT} text/\* [OR]
+RewriteCond %{HTTP_ACCEPT} \*/turtle 
+RewriteRule ^$ ontology.ttl [R=303,L]
+
+RewriteCond %{HTTP_ACCEPT} .+
+RewriteRule ^$ 406.html [R=406,L]
+# Default response
+# ---------------------------
+# Rewrite rule to serve the RDF/XML content from the vocabulary URI by default
+RewriteRule ^$ ontology.xml [R=303,L]