Release 1.0.0 (develop) (#27)

FAIRDataTeam · Jan 20, 2020 · e5eef27 · e5eef27
1 parent 59572d6
commit e5eef27
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -7,6 +7,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+## [1.0.0]
+
 Initial version based on reproducing functionality of deprecated [FAIRifier](https://github.com/FAIRDataTeam/FAIRifier).
 
 ### Added
@@ -21,3 +23,6 @@ Initial version based on reproducing functionality of deprecated [FAIRifier](htt
   supports: FTP, Virtuoso, and Triple Stores with HTTP API
 - About dialog with basic information about the extension and its compatibility
 - Report a bug link to create a GitHub issue easily
+
+[Unreleased]: /../../compare/v1.0.0...develop
+[1.0.0]: /../../tree/v1.0.0
diff --git a/pom.xml b/pom.xml
@@ -28,7 +28,7 @@
 
     <groupId>solutions.fairdata.openrefine</groupId>
     <artifactId>metadata</artifactId>
-    <version>0.1.0-SNAPSHOT</version>
+    <version>1.0.0</version>
     <packaging>jar</packaging>
 
     <name>OpenRefine - FAIR Metadata extension</name>
@@ -137,6 +137,7 @@
             <groupId>org.eclipse.rdf4j</groupId>
             <artifactId>rdf4j-rio-turtle</artifactId>
             <version>${rdf4j.version}</version>
+            <scope>runtime</scope>
         </dependency>
 
         <dependency>

diff --git a/src/main/java/solutions/fairdata/openrefine/metadata/fdp/FairDataPointClient.java b/src/main/java/solutions/fairdata/openrefine/metadata/fdp/FairDataPointClient.java
@@ -35,11 +35,13 @@
 import nl.dtl.fairmetadata4j.model.DistributionMetadata;
 import nl.dtl.fairmetadata4j.model.FDPMetadata;
 import nl.dtl.fairmetadata4j.utils.MetadataUtils;
+import org.apache.http.HttpHeaders;
 import org.eclipse.rdf4j.model.Statement;
 import org.eclipse.rdf4j.model.impl.SimpleValueFactory;
 import org.eclipse.rdf4j.rio.RDFFormat;
+import org.eclipse.rdf4j.rio.RDFParser;
+import org.eclipse.rdf4j.rio.Rio;
 import org.eclipse.rdf4j.rio.helpers.StatementCollector;
-import org.eclipse.rdf4j.rio.turtle.TurtleParser;
 
 import java.io.BufferedReader;
 import java.io.BufferedWriter;
@@ -84,12 +86,15 @@ public class FairDataPointClient {
             308   // HTTP Permanent Redirect
     ));
 
-    private static final String CATALOG_PART = "/catalog";
-    private static final String DATASET_PART = "/dataset";
-    private static final String DISTRIBUTION_PART = "/distribution";
-    private static final String SPEC_PART = "/spec";
-    private static final String AUTH_PART = "/tokens";;
-    private static final String DASHBOARD_PART = "/dashboard";
+    private static final String CATALOG_PART = "catalog";
+    private static final String DATASET_PART = "dataset";
+    private static final String DISTRIBUTION_PART = "distribution";
+    private static final String SPEC_PART = "spec";
+    private static final String AUTH_PART = "tokens";
+    private static final String DASHBOARD_PART = "dashboard";
+
+    private static final String MEDIA_TYPE_JSON = "application/json";
+    private static final String MEDIA_TYPE_TURTLE = "text/turtle";
 
     private static final String USER_AGENT = MetadataModuleImpl.USER_AGENT;
 
@@ -116,8 +121,8 @@ public FairDataPointClient(String fdpBaseURI, String token, Logger logger) {
      * @throws FairDataPointException in case that FDP responds with an unexpected code
      */
     public TokenDTO postAuthentication(AuthDTO auth) throws IOException, FairDataPointException {
-        HttpURLConnection conn = createConnection(fdpBaseURI + AUTH_PART, "POST", "application/json");
-        conn.addRequestProperty("Content-Type", "application/json; utf-8");
+        HttpURLConnection conn = createConnection(url(fdpBaseURI, AUTH_PART), "POST", MEDIA_TYPE_JSON);
+        conn.addRequestProperty(HttpHeaders.CONTENT_TYPE, MEDIA_TYPE_JSON);
         conn.setDoOutput(true);
         objectMapper.writeValue(conn.getOutputStream(), auth);
 
@@ -136,7 +141,7 @@ public TokenDTO postAuthentication(AuthDTO auth) throws IOException, FairDataPoi
      * @throws FairDataPointException in case that FDP responds with an unexpected code
      */
     public List<DashboardCatalogDTO> getDashboard() throws IOException, FairDataPointException {
-        HttpURLConnection conn = request(fdpBaseURI + DASHBOARD_PART, "GET", "application/json", true);
+        HttpURLConnection conn = request(url(fdpBaseURI,DASHBOARD_PART), "GET", MEDIA_TYPE_JSON, true);
 
         if(conn.getResponseCode() == HttpURLConnection.HTTP_OK) {
             return objectMapper.readValue(conn.getInputStream(), new TypeReference<List<DashboardCatalogDTO>>(){});
@@ -153,7 +158,7 @@ public List<DashboardCatalogDTO> getDashboard() throws IOException, FairDataPoin
      * @throws FairDataPointException in case that FDP responds with an unexpected code
      */
     public FDPMetadataDTO getFairDataPointMetadata() throws IOException, FairDataPointException {
-        HttpURLConnection conn = request(fdpBaseURI, "GET", "text/turtle", true);
+        HttpURLConnection conn = request(fdpBaseURI, "GET", MEDIA_TYPE_TURTLE, true);
 
         if(conn.getResponseCode() == HttpURLConnection.HTTP_OK) {
             String actualURI = conn.getURL().toString();
@@ -178,7 +183,7 @@ public FDPMetadataDTO getFairDataPointMetadata() throws IOException, FairDataPoi
      * @throws FairDataPointException in case that FDP responds with an unexpected code
      */
     public CatalogDTO getCatalogMetadata(String catalogURI) throws IOException, FairDataPointException {
-        HttpURLConnection conn = request(catalogURI, "GET", "text/turtle", true);
+        HttpURLConnection conn = request(catalogURI, "GET", MEDIA_TYPE_TURTLE, true);
 
         if(conn.getResponseCode() == HttpURLConnection.HTTP_OK) {
             String actualURI = conn.getURL().toString();
@@ -203,7 +208,7 @@ public CatalogDTO getCatalogMetadata(String catalogURI) throws IOException, Fair
      * @throws FairDataPointException in case that FDP responds with an unexpected code
      */
     public DatasetDTO getDatasetMetadata(String datasetURI) throws IOException, FairDataPointException {
-        HttpURLConnection conn = request(datasetURI, "GET", "text/turtle", true);
+        HttpURLConnection conn = request(datasetURI, "GET", MEDIA_TYPE_TURTLE, true);
 
         if(conn.getResponseCode() == HttpURLConnection.HTTP_OK) {
             String actualURI = conn.getURL().toString();
@@ -228,7 +233,7 @@ public DatasetDTO getDatasetMetadata(String datasetURI) throws IOException, Fair
      * @throws FairDataPointException in case that FDP responds with an unexpected code
      */
     public DistributionDTO getDistributionMetadata(String distributionURI) throws IOException, FairDataPointException {
-        HttpURLConnection conn = request(distributionURI, "GET", "text/turtle", true);
+        HttpURLConnection conn = request(distributionURI, "GET", MEDIA_TYPE_TURTLE, true);
 
         if(conn.getResponseCode() == HttpURLConnection.HTTP_OK) {
             String actualURI = conn.getURL().toString();
@@ -289,7 +294,7 @@ public Object getDistributionSpec() throws IOException, FairDataPointException {
      * @throws FairDataPointException in case that FDP responds with an unexpected code
      */
     private Object getMetadataSpec(String metadataPart) throws IOException, FairDataPointException {
-        HttpURLConnection conn = request(fdpBaseURI + metadataPart + SPEC_PART, "GET", "application/json", true);
+        HttpURLConnection conn = request(url(fdpBaseURI, metadataPart, SPEC_PART), "GET", MEDIA_TYPE_JSON, true);
 
         if(conn.getResponseCode() == HttpURLConnection.HTTP_OK) {
             return objectMapper.readValue(conn.getInputStream(), Object.class);
@@ -307,12 +312,12 @@ private Object getMetadataSpec(String metadataPart) throws IOException, FairData
      * @throws FairDataPointException in case that FDP responds with an unexpected code
      */
     public CatalogDTO postCatalog(CatalogDTO catalogDTO) throws IOException, MetadataException, FairDataPointException {
-        HttpURLConnection conn = createConnection(fdpBaseURI + CATALOG_PART, "POST", "text/turtle");
-        conn.addRequestProperty("Content-Type", "text/turtle");
+        HttpURLConnection conn = createConnection(fdpBaseURI + CATALOG_PART, "POST", MEDIA_TYPE_TURTLE);
+        conn.addRequestProperty(HttpHeaders.CONTENT_TYPE, MEDIA_TYPE_TURTLE);
         conn.setDoOutput(true);
 
         // Generate random IRI, FDP will replace it with really unique
-        String uri = fdpBaseURI + "/fdp/catalog/" + UUID.randomUUID();
+        String uri = url(fdpBaseURI, CATALOG_PART, UUID.randomUUID().toString());
         catalogDTO.setIri(uri);
 
         CatalogMetadata catalogMetadata = CatalogTransformerUtils.dto2Metadata(catalogDTO);
@@ -326,7 +331,7 @@ public CatalogDTO postCatalog(CatalogDTO catalogDTO) throws IOException, Metadat
         bw.close();
 
         if(conn.getResponseCode() == HttpURLConnection.HTTP_CREATED) {
-            String actualURI = conn.getHeaderField("Location");
+            String actualURI = conn.getHeaderField(HttpHeaders.LOCATION);
             CatalogMetadataParser catalogMetadataParser = new CatalogMetadataParser();
 
             CatalogMetadata returnCatalogMetadata = catalogMetadataParser.parse(
@@ -348,12 +353,12 @@ public CatalogDTO postCatalog(CatalogDTO catalogDTO) throws IOException, Metadat
      * @throws FairDataPointException in case that FDP responds with an unexpected code
      */
     public DatasetDTO postDataset(DatasetDTO datasetDTO) throws IOException, MetadataException, FairDataPointException {
-        HttpURLConnection conn = createConnection(fdpBaseURI + DATASET_PART, "POST", "text/turtle");
-        conn.addRequestProperty("Content-Type", "text/turtle");
+        HttpURLConnection conn = createConnection(fdpBaseURI + DATASET_PART, "POST", MEDIA_TYPE_TURTLE);
+        conn.addRequestProperty(HttpHeaders.CONTENT_TYPE, MEDIA_TYPE_TURTLE);
         conn.setDoOutput(true);
 
         // Generate random IRI, FDP will replace it with really unique
-        String uri = fdpBaseURI + "/fdp/dataset/" + UUID.randomUUID();
+        String uri = url(fdpBaseURI, DATASET_PART, UUID.randomUUID().toString());
         datasetDTO.setIri(uri);
 
         DatasetMetadata datasetMetadata = DatasetTransformerUtils.dto2Metadata(datasetDTO);
@@ -367,7 +372,7 @@ public DatasetDTO postDataset(DatasetDTO datasetDTO) throws IOException, Metadat
         bw.close();
 
         if(conn.getResponseCode() == HttpURLConnection.HTTP_CREATED) {
-            String actualURI = conn.getHeaderField("Location");
+            String actualURI = conn.getHeaderField(HttpHeaders.LOCATION);
             DatasetMetadataParser datasetMetadataParser = new DatasetMetadataParser();
 
             DatasetMetadata returnDatasetMetadata = datasetMetadataParser.parse(
@@ -389,12 +394,12 @@ public DatasetDTO postDataset(DatasetDTO datasetDTO) throws IOException, Metadat
      * @throws FairDataPointException in case that FDP responds with an unexpected code
      */
     public DistributionDTO postDistribution(DistributionDTO distributionDTO) throws IOException, MetadataException, FairDataPointException {
-        HttpURLConnection conn = createConnection(fdpBaseURI + DISTRIBUTION_PART, "POST", "text/turtle");
-        conn.addRequestProperty("Content-Type", "text/turtle");
+        HttpURLConnection conn = createConnection(url(fdpBaseURI, DISTRIBUTION_PART), "POST", MEDIA_TYPE_TURTLE);
+        conn.addRequestProperty(HttpHeaders.CONTENT_TYPE, MEDIA_TYPE_TURTLE);
         conn.setDoOutput(true);
 
         // Generate random IRI, FDP will replace it with really unique
-        String uri = fdpBaseURI + "/fdp/distribution/" + UUID.randomUUID();
+        String uri = url(fdpBaseURI, DISTRIBUTION_PART, UUID.randomUUID().toString());
         distributionDTO.setIri(uri);
 
         DistributionMetadata distributionMetadata = DistributionTransformerUtils.dto2Metadata(distributionDTO);
@@ -408,7 +413,7 @@ public DistributionDTO postDistribution(DistributionDTO distributionDTO) throws
         bw.close();
 
         if(conn.getResponseCode() == HttpURLConnection.HTTP_CREATED) {
-            String actualURI = conn.getHeaderField("Location");
+            String actualURI = conn.getHeaderField(HttpHeaders.LOCATION);
             DistributionMetadataParser distributionMetadataParser = new DistributionMetadataParser();
 
             DistributionMetadata returnDistributionMetadata = distributionMetadataParser.parse(
@@ -430,7 +435,7 @@ public DistributionDTO postDistribution(DistributionDTO distributionDTO) throws
      * @throws IOException in case of communication error with FDP
      */
     private ArrayList<Statement> parseStatements(HttpURLConnection conn, String uri) throws IOException {
-        TurtleParser parser = new TurtleParser();
+        RDFParser parser = Rio.createParser(RDFFormat.TURTLE);
         StatementCollector collector = new StatementCollector();
         parser.setRDFHandler(collector);
 
@@ -450,10 +455,12 @@ private ArrayList<Statement> parseStatements(HttpURLConnection conn, String uri)
     private HttpURLConnection createConnection(String url, String method, String accept) throws IOException {
         HttpURLConnection conn = (HttpURLConnection) new URL(url).openConnection();
         conn.setRequestMethod(method);
-        conn.addRequestProperty("Accept", accept);
-        conn.addRequestProperty("User-Agent", USER_AGENT);
+        conn.addRequestProperty(HttpHeaders.ACCEPT, accept);
+        conn.addRequestProperty(HttpHeaders.USER_AGENT, USER_AGENT);
+        conn.addRequestProperty(HttpHeaders.CONTENT_ENCODING, StandardCharsets.UTF_8.displayName());
+
         if (token != null) {
-            conn.addRequestProperty("Authorization", "Bearer " + token);
+            conn.addRequestProperty(HttpHeaders.AUTHORIZATION, "Bearer " + token);
         }
         return conn;
     }
@@ -480,7 +487,7 @@ private HttpURLConnection request(String url, String method, String accept, bool
             visited.add(url);
 
             while (REDIRECTS.contains(conn.getResponseCode())) {
-                String nextUrl = conn.getHeaderField("Location");
+                String nextUrl = conn.getHeaderField(HttpHeaders.LOCATION);
                 String cookies = conn.getHeaderField("Set-Cookie");
 
                 logger.info("HTTP request (caused by redirect) to " + nextUrl);
@@ -499,4 +506,12 @@ private HttpURLConnection request(String url, String method, String accept, bool
         }
         return conn;
     }
+
+    public static String url(String base, String ... fragment) {
+        StringBuilder sb = new StringBuilder(base);
+        for (String f: fragment) {
+            sb.append("/").append(f);
+        }
+        return sb.toString();
+    }
 }
diff --git a/src/main/java/solutions/fairdata/openrefine/metadata/storage/TripleStoreHTTPStorage.java b/src/main/java/solutions/fairdata/openrefine/metadata/storage/TripleStoreHTTPStorage.java
@@ -30,7 +30,9 @@
 import java.io.ByteArrayInputStream;
 import java.io.IOException;
 import java.io.InputStream;
+import java.util.Arrays;
 import java.util.HashMap;
+import java.util.List;
 
 public class TripleStoreHTTPStorage extends Storage {
 
@@ -39,9 +41,12 @@ public class TripleStoreHTTPStorage extends Storage {
     private final HTTPRepository repository;
 
     static {
-        formats.put("application/x-turtle", RDFFormat.TURTLE);
-        formats.put("text/turtle", RDFFormat.TURTLE);
-        formats.put("application/rdf+xml", RDFFormat.RDFXML);
+        List<RDFFormat> rdfFormats = Arrays.asList(RDFFormat.TURTLE, RDFFormat.RDFXML);
+        for (RDFFormat rdfFormat: rdfFormats) {
+            for (String mimeType: rdfFormat.getMIMETypes()) {
+                formats.put(mimeType, rdfFormat);
+            }
+        }
     }
 
     public TripleStoreHTTPStorage(StorageDTO storageDTO) {

diff --git a/src/main/resources/module/MOD-INF/controller.js b/src/main/resources/module/MOD-INF/controller.js
@@ -1,7 +1,7 @@
 /*
  * Main JS file for FAIR Metadata extension of OpenRefine
  */
-/* global importPackage, module, Packages, ClientSideResourceManager */
+/* global importPackage, Packages, ClientSideResourceManager */
 /* eslint-disable no-unused-vars */
 
 function init() {

diff --git a/src/main/resources/module/scripts/api-client.js b/src/main/resources/module/scripts/api-client.js
@@ -1,4 +1,4 @@
-/* global $, MetadataHelpers */
+/* global MetadataHelpers */
 
 class MetadataApiClient {
 

diff --git a/src/main/resources/module/scripts/dialogs/about-dialog.html b/src/main/resources/module/scripts/dialogs/about-dialog.html
@@ -10,7 +10,7 @@
 
             <dt data-i18n="about-dialog/version"></dt>
             <dd>
-                <div class="version"><a href="https://github.com/FAIRDataTeam/OpenRefine-metadata-extension/releases" target="_blank">X.Y.Z</a></div>
+                <div class="version"><a href="https://github.com/FAIRDataTeam/OpenRefine-metadata-extension/releases/tag/v1.0.0" target="_blank">1.0.0</a></div>
             </dd>
 
             <dt data-i18n="about-dialog/license"></dt>
@@ -37,7 +37,7 @@
             <dt data-i18n="about-dialog/authors"></dt>
             <dd>
                 <ul class="authors">
-                    <li class="author">Marek Suchánek (<a href="https://github.com/MarekSuchanek">@MarekSuchanek</a>&raquo)</li>
+                    <li class="author">Marek Suchánek (<a href="https://github.com/MarekSuchanek">@MarekSuchanek</a>)</li>
                 </ul>
             </dd>
 

diff --git a/src/main/resources/module/scripts/dialogs/about-dialog.js b/src/main/resources/module/scripts/dialogs/about-dialog.js
@@ -1,4 +1,4 @@
-/* global $, DOM, DialogSystem */
+/* global DOM, DialogSystem */
 
 class MetadataAboutDialog {
     constructor(type, specs, callbackFn, prefill) {

diff --git a/src/main/resources/module/scripts/dialogs/metadata-form-dialog.js b/src/main/resources/module/scripts/dialogs/metadata-form-dialog.js
@@ -1,4 +1,4 @@
-/* global $, DOM, DialogSystem, Refine, MetadataApiClient, StoreDataDialog */
+/* global DOM, DialogSystem, Refine, MetadataApiClient, StoreDataDialog */
 
 class MetadataFormDialog {
     constructor(specs, callbackFn, prefill) {
@@ -65,7 +65,7 @@ class MetadataFormDialog {
 
     setValue(fieldId, value) {
         const input = this.elements.metadataForm.find(`#${fieldId}`);
-        if (input != null) {
+        if (input !== null) {
             if (input.is(":radio") && value === true) {
                 input.prop("checked", true);
             } else {
@@ -226,24 +226,31 @@ class MetadataFormDialog {
         });
     }
 
-    makeInputField(field) {
-        const input = $(field.type === "text" ? "<textarea>" : "<input>")
-            .attr("id", field.id)
-            .attr("name", field.id)
-            .attr("type", "text")
-            .attr("title", $.i18n(`metadata/${this.specs.id}/${field.id}/description`))
-            .prop("required", field.required);
-
+    handleInputType(field, input) {
         if (field.hidden) {
             input.attr("type", "hidden");
         } else if (field.type === "iri") {
             input
                 .attr("type", "uri")
                 .attr("placeholder", "http://");
         }
+    }
+
+    handleTypehints(field, input) {
         if (field.typehints) {
             this.makeDataList(field, input);
         }
+    }
+
+    makeInputField(field) {
+        let input = $(field.type === "text" ? "<textarea>" : "<input>")
+            .attr("id", field.id)
+            .attr("name", field.id)
+            .attr("type", "text")
+            .attr("title", $.i18n(`metadata/${this.specs.id}/${field.id}/description`))
+            .prop("required", field.required);
+        this.handleInputType(field, input);
+        this.handleTypehints(field, input);
         return input;
     }