Persist ktbl and tos datastream by master sles edit

app/actions/Enrich.java

@@ -77,6 +77,7 @@ public static String enrichMetadata2(Node node) {
 		try {
 			play.Logger.info("Enrich 2 " + node.getPid());
 			String metadata = node.getMetadata2();
+			play.Logger.debug("metadata2 " + metadata);
 			if (metadata == null || metadata.isEmpty()) {
 				play.Logger.info("No metadata2 to enrich " + node.getPid());
 				return "No metadata2 to enrich " + node.getPid();

app/actions/Modify.java

@@ -1115,8 +1115,9 @@ private static List<String> getType(Node node) {
 		}
 	}
 
-	private String rdfToString(Map<String, Object> result, RDFFormat format) {
+	public String rdfToString(Map<String, Object> result, RDFFormat format) {
 		try {
+			play.Logger.debug("result=" + result.toString());
 			String rdf = RdfUtils.readRdfToString(
 					new ByteArrayInputStream(json(result).getBytes("utf-8")),
 					RDFFormat.JSONLD, format, "");

app/archive/fedora/XmlUtils.java

@@ -80,6 +80,7 @@
  * 
  */
 public class XmlUtils {
+	String doiResolver = Globals.doiResolver;
 
 	public static XmlSchemaValidator validator = new XmlSchemaValidator();
 
@@ -489,8 +490,8 @@ public Map<String, Object> getLd2Lobidify2DeepGreen(
 					String doi = node.getTextContent();
 					play.Logger.debug("DOI: " + doi);
 					Map<String, Object> publisherVersionDoi = new TreeMap<>();
-					publisherVersionDoi.put("@id", "https://doi.org/" + doi);
-					publisherVersionDoi.put("prefLabel", "https://doi.org/" + doi);
+					publisherVersionDoi.put("@id", doiResolver + "/" + doi);
+					publisherVersionDoi.put("prefLabel", doiResolver + "/" + doi);
 					publisherVersions.add(publisherVersionDoi);
 				}
 				if (attrib.getNodeValue().equalsIgnoreCase("pmcid")) {
@@ -922,7 +923,7 @@ else if (elemListCopStatement.getLength() > 0) {
 						int indexOpen = text.indexOf("(");
 						int indexClose = text.indexOf(")");
 						if (indexOpen == -1)
-							licenseId = "https://doi.org/10.1027/a000001";
+							licenseId = doiResolver + "/10.1027/a000001";
 						if (indexOpen >= 0)
 							licenseId = text.substring(indexOpen + 1, indexClose);
 						break;

app/controllers/Resource.java

@@ -29,6 +29,7 @@
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Date;
+import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.Map;
 import java.util.stream.Collectors;
@@ -60,6 +61,7 @@
 import authenticate.BasicAuth;
 import helper.HttpArchiveException;
 import helper.KTBLMapperHelper;
+import helper.Metadata2Helper;
 import helper.RdfHelper;
 import helper.ToscienceHelper;
 import helper.WebgatherUtils;
@@ -546,31 +548,33 @@ public static Promise<Result> updateDeepGreen(@PathParam("pid") String pid,
 	@ApiOperation(produces = "application/json", nickname = "updateKtbl", value = "updateKtbl", notes = "Updates the ktbl datastream of a resource.", response = Message.class, httpMethod = "PUT")
 	@ApiImplicitParams({
 			@ApiImplicitParam(name = "data", value = "data", dataType = "file", required = true, paramType = "body") })
-	public static Promise<Result> updateKtbl(@PathParam("pid") String pid) {
+
+	public static Promise<Result> updateKtblAndTos(@PathParam("pid") String pid) {
 		return new ModifyAction().call(pid, node -> {
 			try {
 
-				play.Logger.debug("Starting KTBL Mapping");
-
+				LinkedHashMap<String, Object> rdf = null;
 				Node readNode = new Read().readNode(pid);
-
 				MultipartFormData body = request().body().asMultipartFormData();
 				FilePart data = body.getFile("data");
 
+				String name = data.getFilename();
+				play.Logger.debug("FileName=" + name);
+
 				if (data == null) {
 					return (Result) JsonMessage(new Message("Missing File.", 400));
 				}
 
 				/**
 				 * 1.KTBL(Json)***************************************
 				 */
+				play.Logger.debug("Starting KTBL Mapping");
+
 				String contentOfFile =
 						KTBLMapperHelper.getStringContentFromJsonFile(data);
-				play.Logger.debug("contentOfFile=" + contentOfFile);
 
-				String ktblMetadata =
-						KTBLMapperHelper.getToPersistKtblMetadata(contentOfFile);
-				play.Logger.debug("ktblMetadata=" + ktblMetadata);
+				String ktblMetadata = KTBLMapperHelper
+						.getToPersistKtblMetadata(contentOfFile, readNode.getPid());
 
 				String result1 = modify.updateMetadata("ktbl", readNode, ktblMetadata);
 
@@ -579,25 +583,42 @@ public static Promise<Result> updateKtbl(@PathParam("pid") String pid) {
 				/**
 				 * 2. TOSCIENCE(Json)***************************************
 				 */
+				play.Logger.debug("Starting TOSCIENCE Mapping");
+
+				String toscienceMetadata = ToscienceHelper
+						.getToPersistTosMetadata(contentOfFile, readNode.getPid());
+
+				play.Logger.debug("toscienceMetadata=" + toscienceMetadata);
+
+				String result2 =
+						modify.updateMetadata("toscience", readNode, toscienceMetadata);
 
-				// String result2 =
-				// modify.updateMetadata("toscience", readNode, ktblMetadata);
+				play.Logger.debug("Done TOSCIENCE Mapping");
 
 				/**
-				 * 3. METADATA2(rdf)***************************************
+				 * 3. METADATA2(rdf)****************************************
 				 */
-				// JSONObject ktblJson = new JSONObject(ktblMetadata);
-				// Map<String, Object> rdf =
-				// KTBLMapperHelper.getMapFromJSONObject(ktblJson);
-				//
-				// String contentRewrite = modify.rewriteContent(rdf.toString(), pid);
-				//
-				// String result3 =
-				// modify.updateMetadata("metadata2", readNode, contentRewrite);
-
-				Globals.fedora.updateNode(readNode);
-
-				return JsonMessage(new Message(result1));
+
+				play.Logger.debug("Starting METADATA2 Mapping");
+
+				rdf = Metadata2Helper
+						.getRdfFromToscience(new JSONObject(toscienceMetadata), readNode);
+
+				play.Logger.debug("rdf=" + rdf.toString());
+
+				String rdfContent = modify.rdfToString(
+						(Map<String, Object>) rdf.get("metadata2"), RDFFormat.NTRIPLES);
+
+				play.Logger.debug("rdfContent=" + rdfContent);
+
+				String result3 =
+						modify.updateMetadata("metadata2", readNode, rdfContent);
+
+				play.Logger.debug("Done METADATA2 Mapping");
+
+				Enrich.enrichMetadata2(readNode);
+
+				return JsonMessage(new Message(result1 + result2 + result3));
 			} catch (Exception e) {
 				throw new HttpArchiveException(500, e);
 			}

app/de/hbz/lobid/helper/JsonConverter.java

@@ -120,6 +120,7 @@ private Map<String, Object> convert(String subject, Object context,
 		mainSubjectOfTheResource = subject;
 		collect(g);
 		Map<String, Object> result = createMap(g);
+		play.Logger.debug("result=" + result.toString());
 		result.put("@context", context);
 		return result;
 	}

app/helper/AdHocUriProvider.java

@@ -0,0 +1,87 @@
+package helper;
+
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.net.URLEncoder;
+import java.nio.charset.StandardCharsets;
+
+import org.json.JSONArray;
+import org.json.JSONObject;
+
+import com.google.common.base.Charsets;
+import com.google.common.io.CharStreams;
+import com.google.common.io.Closeables;
+
+import models.Globals;
+import play.libs.ws.WSResponse;
+
+/**
+ * @author aquast
+ *
+ *         The Class provides a simplified way to create an adHocUri based on a
+ *         new to.science.label Object (formely known as "regal etikett") which
+ *         is required for the lobid metadata format.
+ * 
+ *         Class is based on the method code of Enrich.java
+ *         enrichLRMIData-method simplified in comparisation to this by reducing
+ *         functionality and variables
+ */
+public class AdHocUriProvider {
+
+	private String labelValue = null;
+
+	private InputStream inStream;
+
+	/**
+	 * @param LabelValue the value for which we like to create an AdHocUri
+	 * @return a AdHocUri representing a newly created to.science.label
+	 */
+	public String getAdhocUri(String LabelValue) {
+
+		String adHocUri = null;
+		this.labelValue = LabelValue;
+
+		adHocUri = generateNewAdHocUri();
+
+		return adHocUri;
+	}
+
+	private String generateNewAdHocUri() {
+		String adHocUri = null;
+
+		play.Logger.debug("Start AdHocUri generation for " + labelValue);
+
+		// String encodedValue = labelValue.replace(" ", "+");
+		try {
+			String encodedValue =
+					URLEncoder.encode(labelValue, StandardCharsets.UTF_8.toString())
+							.replaceAll("\\+", "%20").replaceAll("%21", "!")
+							.replaceAll("%27", "'").replaceAll("%28", "(")
+							.replaceAll("%29", ")").replaceAll("%7E", "~");
+			WSResponse response = play.libs.ws.WS
+					.url(Globals.zettelUrl + "/localAutocomplete" + "?q=" + encodedValue)
+					.setFollowRedirects(true).get().get(2000);
+			inStream = response.getBodyAsStream();
+			String formsResponseBody =
+					CharStreams.toString(new InputStreamReader(inStream, Charsets.UTF_8));
+			Closeables.closeQuietly(inStream);
+			// fetch annoying errors from to.science.forms service
+			if (response.getStatus() != 200) {
+				play.Logger.error(
+						"to.science.forms service request localAutocomplete fails for "
+								+ encodedValue + "\nUse URI for setting Label now!");
+			} else {
+				// Parse out uri value from JSON structure
+				JSONArray jFormsResponse = new JSONArray(formsResponseBody);
+				JSONObject jFormsObject = jFormsResponse.getJSONObject(0);
+				adHocUri = new String(jFormsObject.getString("value"));
+				play.Logger.debug("Found adHoc-URI: " + adHocUri);
+			}
+		} catch (Exception e) {
+			play.Logger.error("Content could not be enriched!", e);
+			throw new RuntimeException("LRMI.json could not be enriched", e);
+		}
+
+		return adHocUri;
+	}
+}

app/helper/DataciteClient.java

@@ -35,6 +35,7 @@
 import com.sun.jersey.client.urlconnection.HTTPSProperties;
 import com.sun.jersey.multipart.FormDataMultiPart;
 import com.sun.jersey.multipart.impl.MultiPartWriter;
+import com.typesafe.config.ConfigFactory;
 
 /**
  * @author Jan Schnasse
@@ -45,14 +46,16 @@ public class DataciteClient {
 	Client webclient = null;
 	boolean testMode = false;
 	int status = 200;
+	String user = Globals.dataCiteUser;
+	String password = Globals.dataCitePasswd;
+	// URL of Datacite-Repository(Prod | Test)
+	String dataciteURL = Globals.datCiteUrl;
 
 	/**
 	 * The DataciteClient can mint and register dois via the datacite api
 	 */
 	public DataciteClient() {
 		status = 200;
-		String user = Globals.dataCiteUser;
-		String password = Globals.dataCitePasswd;
 		ClientConfig cc = new DefaultClientConfig();
 		cc.getClasses().add(MultiPartWriter.class);
 		cc.getClasses().add(FormDataMultiPart.class);
@@ -103,14 +106,18 @@ public void setTestMode(boolean t) {
 	 */
 	public String mintDoiAtDatacite(String doi, String objectUrl) {
 		try {
+			play.Logger.debug("mintDoiAtDatacite is called");
+			play.Logger.debug("objectUrl=" + objectUrl);
 			status = 200;
-			String url = testMode ? "https://mds.datacite.org/doi?testMode=true"
-					: "https://mds.datacite.org/doi";
+			String url =
+					testMode ? dataciteURL + "/doi?testMode=true" : dataciteURL + "/doi";
 			WebResource resource = webclient.resource(url);
+			play.Logger.debug("resource=" + resource.toString());
 			String postBody = "doi=" + doi + "\nurl=" + objectUrl + "\n";
-			play.Logger.info("PostBody:\n" + postBody);
+			play.Logger.debug("PostBody=" + postBody);
 			String response =
 					resource.type("application/xml").post(String.class, postBody);
+			play.Logger.debug("response" + response);
 			return response;
 		} catch (UniformInterfaceException e) {
 			setStatus(e.getResponse().getStatus());
@@ -125,9 +132,13 @@ public String mintDoiAtDatacite(String doi, String objectUrl) {
 	 */
 	public String registerMetadataAtDatacite(Node node, String xml) {
 		try {
+			play.Logger.debug("registerMetadataAtDatacite is called");
+			play.Logger.debug("dataciteURL=" + dataciteURL);
 			status = 200;
-			String url = testMode ? "https://mds.datacite.org/metadata?testMode=true"
-					: "https://mds.datacite.org/metadata";
+			String url = testMode ? dataciteURL + "/metadata?testMode=true"
+					: dataciteURL + "/metadata";
+
+			play.Logger.debug("url=" + url);
 			WebResource resource = webclient.resource(url);
 			String response = resource.type("application/xml;charset=UTF-8")
 					.post(String.class, xml);

app/helper/KTBLMapperHelper.java

@@ -12,6 +12,7 @@
 import play.mvc.Http.MultipartFormData.FilePart;
 import org.json.JSONException;
 import java.io.IOException;
+import models.Globals;
 
 /**
  * 
@@ -64,22 +65,37 @@ static public String getStringContentFromJsonFile(FilePart fp) {
 	 * @param allKtblMetadata
 	 * @return required KTBL metadata, which must be persisted
 	 */
-	static public String getToPersistKtblMetadata(String contentJsFile) {
+	static public String getToPersistKtblMetadata(String contentJsFile,
+			String pid) {
 
 		JSONObject wantedKtblMetadata = null;
 		JSONObject allKtblMetadata = null;
+
 		try {
+			String resource_id =
+					new String(Globals.protocol + Globals.server + "/resource/" + pid);
+
 			allKtblMetadata = new JSONObject(contentJsFile);
 			wantedKtblMetadata = new JSONObject();
+			play.Logger.debug("resource_id= " + resource_id);
+			if (resource_id != null) {
+				wantedKtblMetadata.put("id", resource_id);
+			}
 
-			wantedKtblMetadata.put("recordingPeriod",
-					allKtblMetadata.getJSONArray("recordingPeriod"));
-			wantedKtblMetadata.put("relatedDatasets",
-					allKtblMetadata.getJSONArray("relatedDatasets"));
-			wantedKtblMetadata.put("info", allKtblMetadata.get("info"));
+			if (allKtblMetadata.has("recordingPeriod")) {
+				wantedKtblMetadata.put("recordingPeriod",
+						allKtblMetadata.getJSONArray("recordingPeriod"));
+			}
+			if (allKtblMetadata.has("relatedDatasets")) {
+				wantedKtblMetadata.put("relatedDatasets",
+						allKtblMetadata.getJSONArray("relatedDatasets"));
+			}
+			if (allKtblMetadata.has("info")) {
+				wantedKtblMetadata.put("info", allKtblMetadata.get("info"));
+			}
 
-		} catch (JSONException e) {
-			play.Logger.debug("JSONException:getToPersistKtblMetadata()");
+		} catch (Exception e) {
+			play.Logger.debug("Unable to create JSONObject");
 		}
 
 		return wantedKtblMetadata.toString();