Implement DataCite API support

IQSS · Feb 4, 2016 · 22a5e93 · 22a5e93
1 parent bebf135
commit 22a5e93
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Showing 8 changed files with 91 additions and 15 deletions.
diff --git a/pom.xml b/pom.xml
@@ -318,6 +318,21 @@
             <version>0.7.5.201505241946</version>
         </dependency>
         <!-- Added for DataCite -->
+        <dependency>
+            <groupId>org.slf4j</groupId>
+            <artifactId>slf4j-log4j12</artifactId>
+            <version>1.6.1</version>
+        </dependency>
+        <dependency>
+            <groupId>axis</groupId>
+            <artifactId>axis</artifactId>
+            <version>1.4</version>
+        </dependency>
+        <dependency>
+            <groupId>io.searchbox</groupId>
+            <artifactId>jest</artifactId>
+            <version>0.1.7</version>
+        </dependency>
         <dependency>
             <groupId>org.apache.httpcomponents</groupId>
             <artifactId>httpclient</artifactId>
@@ -328,6 +343,31 @@
             <artifactId>httpcore</artifactId>
             <version>4.4.1</version>
         </dependency>
+        <dependency>
+            <groupId>commons-codec</groupId>
+            <artifactId>commons-codec</artifactId>
+            <version>1.9</version>
+        </dependency>
+        <dependency>
+            <groupId>com.maxmind.geoip2</groupId>
+            <artifactId>geoip2</artifactId>
+            <version>2.3.1</version>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.commons</groupId>
+            <artifactId>commons-csv</artifactId>
+            <version>1.2</version>
+        </dependency>
+        <dependency>
+            <groupId>net.sf.ehcache</groupId>
+            <artifactId>ehcache</artifactId>
+            <version>2.10.1</version>
+        </dependency>
+        <dependency>
+            <groupId>log4j</groupId>
+            <artifactId>log4j</artifactId>
+            <version>1.2.17</version>
+        </dependency>
 
     </dependencies>
 

diff --git a/src/main/java/edu/harvard/iq/dataverse/DOIDataCiteRegisterService.java b/src/main/java/edu/harvard/iq/dataverse/DOIDataCiteRegisterService.java
@@ -66,6 +66,7 @@ public String createIdentifier(String identifier, HashMap<String, String> metada
                     metadata.get("datacite.title"), metadata.get("datacite.publisher"),
                     metadata.get("datacite.publicationyear")});
         String xmlMetadata = metadataTemplate.generateXML();
+         logger.log(Level.INFO, "xmlMetadata 70 " + xmlMetadata.toString() );
         String status = metadata.get("_status").trim();
         String target = metadata.get("_target");
         String retString = "";
@@ -206,6 +207,7 @@ public DataCiteMetadataTemplate(String xmlMetaData){
     }
 
     public String generateXML() {
+        System.out.print("in generate xml...");
         xmlMetadata = template.replace("${identifier}", this.identifier.trim())
                 .replace("${title}", this.title)
                 .replace("${publisher}", this.publisher)

diff --git a/src/main/java/edu/harvard/iq/dataverse/DOIDataCiteServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/DOIDataCiteServiceBean.java
@@ -48,6 +48,7 @@ public String createIdentifier(Dataset dataset) {
         HashMap metadata = getMetadataFromStudyForCreateIndicator(dataset);
         metadata.put("_status", "reserved");
         try {
+            logger.log(Level.INFO, "doiDataCiteRegisterService.toString : " + doiDataCiteRegisterService.toString());
             retString = doiDataCiteRegisterService.createIdentifier(identifier, metadata);
             logger.log(Level.INFO, "create DOI identifier retString : " + retString);
         } catch (Exception e) {
@@ -140,7 +141,7 @@ public void deleteIdentifier(Dataset datasetIn) {
             return;
         }
         if (idStatus.equals("public")) {
-            //if public then it has been released set to unavaialble and reset target to n2t url
+            //if public then it has been released set to unavailable and reset target to n2t url
             updateIdentifierStatus(datasetIn, "unavailable");
         }
     }

diff --git a/src/main/java/edu/harvard/iq/dataverse/DataCiteRESTfullClient.java b/src/main/java/edu/harvard/iq/dataverse/DataCiteRESTfullClient.java
@@ -5,7 +5,9 @@
  */
 package edu.harvard.iq.dataverse;
 
+
 import java.io.IOException;
+
 import java.io.UnsupportedEncodingException;
 
 import java.util.logging.Level;
@@ -43,7 +45,7 @@ public class DataCiteRESTfullClient {
     private CloseableHttpClient httpClient;
     private HttpClientContext context;
     private String encoding = "utf-8";
-
+    
     public DataCiteRESTfullClient(String url, String username, String password) {
         this.url = url;
         try {
@@ -149,10 +151,14 @@ public String postMetadata(String metadata) throws UnsupportedEncodingException
         HttpPost httpPost = new HttpPost(this.url + "/metadata");
         httpPost.setHeader("Content-Type", "application/xml;charset=UTF-8");
         httpPost.setEntity(new StringEntity(metadata, "utf-8"));
-
+        System.out.print("in post metadata entity: " + httpPost.getEntity().toString());
+            System.out.print("In PostMetadata httpClient " + httpClient.toString());
+            System.out.print("In PostMetadata credentials " + context.getCredentialsProvider().getCredentials(AuthScope.ANY));
         try {
             HttpResponse response = httpClient.execute(httpPost,context);
+
             String data = EntityUtils.toString(response.getEntity(), encoding);
+            System.out.print("response " + data);
             if (response.getStatusLine().getStatusCode() != 201) {
                 String errMsg = "Response code: " + response.getStatusLine().getStatusCode() + ", " + data;
                 logger.log(Level.SEVERE, errMsg);
@@ -190,7 +196,7 @@ public String inactiveDataset(String doi) {
 
     public static void main(String[] args) throws Exception {
         String doi = "10.5072/DVN/274533";
-        DataCiteRESTfullClient client = new DataCiteRESTfullClient("https://mds.test.datacite.org", "TIB.PUB", "62751062");
+        DataCiteRESTfullClient client = new DataCiteRESTfullClient("https://mds.test.datacite.org", "DATACITE.HARVARD", "DVNapitest");
 //		System.out.println(client.getUrl(doi));
 //		System.out.println(client.getMetadata(doi));
 //        System.out.println(client.postMetadata(readAndClose("C:/Users/luopc/Desktop/datacite.xml", "utf-8")));

diff --git a/src/main/java/edu/harvard/iq/dataverse/DatasetPage.java b/src/main/java/edu/harvard/iq/dataverse/DatasetPage.java
@@ -1455,7 +1455,7 @@ public String saveGuestbookResponse(String type) {
                 } else {
                     for (FileMetadata fmd : this.selectedFiles) {
                         DataFile df = fmd.getDataFile();
-                        if (df != null) {
+                        if (df != null  && canDownloadFile(fmd)) {
                             this.guestbookResponse.setDataFile(df);
                             cmd = new CreateGuestbookResponseCommand(dvRequestService.getDataverseRequest(), this.guestbookResponse, dataset);
                             commandEngine.submit(cmd);
@@ -2089,8 +2089,19 @@ public String getSelectedFilesIdsString() {
             }
             downloadIdString += fmd.getDataFile().getId();
         }
-        return downloadIdString;
-
+        return downloadIdString;     
+    }
+
+        // helper Method
+    public String getSelectedFilesIdsStringForDownload() {        
+        String downloadIdString = "";
+        for (FileMetadata fmd : this.selectedFiles){
+            if (!StringUtil.isEmpty(downloadIdString)) {
+                downloadIdString += ",";
+            }
+            downloadIdString += fmd.getDataFile().getId();
+        }
+        return downloadIdString;     
     }
 
     public void updateFileCounts(){

diff --git a/...n/java/edu/harvard/iq/dataverse/engine/command/impl/DeaccessionDatasetVersionCommand.java b/...n/java/edu/harvard/iq/dataverse/engine/command/impl/DeaccessionDatasetVersionCommand.java
@@ -41,14 +41,18 @@ public DatasetVersion execute(CommandContext ctxt) throws CommandException {
 
         theVersion.setVersionState(DatasetVersion.VersionState.DEACCESSIONED);
 
-        if (deleteDOIIdentifier){
-                    String nonNullDefaultIfKeyNotFound = "";
+        if (deleteDOIIdentifier) {
+            String nonNullDefaultIfKeyNotFound = "";
 
-        String    doiProvider = ctxt.settings().getValueForKey(SettingsServiceBean.Key.DoiProvider, nonNullDefaultIfKeyNotFound);
-
-           if (doiProvider.equals("EZID")) ctxt.doiEZId().deleteIdentifier(ds);
-           if (doiProvider.equals("DataCite")) ctxt.doiDataCite().deleteIdentifier(ds);
-        }       
+            String doiProvider = ctxt.settings().getValueForKey(SettingsServiceBean.Key.DoiProvider, nonNullDefaultIfKeyNotFound);
+
+            if (doiProvider.equals("EZID")) {
+                ctxt.doiEZId().deleteIdentifier(ds);
+            }
+            if (doiProvider.equals("DataCite")) {
+                ctxt.doiDataCite().deleteIdentifier(ds);
+            }
+        }      
         DatasetVersion managed = ctxt.em().merge(theVersion);
 
         boolean doNormalSolrDocCleanUp = true;

diff --git a/src/main/java/edu/harvard/iq/dataverse/settings/SettingsServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/settings/SettingsServiceBean.java
@@ -2,7 +2,7 @@
 
 import edu.harvard.iq.dataverse.actionlogging.ActionLogRecord;
 import edu.harvard.iq.dataverse.actionlogging.ActionLogServiceBean;
-import edu.harvard.iq.dataverse.api.ApiBlockingFilter;
+//import edu.harvard.iq.dataverse.api.ApiBlockingFilter;
 import java.util.Arrays;
 import java.util.Collections;
 import java.util.HashSet;

diff --git a/src/main/resources/edu/harvard/iq/dataverse/datacite_metadata_template.xml b/src/main/resources/edu/harvard/iq/dataverse/datacite_metadata_template.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<resource xsi:schemaLocation="http://datacite.org/schema/kernel-3 http://schema.datacite.org/meta/kernel-3/metadata.xsd"
+          xmlns="http://datacite.org/schema/kernel-3"
+          xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+    <identifier identifierType="DOI">${identifier}</identifier>
+    <creators>${creators}</creators>
+    <titles>
+        <title>${title}</title>
+    </titles>
+    <publisher>${publisher}</publisher>
+    <publicationYear>${publisherYear}</publicationYear>
+</resource>