Merge branch 'develop' into 5253-metrics-block-ui #5253

.travis.yml

@@ -1,5 +1,5 @@
 language: java
 jdk:
-  - oraclejdk8
+  - openjdk8
 script: mvn -DcompilerArgument=-Xlint:unchecked test -P all-unit-tests
 after_success: mvn jacoco:report coveralls:report 

doc/release-notes/5687-invalid-notifications.md

@@ -0,0 +1,6 @@
+The following needs to be added to the release notes and/or upgrade instructions: 
+
+In making this fix we discovered that notifications created prior to 2018 may have been invalidated.  With this release we advise that these older notifications are deleted from the database. The following query can be used for this purpose:
+
+delete from usernotification where date_part('year', senddate) < 2018;
+

doc/release-notes/5766-citation-tsv

@@ -0,0 +1,4 @@
+Update citation metadata block
+curl http://localhost:8080/api/admin/datasetfield/load -X POST --data-binary @citation.tsv -H "Content-type: text/tab-separated-values"
+
+Run ReExportall to update the citation metadata block to remove an errant tab: http://guides.dataverse.org/en/4.16/admin/metadataexport.html?highlight=export#batch-exports-through-the-api

doc/release-notes/5967-custom-analytics-fix.md

@@ -0,0 +1 @@
+Update your custom analytics code to include CDATA sections, inside the `script` tags, around the javascript code. We have updated the documentation and sample analytics code snippet provided in [Installation Guide > Configuration > Web Analytics Code](http://guides.dataverse.org/en/latest/installation/config.html#web-analytics-code) to fix a bug that broke the rendering of the 403 and 500 custom error pgs (#5967).

doc/sphinx-guides/source/_static/installation/files/var/www/dataverse/branding/analytics-code.html

@@ -1,11 +1,11 @@
 <!-- Global site tag (gtag.js) - Google Analytics -->
 <script async="async" src="https://www.googletagmanager.com/gtag/js?id=YOUR ACCOUNT CODE"></script>
 <script>
+  //<![CDATA[
   window.dataLayer = window.dataLayer || [];
   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date()); gtag('config', 'YOUR ACCOUNT CODE');
-</script>
-<script>
+
   window.addEventListener("load", enableAnalyticsEventCapture, false);
 
   function enableAnalyticsEventCapture() {
@@ -145,4 +145,5 @@
     label = label.substring(label.indexOf('/dataverse/') + 11, index).split(/[?#]/)[0];
     return(label);
   }
+  //]]>
 </script>

doc/sphinx-guides/source/developers/documentation.rst

@@ -8,20 +8,41 @@ Documentation
 Quick Fix
 -----------
 
-If you find a typo or a small error in the documentation you can easily fix it using GitHub.
+If you find a typo or a small error in the documentation you can fix it using GitHub's online web editor. Generally speaking, we will be following https://help.github.com/en/articles/editing-files-in-another-users-repository
 
-- Fork the repository
-- Go to [your GitHub username]/dataverse/doc/sphinx-guides/source and access the file you would like to fix
-- Switch to the branch that is currently under development
-- Click the Edit button in the upper-right corner and fix the error
-- Submit a pull request
+- Navigate to https://github.com/IQSS/dataverse/tree/develop/doc/sphinx-guides/source where you will see folders for each of the guides:
+
+  - `admin`_
+  - `api`_
+  - `developers`_
+  - `installation`_
+  - `user`_
+
+- Find the file you want to edit under one of the folders above.
+- Click the pencil icon in the upper-right corner. If this is your first contribution to Dataverse, the hover text over the pencil icon will say "Fork this project and edit this file".
+- Make changes to the file and preview them.
+- In the **Commit changes** box, enter a description of the changes you have made and click **Propose file change**.
+- Under the **Write** tab, delete the long welcome message and write a few words about what you fixed.
+- Click **Create Pull Request**.
+
+That's it! Thank you for your contribution! Your pull request will be added manually to the main Dataverse project board at https://github.com/orgs/IQSS/projects/2 and will go through code review and QA before it is merged into the "develop" branch. Along the way, developers might suggest changes or make them on your behalf. Once your pull request has been merged you will be listed as a contributor at https://github.com/IQSS/dataverse/graphs/contributors
+
+Please see https://github.com/IQSS/dataverse/pull/5857 for an example of a quick fix that was merged (the "Files changed" tab shows how a typo was fixed).
+
+If you would like to read more about the Dataverse project's use of GitHub, please see the :doc:`version-control` section. For bug fixes and features we request that you create an issue before making a pull request but this is not at all necessary for quick fixes to the documentation.
+
+.. _admin: https://github.com/IQSS/dataverse/tree/develop/doc/sphinx-guides/source/admin
+.. _api: https://github.com/IQSS/dataverse/tree/develop/doc/sphinx-guides/source/api
+.. _developers: https://github.com/IQSS/dataverse/tree/develop/doc/sphinx-guides/source/developers
+.. _installation: https://github.com/IQSS/dataverse/tree/develop/doc/sphinx-guides/source/installation
+.. _user: https://github.com/IQSS/dataverse/tree/develop/doc/sphinx-guides/source/user
 
 Other Changes (Sphinx)
 ----------------------
 
 The documentation for Dataverse was written using Sphinx (http://sphinx-doc.org/). 
 If you are interested in suggesting changes or updates we recommend that you create 
-the html files using Sphinx locally and the submit a pull request through GitHub. Here are the instructions on how to proceed:
+the html files using Sphinx locally and then submit a pull request through GitHub. Here are the instructions on how to proceed:
 
 
 Installing Sphinx
@@ -50,7 +71,11 @@ Using Sphinx
 
 First, you will need to make a fork of the dataverse repository in GitHub. Then, you will need to make a clone of your fork so you can manipulate the files outside GitHub.
 
-To edit the existing documentation go to ~/dataverse/doc/sphinx-guides/source directory inside your clone. There, you will find the .rst files that correspond to the guides in the dataverse page (http://guides.dataverse.org/en/latest/user/index.html). Now, using your preferred text editor, open and edit these files, or create new .rst files and edit the others accordingly. 
+To edit the existing documentation:
+
+- Create a branch (refer to http://guides.dataverse.org/en/latest/developers/version-control.html > *Create a New Branch off the develop Branch*) to record the changes you are about to perform.
+- Go to ~/dataverse/doc/sphinx-guides/source directory inside your clone. There, you will find the .rst files that correspond to the guides in the dataverse page (http://guides.dataverse.org/en/latest/).
+- Using your preferred text editor, open and edit the necessary files, or create new ones.
 
 Once you are done, open a terminal and change directories to ~/dataverse/doc/sphinx-guides . Then, run the following commands:
 
@@ -61,7 +86,7 @@ Once you are done, open a terminal and change directories to ~/dataverse/doc/sph
 After sphinx is done processing the files you should notice that the html folder in ~/dataverse/doc/sphinx-guides/build directory has been updated.
 You can click on the files in the html folder to preview the changes.
 
-Now you can make a commit with the changes to your own fork in GitHub and submit a pull request to the dataverse repository.
+Now you can make a commit with the changes to your own fork in GitHub and submit a pull request to the original (upstream) dataverse repository.
 
 Table of Contents
 -----------------

doc/sphinx-guides/source/installation/config.rst

@@ -634,11 +634,13 @@ Create your own ``analytics-code.html`` file using the analytics code snippet pr
     <!-- Global Site Tag (gtag.js) - Google Analytics -->
     <script async="async" src="https://www.googletagmanager.com/gtag/js?id=YOUR-ACCOUNT-CODE"></script>
     <script>
+        //<![CDATA[
 	window.dataLayer = window.dataLayer || [];
 	function gtag(){dataLayer.push(arguments);}
 	gtag('js', new Date());
 
 	gtag('config', 'YOUR-ACCOUNT-CODE');
+        //]]>
     </script>
 
 **IMPORTANT:** Note the "async" attribute in the first script line above. In the documentation provided by Google, its value is left blank (as in ``<script async src="...">``). It must be set as in the example above (``<script async="async" src="...">``), otherwise it may cause problems with some browsers.

scripts/api/data/metadatablocks/citation.tsv

@@ -32,7 +32,7 @@
 	publication	Related Publication	Publications that use the data from this Dataset.		none	28		FALSE	FALSE	TRUE	FALSE	TRUE	FALSE		citation	http://purl.org/dc/terms/isReferencedBy
 	publicationCitation	Citation	The full bibliographic citation for this related publication.		textbox	29	#VALUE	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	publication	citation	http://purl.org/dc/terms/bibliographicCitation
 	publicationIDType	ID Type	The type of digital identifier used for this publication (e.g., Digital Object Identifier (DOI)).		text	30	#VALUE: 	TRUE	TRUE	FALSE	FALSE	TRUE	FALSE	publication	citation	http://purl.org/spar/datacite/ResourceIdentifierScheme
-	publicationIDNumber	ID Number	The identifier for the selected ID type.		text	31	#VALUE	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	publication	citation		http://purl.org/spar/datacite/ResourceIdentifier
+	publicationIDNumber	ID Number	The identifier for the selected ID type.		text	31	#VALUE	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	publication	citation	http://purl.org/spar/datacite/ResourceIdentifier
 	publicationURL	URL	Link to the publication web page (e.g., journal article page, archive record page, or other).	Enter full URL, starting with http://	url	32	<a href="#VALUE" target="_blank">#VALUE</a>	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	publication	citation	https://schema.org/distribution
 	notesText	Notes	Additional important information about the Dataset.		textbox	33		FALSE	FALSE	FALSE	FALSE	TRUE	FALSE		citation
 	language	Language	Language of the Dataset		text	34		TRUE	TRUE	TRUE	TRUE	FALSE	FALSE		citation	http://purl.org/dc/terms/language
@@ -95,7 +95,7 @@
 	subject	Social Sciences	D11	12											
 	subject	Other	D12	13											
 	publicationIDType	ark		0											
-	publicationIDType	arXiv		1	arxiv										
+	publicationIDType	arXiv		1											
 	publicationIDType	bibcode		2											
 	publicationIDType	doi		3											
 	publicationIDType	ean13		4											

src/main/java/edu/harvard/iq/dataverse/DataCiteRESTfullClient.java

@@ -223,7 +223,7 @@ 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", "DATACITE.HARVARD", "DVNapitest");
+        DataCiteRESTfullClient client = new DataCiteRESTfullClient("https://mds.test.datacite.org", "DATACITE_TEST_USERNAME", "DATACITE_TEST_PASSWORD");
 //		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")));

src/main/java/edu/harvard/iq/dataverse/DatasetPage.java

@@ -124,6 +124,7 @@
 import edu.harvard.iq.dataverse.search.SearchFields;
 import edu.harvard.iq.dataverse.search.SearchServiceBean;
 import edu.harvard.iq.dataverse.search.SearchUtil;
+import edu.harvard.iq.dataverse.search.SolrClientService;
 import java.util.Comparator;
 import java.util.TimeZone;
 import javax.servlet.http.HttpServletRequest;
@@ -212,6 +213,8 @@ public enum DisplayMode {
     PrivateUrlServiceBean privateUrlService;
     @EJB
     ExternalToolServiceBean externalToolService;
+    @EJB
+    SolrClientService solrClientService;
     @Inject
     DataverseRequestServiceBean dvRequestService;
     @Inject
@@ -725,7 +728,7 @@ public boolean isThisVersionSearchable() {
         QueryResponse queryResponse = null;
 
         try {
-            queryResponse = getSolrServer().query(solrQuery);
+            queryResponse = solrClientService.getSolrClient().query(solrQuery);
         } catch (Exception ex) {
             logger.fine("Solr exception: " + ex.getLocalizedMessage());
             // solr maybe down/some error may have occurred... 
@@ -840,7 +843,7 @@ public Set<Long> getFileIdsInVersionFromSolr(Long datasetVersionId, String patte
         Set<Long> resultIds = new HashSet<>();
 
         try {
-            queryResponse = getSolrServer().query(solrQuery);
+            queryResponse = solrClientService.getSolrClient().query(solrQuery);
         } catch (HttpSolrClient.RemoteSolrException ex) {
             logger.fine("Remote Solr Exception: " + ex.getLocalizedMessage());
             String msg = ex.getLocalizedMessage(); 
@@ -858,7 +861,7 @@ public Set<Long> getFileIdsInVersionFromSolr(Long datasetVersionId, String patte
             logger.fine("Solr query (trying again): " + solrQuery);
 
             try {
-                queryResponse = getSolrServer().query(solrQuery);
+                queryResponse = solrClientService.getSolrClient().query(solrQuery);
             } catch (Exception ex) {
                 logger.warning("Caught a Solr exception (again!): " + ex.getLocalizedMessage());
                 return resultIds;
@@ -4828,6 +4831,25 @@ public void setPrivateUrlJustCreatedToFalse() {
         privateUrlWasJustCreated = false;
     }
 
+    public boolean isShowLinkingPopup() {
+        return showLinkingPopup;
+    }
+
+    public void setShowLinkingPopup(boolean showLinkingPopup) {
+        this.showLinkingPopup = showLinkingPopup;
+    }    
+
+    private boolean showLinkingPopup = false;
+
+    //
+
+    /*
+        public void setSelectedGroup(ExplicitGroup selectedGroup) {
+        setShowDeletePopup(true);
+        this.selectedGroup = selectedGroup;
+    }
+    */
+
     public void createPrivateUrl() {
         try {
             PrivateUrl createdPrivateUrl = commandEngine.submit(new CreatePrivateUrlCommand(dvRequestService.getDataverseRequest(), dataset));
@@ -5131,13 +5153,7 @@ public void archiveVersion(Long id) {
             }
         }
     }
-
-    private SolrClient solrServer = null;
-
-    private SolrClient getSolrServer () {
-        return searchService.getSolrServer();       
-    }
-
+
     private static Date getFileDateToCompare(FileMetadata fileMetadata) {
         DataFile datafile = fileMetadata.getDataFile();