Merge pull request #6129 from IQSS/develop

v4.16

.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/4.16-release-notes.md

@@ -0,0 +1,100 @@
+# Dataverse 4.16
+
+This release brings new features, enhancements, and bug fixes to Dataverse. Thank you to all of the community members who contributed code, suggestions, bug reports, and other assistance across the project.
+
+## Release Highlights
+
+### Metrics Redesign
+
+The metrics view at both the Dataset and File level has been redesigned. The main driver of this redesign has been the expanded metrics (citations and views) provided through an integration with Make Data Count, but installations that do not adopt Make Data Count will also be able to take advantage of the new metrics panel.
+
+### HTML Codebook Export
+
+Users will now be able to download HTML Codebooks as an additional Dataset Export type. This codebook is a more human-readable version of the DDI Codebook 2.5 metadata export and provides valuable information about the contents and structure of a dataset and will increase reusability of the datasets in Dataverse.
+
+### Harvesting Improvements
+
+The Harvesting code will now better handle problematic records during incremental harvests. Fixing this will mean not only fewer manual interventions by installation administrators to keep harvesting running, but it will also mean users can more easily find and access data that is important to their research.
+
+## Major Use Cases
+
+Newly-supported use cases in this release include:
+
+- As a user, I can view the works that have cited a dataset.
+- As a user, I can view the downloads and views for a dataset, based on the Make Data Count standard.
+- As a user, I can export an HTML codebook for a dataset.
+- As a user, I can expect harvested datasets to be made available more regularly.
+- As a user, I'll encounter fewer locks as I go through the publishing process.
+- As an installation administrator, I no longer need to destroy a PID in another system after destroying a dataset in Dataverse.
+
+## Notes for Dataverse Installation Administrators
+
+### Run ReExportall
+
+We made changes to the citation block in this release that will require installations to run ReExportall as part of the upgrade process. We've included this in the detailed instructions below.
+
+### Custom Analytics Code Changes
+
+You should 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).
+
+### Destroy Updates
+
+Destroying Datasets in Dataverse will now unregister/delete the PID with the PID provider. This eliminates the need for an extra step to "clean up" a PID registration after destroying a Dataset.
+
+### Deleting Notifications
+
+In making the fix for #5687 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;`
+
+### Lock Improvements
+
+In 4.15 a new lock was added to prevent parallel edits. After seeing that the lock was not being released as expected, which required administrator intervention, we've adjusted this code to release the lock as expected.
+
+### New Database Settings
+
+:AllowCors - Allows Cross-Origin Resource sharing(CORS). By default this setting is absent and Dataverse assumes it to be true.
+
+## Notes for Tool Developers and Integrators
+
+### OpenAIRE Export Changes
+
+The OpenAIRE metadata export now correctly expresses information about a dataset's Production Place and GeoSpatial Bounding Box. When users add metadata to Dataverse's Production Place and GeoSpatial Bounding Box fields, those fields are now mapped to separate DataCite geoLocation properties.
+
+Metadata about the software name and version used to create a dataset, Software Name and Software Version, are re-mapped from DataCite's more general descriptionType="Methods" property to descriptionType="TechnicalInfo", which was added in a recent version of the DataCite schema in order to improve discoverability of metadata about the software used to create datasets.
+
+## Complete List of Changes
+
+For the complete list of code changes in this release, see the <a href="https://github.com/IQSS/dataverse/milestone/83?closed=1">4.16 milestone</a> in Github.
+
+For help with upgrading, installing, or general questions please post to the <a href="https://groups.google.com/forum/#!forum/dataverse-community">Dataverse Google Group</a> or email [email protected].
+
+## Installation
+
+If this is a new installation, please see our <a href=http://guides.dataverse.org/en/4.16/installation/>Installation Guide</a>.
+
+## Upgrade
+
+1. Undeploy the previous version.
+
+- &lt;glassfish install path&gt;/glassfish4/bin/asadmin list-applications
+- &lt;glassfish install path&gt;/glassfish4/bin/asadmin undeploy dataverse
+
+2. Stop glassfish and remove the generated directory, start
+
+- service glassfish stop
+- remove the generated directory: rm -rf &lt;glassfish install path&gt;glassfish4/glassfish/domains/domain1/generated
+- service glassfish start
+
+3. Deploy this version.
+
+- &lt;glassfish install path&gt;/glassfish4/bin/asadmin deploy &lt;path&gt;dataverse-4.16.war
+
+4. Restart glassfish  
+5. 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"`  
+
+6. Run ReExportall to update the citations  
+
+   <http://guides.dataverse.org/en/4.16/admin/metadataexport.html?highlight=export#batch-exports-through-the-api>

doc/sphinx-guides/source/_static/api/define-metadatablocks.json

@@ -0,0 +1,8 @@
+[
+  "citation",
+  "geospatial",
+  "socialscience",
+  "astrophysics",
+  "biomedical",
+  "journal"
+]

doc/sphinx-guides/source/_static/docsdataverse_org.css

@@ -114,4 +114,8 @@ div.form-group .glyphicon.glyphicon-asterisk {font-size: .5em; vertical-align: t
 
 /* #sidebar.bs-sidenav.affix {
 	position: static;
-} REMOVED STATIC ToC */
+} REMOVED STATIC ToC */
+
+pre {
+    white-space: pre-wrap;
+}

doc/sphinx-guides/source/_static/installation/files/etc/maintenance/maintenance.xhtml

@@ -13,19 +13,14 @@
 
         <link type="image/png" rel="image_src" href="https://cdn.rawgit.com/IQSS/dataverse/87cf58b5c3e8e01cf0f4891465df02334852eed3/src/main/webapp/resources/images/dataverseproject.png.xhtml" />
 
-        <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.2/css/bootstrap.min.css" />
+        <link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/3.4.1/css/bootstrap.min.css" />
 
-        <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.2/css/bootstrap-theme.min.css" />
-
-        <link rel="stylesheet" href="https://cdn.rawgit.com/IQSS/dataverse/87cf58b5c3e8e01cf0f4891465df02334852eed3/src/main/webapp/resources/css/fontcustom.css" />
-
-        <link rel="stylesheet" href="https://cdn.rawgit.com/IQSS/dataverse/87cf58b5c3e8e01cf0f4891465df02334852eed3/src/main/webapp/resources/css/socicon.css" />
+        <link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/3.4.1/css/bootstrap-theme.min.css" />
 
         <link rel="stylesheet" href="https://cdn.rawgit.com/IQSS/dataverse/87cf58b5c3e8e01cf0f4891465df02334852eed3/src/main/webapp/resources/css/structure.css" />
 
-        <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.2/js/bootstrap.min.js"></script>
-
         <style type="text/css">
+            /* FontCustom CSS */
             @font-face {
               font-family: "fontcustom";
               src: url("https://cdn.rawgit.com/IQSS/dataverse/87cf58b5c3e8e01cf0f4891465df02334852eed3/src/main/webapp/resources/fontcustom/fontcustom_0cdeefae934823416d24b6c2132ac702.eot");
@@ -37,25 +32,32 @@
               font-style: normal;
             }
 
-            @font-face {
-                font-family: 'socicon';
-                src: url('https://cdn.rawgit.com/IQSS/dataverse/87cf58b5c3e8e01cf0f4891465df02334852eed3/src/main/webapp/resources/socicon-font/socicon-webfont.eot');
-                src: url('https://cdn.rawgit.com/IQSS/dataverse/87cf58b5c3e8e01cf0f4891465df02334852eed3/src/main/webapp/resources/socicon-font/socicon-webfont.eot?#iefix') format('embedded-opentype'),
-                     url('https://cdn.rawgit.com/IQSS/dataverse/87cf58b5c3e8e01cf0f4891465df02334852eed3/src/main/webapp/resources/socicon-font/socicon-webfont.woff') format('woff'),
-                     url('https://cdn.rawgit.com/IQSS/dataverse/87cf58b5c3e8e01cf0f4891465df02334852eed3/src/main/webapp/resources/socicon-font/socicon-webfont.woff2') format('woff2'),
-                     url('https://cdn.rawgit.com/IQSS/dataverse/87cf58b5c3e8e01cf0f4891465df02334852eed3/src/main/webapp/resources/socicon-font/socicon-webfont.ttf') format('truetype'),
-                     url('https://cdn.rawgit.com/IQSS/dataverse/87cf58b5c3e8e01cf0f4891465df02334852eed3/src/main/webapp/resources/socicon-font/socicon-webfont.svg#sociconregular') format('svg');
-                font-weight: normal;
-                font-style: normal;
-                text-transform: initial;
-            }
-
             @media screen and (-webkit-min-device-pixel-ratio:0) {
               @font-face {
                 font-family: "fontcustom";
                 src: url("https://cdn.rawgit.com/IQSS/dataverse/87cf58b5c3e8e01cf0f4891465df02334852eed3/src/main/webapp/resources/fontcustom/fontcustom_0cdeefae934823416d24b6c2132ac702.svg#fontcustom") format("svg");
               }
             }
+
+            [data-icon]:before { content: attr(data-icon); }
+
+            [data-icon]:before,
+            .icon-dataverse:before {
+              display: inline-block;
+              font-family: "fontcustom";
+              font-style: normal;
+              font-weight: normal;
+              font-variant: normal;
+              line-height: 1;
+              text-decoration: inherit;
+              text-rendering: optimizeLegibility;
+              text-transform: none;
+              -moz-osx-font-smoothing: grayscale;
+              -webkit-font-smoothing: antialiased;
+              font-smoothing: antialiased;
+            }
+
+            .icon-dataverse:before { content: "\f100"; }
         </style>
     </head>
     <body>
@@ -98,15 +100,17 @@
                 <p>If you have any comments, questions or concerns, please reach out to [email protected].</p>
             </div>
         </div>
-        <div class="container" id="footer">
-            <div class="row">
-                <div class="col-sm-8 small">
-                    <p>Copyright &#169; 2018</p>
-                </div>
-                <div class="col-sm-4 text-right">
-                    <div class="poweredbylogo">
-                        <span>Powered by</span> 
-                        <a href="http://dataverse.org/" title="The Dataverse Project" target="_blank"><img src="https://cdn.rawgit.com/IQSS/dataverse/87cf58b5c3e8e01cf0f4891465df02334852eed3/src/main/webapp/resources/images/dataverseproject_logo.jpg" alt="The Dataverse Project" /></a>
+        <div id="footer">
+            <div class="container">
+                <div class="row">
+                    <div class="col-sm-8 small">
+                        <p>Copyright &#169; 2019</p>
+                    </div>
+                    <div class="col-sm-4 text-right">
+                        <div class="poweredbylogo">
+                            <span>Powered by</span> 
+                            <a href="http://dataverse.org/" title="The Dataverse Project" target="_blank"><img src="https://cdn.rawgit.com/IQSS/dataverse/87cf58b5c3e8e01cf0f4891465df02334852eed3/src/main/webapp/resources/images/dataverseproject_logo.jpg" alt="The Dataverse Project" /></a>
+                        </div>
                     </div>
                 </div>
             </div>

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/_static/navbarscroll.js

@@ -7,7 +7,7 @@ $jqTheme(document).ready(function() {
     if (location.pathname.replace(/^\//,'') == this.pathname.replace(/^\//,'') 
 && location.hostname == this.hostname) {
       var target = $jqTheme(this.hash);
-      target = target.length ? target : $('a.headerlink[href="#' + this.hash.slice(1) +'""]');
+      target = target.length ? target : $jqTheme('a.headerlink[href="#' + this.hash.slice(1) +'""]');
       if (target.length) {
         $jqTheme('html,body').animate({
           scrollTop: target.offset().top - 60 //offsets for fixed header
@@ -18,7 +18,7 @@ $jqTheme(document).ready(function() {
   });
   //Executed on page load with URL containing an anchor tag.
   if($jqTheme(location.href.split("#")[1])) {
-      var target = $('#'+location.href.split("#")[1]);
+      var target = $jqTheme('#'+location.href.split("#")[1]);
       if (target.length) {
         $jqTheme('html,body').animate({
           scrollTop: target.offset().top - 60 //offset height of header here too.