Merge branch 'develop' into 6574-filenames #6574

conf/docker-aio/c7.dockerfile

@@ -1,6 +1,6 @@
 FROM centos:7
 # OS dependencies
-RUN yum install -y https://download.postgresql.org/pub/repos/yum/9.6/redhat/rhel-7-x86_64/pgdg-redhat-repo-latest.noarch.rpm
+RUN yum install -y https://download.postgresql.org/pub/repos/yum/reporpms/EL-7-x86_64/pgdg-redhat-repo-latest.noarch.rpm
 #RUN yum install -y java-1.8.0-openjdk-headless postgresql-server sudo epel-release unzip perl curl httpd
 RUN yum install -y java-1.8.0-openjdk-devel postgresql96-server sudo epel-release unzip perl curl httpd
 RUN yum install -y jq lsof awscli

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

@@ -191,7 +191,7 @@ Without this "burrito" key in place, REST Assured will not be able to create use
 Root Dataverse Permissions
 ^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-In your browser, log in as dataverseAdmin (password: admin) and click the "Edit" button for your root dataverse. Navigate to Permissions, then the Edit Access button. Under "Who can add to this dataverse?" choose "Anyone with a dataverse account can add sub dataverses" if it isn't set to this already.
+In your browser, log in as dataverseAdmin (password: admin) and click the "Edit" button for your root dataverse. Navigate to Permissions, then the Edit Access button. Under "Who can add to this dataverse?" choose "Anyone with a Dataverse account can add sub dataverses and datasets" if it isn't set to this already.
 
 Alternatively, this same step can be done with this script: ``scripts/search/tests/grant-authusers-add-on-root``
 

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

@@ -1459,6 +1459,14 @@ Note: The "About" link will not appear in the navbar until this option is set.
 
 ``curl -X PUT -d http://dataverse.example.edu http://localhost:8080/api/admin/settings/:NavbarAboutUrl``
 
+:NavbarGuidesUrl
+++++++++++++++++
+
+Set ``:NavbarGuidesUrl`` to a fully-qualified URL which will be used for the "User Guide" link in the navbar.
+
+Note: by default, the URL is composed from the settings ``:GuidesBaseUrl`` and ``:GuidesVersion`` below.
+
+``curl -X PUT -d http://example.edu/fancy-dataverse-guide http://localhost:8080/api/admin/settings/:NavbarGuidesUrl``
 
 :GuidesBaseUrl
 ++++++++++++++

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

@@ -101,16 +101,16 @@ Installing PostgreSQL
 
 Version 9.6 is strongly recommended because it is the version developers and QA test with::
 
-	# yum install -y https://download.postgresql.org/pub/repos/yum/9.6/redhat/rhel-7-x86_64/pgdg-centos96-9.6-3.noarch.rpm
+	# yum install -y https://download.postgresql.org/pub/repos/yum/reporpms/EL-7-x86_64/pgdg-redhat-repo-latest.noarch.rpm
 	# yum makecache fast
 	# yum install -y postgresql96-server
 	# /usr/pgsql-9.6/bin/postgresql96-setup initdb
 	# /usr/bin/systemctl start postgresql-9.6
 	# /usr/bin/systemctl enable postgresql-9.6
 
-Note that the steps above are specific to RHEL/CentOS 7. For RHEL/CentOS 6 use::
+Note that the steps above are specific to RHEL/CentOS 7. For RHEL/CentOS 8 use::
 
-	# yum install -y https://download.postgresql.org/pub/repos/yum/9.6/redhat/rhel-6-x86_64/pgdg-centos96-9.6-3.noarch.rpm
+	# yum install -y https://download.postgresql.org/pub/repos/yum/reporpms/EL-8-x86_64/pgdg-redhat-repo-latest.noarch.rpm
 	# yum makecache fast
 	# yum install -y postgresql96-server
 	# service postgresql-9.6 initdb

scripts/vagrant/setup.sh

@@ -23,7 +23,7 @@ java -version
 javac -version
 
 # switching to postgresql-9.6 per #4709
-yum install -y https://download.postgresql.org/pub/repos/yum/9.6/redhat/rhel-7-x86_64/pgdg-redhat-repo-latest.noarch.rpm
+yum install -y https://download.postgresql.org/pub/repos/yum/reporpms/EL-7-x86_64/pgdg-redhat-repo-latest.noarch.rpm
 yum makecache fast
 yum install -y postgresql96-server
 /usr/pgsql-9.6/bin/postgresql96-setup initdb

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

@@ -19,6 +19,7 @@
 import edu.harvard.iq.dataverse.util.FileUtil;
 import edu.harvard.iq.dataverse.util.ShapefileHandler;
 import edu.harvard.iq.dataverse.util.StringUtil;
+import edu.harvard.iq.dataverse.worldmapauth.WorldMapToken;
 import java.io.IOException;
 import java.util.List;
 import java.util.ArrayList;
@@ -214,6 +215,13 @@ public void setGuestbookResponses(List<GuestbookResponse> guestbookResponses) {
         this.guestbookResponses = guestbookResponses;
     }
 
+    // The WorldMap LayerMetadata and AuthToken are here to facilitate a
+    // clean cascade delete when the DataFile is deleted:
+    @OneToOne(mappedBy="dataFile", orphanRemoval = true, cascade={CascadeType.REMOVE, CascadeType.MERGE, CascadeType.PERSIST})
+    private MapLayerMetadata mapLayerMetadata;    
+    @OneToMany(mappedBy="dataFile", orphanRemoval = true, cascade={CascadeType.REMOVE, CascadeType.MERGE, CascadeType.PERSIST})
+    private List<WorldMapToken> worldMapTokens;
+
     private char ingestStatus = INGEST_STATUS_NONE; 
 
     @OneToOne(mappedBy = "thumbnailFile")

src/main/java/edu/harvard/iq/dataverse/engine/command/impl/DeleteDataFileCommand.java

@@ -24,6 +24,9 @@
 import java.util.logging.Level;
 import java.util.logging.Logger;
 import edu.harvard.iq.dataverse.GlobalIdServiceBean;
+import edu.harvard.iq.dataverse.UserNotification;
+import java.sql.Timestamp;
+import java.util.Date;
 
 /**
  * Deletes a data file, both DB entity and filesystem object.
@@ -210,6 +213,31 @@ public FileVisitResult postVisitDirectory(final Path dir, final IOException e)
         } catch (Exception e) {
             logger.log(Level.WARNING, "Identifier deletion was not successfull:", e.getMessage());
         }
+
+        // If there is a Map Layer associated with this file, we may need to 
+        // try and remove the layer data on the WorldMap side. 
+        if (ctxt.mapLayerMetadata().findMetadataByDatafile(doomed) != null) {
+            // (We need an AuthenticatedUser in order to produce a WorldMap token!)
+            String id = getUser().getIdentifier();
+            id = id.startsWith("@") ? id.substring(1) : id;
+            AuthenticatedUser authenticatedUser = ctxt.authentication().getAuthenticatedUser(id);
+            try {
+                ctxt.mapLayerMetadata().deleteMapLayerFromWorldMap(doomed, authenticatedUser);
+
+                // We have the dedicatd command DeleteMapLayerMetadataCommand, but 
+                // there's no need to use it explicitly, since the Dataverse-side
+                // MapLayerMetadata entity will be deleted by the database 
+                // cascade on the DataFile. -- L.A. Apr. 2020
+
+            } catch (Exception ex) {
+                // We are not going to treat it as a fatal condition and bail out, 
+                // but we will send a notification to the user, warning them 
+                // there may still be some data associated with the mapped layer, 
+                // on the WorldMap side, un-deleted:
+                ctxt.notifications().sendNotification(authenticatedUser, new Timestamp(new Date().getTime()), UserNotification.Type.MAPLAYERDELETEFAILED, doomed.getFileMetadata().getId());
+            }
+
+        }
         DataFile doomedAndMerged = ctxt.em().merge(doomed);
         ctxt.em().remove(doomedAndMerged);
         /**

src/main/webapp/addDataFormFragment.xhtml

@@ -0,0 +1,19 @@
+<ui:composition xmlns:h="http://java.sun.com/jsf/html"
+    xmlns:f="http://java.sun.com/jsf/core"
+    xmlns:ui="http://java.sun.com/jsf/facelets"
+    xmlns:c="http://java.sun.com/jsp/jstl/core"
+    xmlns:p="http://primefaces.org/ui"
+    xmlns:jsf="http://xmlns.jcp.org/jsf">
+    <!-- Add Data Form - not logged in... -->
+    <p:dialog id="addDataGuest" header="#{bundle['dataverse.results.dialog.addDataGuest.header']}" widgetVar="addData_popup" modal="true">
+        <p class="help-block">
+            <h:outputText value="#{dataverseHeaderFragment.signupAllowed ? bundle['dataverse.results.dialog.addDataGuest.msg.signup'] : bundle['dataverse.results.dialog.addDataGuest.msg']}" escape="false"></h:outputText>
+        </p>
+        <div class="button-block">
+            <ui:fragment rendered="#{dataverseHeaderFragment.signupAllowed}">
+                <a class="btn btn-default" href="#{dataverseHeaderFragment.getSignupUrl(navigationWrapper.redirectPage)}" title="#{bundle['dataverse.results.dialog.addDataGuest.signup.title']}">#{bundle['signup']}</a>
+            </ui:fragment>
+            <a class="btn btn-default" href="/loginpage.xhtml#{navigationWrapper.redirectPage}" title="#{bundle['dataverse.results.dialog.addDataGuest.login.title']}">#{bundle['login']}</a>
+        </div>
+    </p:dialog>
+</ui:composition>

src/main/webapp/dataverse_header.xhtml

@@ -10,6 +10,11 @@
                 xmlns:of="http://omnifaces.org/functions"
                 xmlns:iqbs="http://xmlns.jcp.org/jsf/composite/iqbs">
     <o:resourceInclude path="/CustomizationFilesServlet?customFileType=header" rendered="#{!widgetWrapper.widgetView}"/>
+    <o:importFunctions type="edu.harvard.iq.dataverse.authorization.groups.impl.builtin.AuthenticatedUsers" />
+    <ui:param name="showAddDataverseLink" value="#{permissionServiceBean.userOn(AuthenticatedUsers:get(),dataverseServiceBean.findRootDataverse()).canIssueCommand('CreateDataverseCommand') }"/>
+    <ui:param name="showAddDatasetLink" value="#{permissionServiceBean.userOn(AuthenticatedUsers:get(),dataverseServiceBean.findRootDataverse()).canIssueCommand('AbstractCreateDatasetCommand') }"/>
+    <ui:param name="showAddDataGroup" value="#{showAddDataverseLink or showAddDatasetLink}"/>
+
     <div id="dataverse-header-block">
         <!-- Navbar Panel -->
         <nav id="navbarFixed" class="navbar navbar-default navbar-fixed-top" jsf:rendered="#{!widgetWrapper.widgetView}">
@@ -31,15 +36,15 @@
                 </div>
                 <div class="collapse navbar-collapse" id="topNavBar">
                     <ul class="nav navbar-nav navbar-right">
-                        <li class="dropdown">
+                        <li class="dropdown" jsf:rendered="#{showAddDataGroup}">
                             <a href="#" class="dropdown-toggle" data-toggle="dropdown">#{bundle['dataverse.results.btn.addData']} <b class="caret"></b></a>
                             <ul class="dropdown-menu">
-                                <li>
+                                <li jsf:rendered="#{showAddDataverseLink}">
                                     <h:outputLink value="/dataverse.xhtml?ownerId=#{dataverseServiceBean.findRootDataverse().id}">
                                         <h:outputText value="#{bundle['dataverse.results.btn.addData.newDataverse']}"/>
                                     </h:outputLink>
                                 </li>
-                                <li>
+                                <li jsf:rendered="#{showAddDatasetLink}">
                                     <h:outputLink value="/dataset.xhtml?ownerId=#{dataverseServiceBean.findRootDataverse().id}">
                                         <h:outputText value="#{bundle['dataverse.results.btn.addData.newDataset']}"/>
                                     </h:outputLink>
@@ -69,7 +74,7 @@
                             </h:outputLink>
                         </li>
                         <li>
-                            <h:outputLink value="#{settingsWrapper.guidesBaseUrl}/#{systemConfig.guidesVersion}/user" target="_blank" rel="noopener">
+                            <h:outputLink value="#{settingsWrapper.get(':NavbarGuidesUrl', settingsWrapper.guidesBaseUrl.concat('/').concat(systemConfig.guidesVersion).concat('/user'))}" target="_blank" rel="noopener">
                                 <h:outputText value="#{bundle['header.guides.user']}"/>
                             </h:outputLink>
                         </li>

src/main/webapp/search-include-fragment.xhtml

@@ -657,15 +657,6 @@
                          actionListener="#{SearchIncludeFragment.setDisplayCardValues()}" />
     </h:form>
 
-    <p:dialog id="addDataGuest" header="#{bundle['dataverse.results.dialog.addDataGuest.header']}" widgetVar="addData_popup" modal="true">
-        <p class="help-block">
-            <h:outputText value="#{dataverseHeaderFragment.signupAllowed ? bundle['dataverse.results.dialog.addDataGuest.msg.signup'] : bundle['dataverse.results.dialog.addDataGuest.msg']}" escape="false"></h:outputText>
-        </p>
-        <div class="button-block">
-            <ui:fragment rendered="#{dataverseHeaderFragment.signupAllowed}">
-                <a class="btn btn-default" href="#{dataverseHeaderFragment.getSignupUrl(navigationWrapper.redirectPage)}" title="#{bundle['dataverse.results.dialog.addDataGuest.signup.title']}">#{bundle['signup']}</a>
-            </ui:fragment>
-            <a class="btn btn-default" href="/loginpage.xhtml#{navigationWrapper.redirectPage}" title="#{bundle['dataverse.results.dialog.addDataGuest.login.title']}">#{bundle['login']}</a>
-        </div>
-    </p:dialog>
+    <ui:include src="addDataFormFragment.xhtml"></ui:include>
+
 </ui:composition>

src/test/java/edu/harvard/iq/dataverse/api/FileMetadataIT.java

@@ -13,7 +13,7 @@
 import java.util.UUID;
 
 import static com.jayway.restassured.RestAssured.given;
-import static javax.ws.rs.core.Response.Status.FORBIDDEN;
+import static javax.ws.rs.core.Response.Status.OK;
 import static junit.framework.Assert.assertEquals;
 import static junit.framework.Assert.fail;
 import static org.hamcrest.CoreMatchers.equalTo;
@@ -118,6 +118,8 @@ public void tearDownDataverse() {
     @Test
     public void testJsonParserWithDirectoryLabels() {
         try {
+            //SEK 4/14/2020 need to be super user to add a dataset with files
+            UtilIT.makeSuperUser(testName).then().assertThat().statusCode(OK.getStatusCode());
 
             // try to create a dataset with directory labels that contain both leading and trailing file separators
             //Should work now
@@ -134,8 +136,6 @@ public void testJsonParserWithDirectoryLabels() {
 
             // create dataset and set id
             System.out.println("Creating dataset....");
-            //SEK 4/14/2020 need to be super user to add a dataset with files
-            UtilIT.makeSuperUser(testName);
             dsId = given()
                     .header(keyString, token)
                     .body(IOUtils.toString(classLoader.getResourceAsStream("json/complete-dataset-with-files.json")))