Merge branch 'develop' into 2960-download-manager-help-msg

doc/sphinx-guides/source/developers/dev-environment.rst

@@ -169,7 +169,9 @@ After the script has finished, you should be able to log into Dataverse with the
 Configure Your Development Environment for Publishing
 -----------------------------------------------------
 
-In order to publish datasets, you must configure Dataverse with a username and password for a persistent ID provider. The installer configures your development environment to use DOIs (rather than Handles) for persistent IDs with DataCite's test server at https://mds.test.datacite.org as the provider. In order to publish datasets with this provider, you must email [email protected] and ask for a test account. Once you have your DataCite username and password, you must add them as JVM options (``doi.username`` and ``doi.password``) as described under "Persistent Identifiers and Publishing Datasets" in the :doc:`/installation/config` section of the Installation Guide.
+Run the following command:
+
+``curl http://localhost:8080/api/admin/settings/:DoiProvider -X PUT -d FAKE``
 
 Next Steps
 ----------

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

@@ -884,7 +884,7 @@ By default the footer says "Copyright © [YYYY]" but you can add text after the
 :DoiProvider
 ++++++++++++
 
-As of this writing "DataCite" and "EZID" are the only valid options. ``:DoiProvider`` is only needed if you are using DOI.
+As of this writing "DataCite" and "EZID" are the only valid options for production installations. Developers are welcome to use "FAKE". ``:DoiProvider`` is only needed if you are using DOI.
 
 ``curl -X PUT -d DataCite http://localhost:8080/api/admin/settings/:DoiProvider``
 

scripts/deploy/phoenix.dataverse.org/post

@@ -5,7 +5,7 @@ cd ../..
 psql -U dvnapp dvndb -f scripts/database/reference_data.sql
 psql -U dvnapp dvndb -f doc/sphinx-guides/source/_static/util/pg8-createsequence-prep.sql
 psql -U dvnapp dvndb -f doc/sphinx-guides/source/_static/util/createsequence.sql
-curl http://localhost:8080/api/admin/settings/:DoiProvider -X PUT -d DataCite
+curl http://localhost:8080/api/admin/settings/:DoiProvider -X PUT -d FAKE
 scripts/search/tests/publish-dataverse-root
 git checkout scripts/api/data/dv-root.json
 scripts/search/tests/grant-authusers-add-on-root

src/main/java/Bundle.properties

@@ -1184,7 +1184,7 @@ dataset.submitBtn=Submit for Review
 dataset.disabledSubmittedBtn=Submitted for Review
 dataset.submitMessage=You will not be able to make changes to this dataset while it is in review.
 dataset.submit.success=Your dataset has been submitted for review.
-dataset.inreview.infoMessage=\u2013 This dataset is currently under review prior to publication.
+dataset.inreview.infoMessage=The draft version of this dataset is currently under review prior to publication.
 dataset.submit.failure=Dataset Submission Failed - {0}
 dataset.submit.failure.null=Can't submit for review. Dataset is null.
 dataset.submit.failure.isReleased=Latest version of dataset is already released. Only draft versions can be submitted for review.
@@ -1220,6 +1220,7 @@ dataset.share.datasetShare=Share Dataset
 dataset.share.datasetShare.tip=Share this dataset on your favorite social media networks.
 dataset.share.datasetShare.shareText=View this dataset.
 dataset.locked.message=Dataset Locked
+dataset.locked.message.details=This dataset is locked until publication.
 dataset.locked.inReview.message=Submitted for Review
 dataset.publish.error=This dataset may not be published due to an error when contacting the <a href=\{1} target=\"_blank\"/> {0} </a> Service. Please try again.
 dataset.publish.error.doi=This dataset may not be published because the DOI update failed.
@@ -1236,8 +1237,9 @@ dataset.compute.computeBatchListHeader=Compute Batch
 dataset.compute.computeBatchRestricted=This dataset contains restricted files you may not compute on because you have not been granted access.
 dataset.delete.error=Could not deaccession the dataset because the {0} update failed.
 dataset.publish.worldMap.deleteConfirm=Please note that your data and map on WorldMap will be removed due to restricted file access changes in this dataset version which you are publishing. Do you want to continue?
-dataset.publish.workflow.inprogress=Publish workflow in progress
-dataset.pidRegister.workflow.inprogress=Register/update file persistent identifiers workflow in progress
+dataset.publish.workflow.message=Publish in Progress
+dataset.publish.workflow.inprogress=This dataset is locked until publication.
+dataset.pidRegister.workflow.inprogress=This dataset is locked while the file persistent identifiers are being registered or updated.
 dataset.versionUI.draft=Draft
 dataset.versionUI.inReview=In Review
 dataset.versionUI.unpublished=Unpublished
@@ -1401,8 +1403,8 @@ file.rsyncUpload.step2=Download this file upload script:
 file.rsyncUpload.step2.downloadScriptButton=Download DCM Script
 file.rsyncUpload.step3=Open a terminal window in the same directory you saved the script and run this command: <code>bash ./{0}</code>
 file.rsyncUpload.step4=Follow the instructions in the script. It will ask for a full path (beginning with "/") to the directory containing your data. Note: this script will expire after 7 days.
-file.rsyncUpload.inProgressMessage.summary=DCM File Upload
-file.rsyncUpload.inProgressMessage.details=This dataset is locked until the data files have been transferred and verified.
+file.rsyncUpload.inProgressMessage.summary=File Upload in Progress
+file.rsyncUpload.inProgressMessage.details=This dataset is locked while the data files are being transferred and verified.
 file.rsyncUpload.httpUploadDisabledDueToRsyncFileExisting=HTTP upload is disabled for this dataset because you have already uploaded files via rsync. If you would like to switch to HTTP upload, please contact {0}.
 file.rsyncUpload.httpUploadDisabledDueToRsyncFileExistingAndPublished=HTTP upload is disabled for this dataset because you have already uploaded files via rsync and published the dataset.
 file.rsyncUpload.rsyncUploadDisabledDueFileUploadedViaHttp=Upload with rsync + SSH is disabled for this dataset because you have already uploaded files via HTTP. If you would like to switch to rsync upload, then you must first remove all uploaded files from this dataset. Once this dataset is published, the chosen upload method is permanently locked in.

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

@@ -1552,10 +1552,10 @@ private String init(boolean initFull) {
         }
 
         // Various info messages, when the dataset is locked (for various reasons):
-        if (dataset.isLocked()) {
+        if (dataset.isLocked() && canUpdateDataset()) {
             if (dataset.isLockedFor(DatasetLock.Reason.Workflow)) {
                 JH.addMessage(FacesMessage.SEVERITY_WARN, BundleUtil.getStringFromBundle("dataset.locked.message"),
-                        BundleUtil.getStringFromBundle("dataset.publish.workflow.inprogress"));
+                        BundleUtil.getStringFromBundle("dataset.locked.message.details"));
             }
             if (dataset.isLockedFor(DatasetLock.Reason.InReview)) {
                 JH.addMessage(FacesMessage.SEVERITY_WARN, BundleUtil.getStringFromBundle("dataset.locked.inReview.message"),
@@ -1573,8 +1573,8 @@ private String init(boolean initFull) {
                     datasetService.removeDatasetLocks(dataset.getId(), DatasetLock.Reason.pidRegister);
                 }*/
             if (dataset.isLockedFor(DatasetLock.Reason.pidRegister)) {
-                JH.addMessage(FacesMessage.SEVERITY_WARN, BundleUtil.getStringFromBundle("dataset.pidRegister.workflow.inprogress"),
-                        BundleUtil.getStringFromBundle("dataset.publish.workflow.inprogress"));
+                JH.addMessage(FacesMessage.SEVERITY_WARN, BundleUtil.getStringFromBundle("dataset.publish.workflow.message"),
+                        BundleUtil.getStringFromBundle("dataset.pidRegister.workflow.inprogress"));
             }
         }
 
@@ -1943,7 +1943,7 @@ private String releaseDataset(boolean minor) {
                 if ( result.isCompleted() ) {
                     JsfHelper.addSuccessMessage(BundleUtil.getStringFromBundle("dataset.message.publishSuccess"));
                 } else {
-                    JH.addMessage(FacesMessage.SEVERITY_WARN, BundleUtil.getStringFromBundle("dataset.locked.message"), BundleUtil.getStringFromBundle("dataset.publish.workflow.inprogress"));
+                    JH.addMessage(FacesMessage.SEVERITY_WARN, BundleUtil.getStringFromBundle("dataset.locked.message"), BundleUtil.getStringFromBundle("dataset.locked.message.details"));
                 }
 
             } catch (CommandException ex) {

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

@@ -15,6 +15,7 @@
 import edu.harvard.iq.dataverse.engine.command.exception.CommandException;
 import edu.harvard.iq.dataverse.engine.command.exception.PermissionException;
 import edu.harvard.iq.dataverse.ingest.IngestServiceBean;
+import edu.harvard.iq.dataverse.pidproviders.FakePidProviderServiceBean;
 import edu.harvard.iq.dataverse.privateurl.PrivateUrlServiceBean;
 import edu.harvard.iq.dataverse.search.IndexBatchServiceBean;
 import edu.harvard.iq.dataverse.search.IndexServiceBean;
@@ -108,7 +109,10 @@ public class EjbDataverseEngine {
 
     @EJB
     DOIDataCiteServiceBean doiDataCite;
-
+
+    @EJB
+    FakePidProviderServiceBean fakePidProvider;
+
     @EJB
     HandlenetServiceBean handleNet;
 
@@ -372,7 +376,12 @@ public DOIEZIdServiceBean doiEZId() {
                 public DOIDataCiteServiceBean doiDataCite() {
                     return doiDataCite;
                 }
-
+
+                @Override
+                public FakePidProviderServiceBean fakePidProvider() {
+                    return fakePidProvider;
+                }
+
                 @Override
                 public HandlenetServiceBean handleNet() {
                     return handleNet;

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

@@ -78,6 +78,7 @@ class BeanDispatcher {
             switch ( doiProvider ) {
                 case "EZID": return ctxt.doiEZId();
                 case "DataCite": return ctxt.doiDataCite();
+                case "FAKE": return ctxt.fakePidProvider();
                 default: 
                     logger.log(Level.SEVERE, "Unknown doiProvider: {0}", doiProvider);
                     return null;

src/main/java/edu/harvard/iq/dataverse/dataaccess/SwiftAccessIO.java

@@ -518,13 +518,17 @@ private StoredObject initializeSwiftFileObject(boolean writeAccess, String auxIt
                 Properties p = getSwiftProperties();
                 swiftEndPoint = p.getProperty("swift.default.endpoint");
 
+                // Swift uses this to create pseudo-hierarchical folders
+                String swiftPseudoFolderPathSeparator = "/";
+
                 //swiftFolderPath = dataFile.getOwner().getDisplayName();
                 String swiftFolderPathSeparator = "-";
                 String authorityNoSlashes = owner.getAuthority().replace("/", swiftFolderPathSeparator);
                 swiftFolderPath = owner.getProtocolForFileStorage() + swiftFolderPathSeparator
-                                  + authorityNoSlashes.replace(".", swiftFolderPathSeparator)
-                                  + swiftFolderPathSeparator + owner.getIdentifierForFileStorage();
-                swiftFileName = storageIdentifier;
+                                  + authorityNoSlashes.replace(".", swiftFolderPathSeparator);
+
+                swiftFileName = owner.getIdentifierForFileStorage() + swiftPseudoFolderPathSeparator
+                                + storageIdentifier;
                 //setSwiftContainerName(swiftFolderPath);
                 //swiftFileName = dataFile.getDisplayName();
                 //Storage Identifier is now updated after the object is uploaded on Swift.
@@ -569,10 +573,14 @@ private StoredObject initializeSwiftFileObject(boolean writeAccess, String auxIt
                 Properties p = getSwiftProperties();
                 swiftEndPoint = p.getProperty("swift.default.endpoint");
                 String swiftFolderPathSeparator = "-";
+
+                // Swift uses this to create pseudo-hierarchical folders
+                String swiftPseudoFolderPathSeparator = "/";
+
                 String authorityNoSlashes = dataset.getAuthorityForFileStorage().replace("/", swiftFolderPathSeparator);
                 swiftFolderPath = dataset.getProtocolForFileStorage() + swiftFolderPathSeparator +
                     authorityNoSlashes.replace(".", swiftFolderPathSeparator) +
-                    swiftFolderPathSeparator + dataset.getIdentifierForFileStorage();
+                    swiftPseudoFolderPathSeparator + dataset.getIdentifierForFileStorage();
 
                 swiftFileName = auxItemTag;
                 dvObject.setStorageIdentifier("swift://" + swiftEndPoint + ":" + swiftFolderPath);

src/main/java/edu/harvard/iq/dataverse/engine/command/CommandContext.java

@@ -31,6 +31,7 @@
 import edu.harvard.iq.dataverse.datacapturemodule.DataCaptureModuleServiceBean;
 import edu.harvard.iq.dataverse.engine.DataverseEngine;
 import edu.harvard.iq.dataverse.ingest.IngestServiceBean;
+import edu.harvard.iq.dataverse.pidproviders.FakePidProviderServiceBean;
 import edu.harvard.iq.dataverse.privateurl.PrivateUrlServiceBean;
 import edu.harvard.iq.dataverse.search.IndexBatchServiceBean;
 import edu.harvard.iq.dataverse.search.SolrIndexServiceBean;
@@ -99,6 +100,8 @@ public interface CommandContext {
 
     public DOIDataCiteServiceBean doiDataCite();
 
+    public FakePidProviderServiceBean fakePidProvider();
+
     public HandlenetServiceBean handleNet();
 
     public GuestbookServiceBean guestbooks();

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

@@ -22,6 +22,7 @@
 import static java.util.stream.Collectors.joining;
 import javax.validation.ConstraintViolation;
 import edu.harvard.iq.dataverse.GlobalIdServiceBean;
+import edu.harvard.iq.dataverse.pidproviders.FakePidProviderServiceBean;
 
 /**
  *
@@ -158,6 +159,16 @@ protected void registerExternalIdentifier(Dataset theDataset, CommandContext ctx
         if (!theDataset.isIdentifierRegistered()) {
             GlobalIdServiceBean globalIdServiceBean = GlobalIdServiceBean.getBean(theDataset.getProtocol(), ctxt);
             if ( globalIdServiceBean != null ) {
+                if (globalIdServiceBean instanceof FakePidProviderServiceBean) {
+                    try {
+                        globalIdServiceBean.createIdentifier(theDataset);
+                    } catch (Throwable ex) {
+                        logger.warning("Problem running createIdentifier for FakePidProvider: " + ex);
+                    }
+                    theDataset.setGlobalIdCreateTime(getTimestamp());
+                    theDataset.setIdentifierRegistered(true);
+                    return;
+                }
                 try {
                     if (globalIdServiceBean.alreadyExists(theDataset)) {
                         int attempts = 0;

src/main/java/edu/harvard/iq/dataverse/pidproviders/FakePidProviderServiceBean.java

@@ -0,0 +1,66 @@
+package edu.harvard.iq.dataverse.pidproviders;
+
+import edu.harvard.iq.dataverse.AbstractGlobalIdServiceBean;
+import edu.harvard.iq.dataverse.DvObject;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import javax.ejb.Stateless;
+
+@Stateless
+public class FakePidProviderServiceBean extends AbstractGlobalIdServiceBean {
+
+    @Override
+    public boolean alreadyExists(DvObject dvo) throws Exception {
+        return true;
+    }
+
+    @Override
+    public boolean registerWhenPublished() {
+        return false;
+    }
+
+    @Override
+    public List<String> getProviderInformation() {
+        ArrayList<String> providerInfo = new ArrayList<>();
+        String providerName = "FAKE";
+        String providerLink = "http://dataverse.org";
+        providerInfo.add(providerName);
+        providerInfo.add(providerLink);
+        return providerInfo;
+    }
+
+    @Override
+    public String createIdentifier(DvObject dvo) throws Throwable {
+        return "fakeIdentifier";
+    }
+
+    @Override
+    public Map<String, String> getIdentifierMetadata(DvObject dvo) {
+        Map<String, String> map = new HashMap<>();
+        return map;
+    }
+
+    @Override
+    public String modifyIdentifierTargetURL(DvObject dvo) throws Exception {
+        return "fakeModifyIdentifierTargetURL";
+    }
+
+    @Override
+    public void deleteIdentifier(DvObject dvo) throws Exception {
+        // no-op
+    }
+
+    @Override
+    public Map<String, String> lookupMetadataFromIdentifier(String protocol, String authority, String identifier) {
+        Map<String, String> map = new HashMap<>();
+        return map;
+    }
+
+    @Override
+    public boolean publicizeIdentifier(DvObject studyIn) {
+        return true;
+    }
+
+}

src/main/webapp/403.xhtml

@@ -5,7 +5,6 @@
       xmlns:ui="http://java.sun.com/jsf/facelets"
       xmlns:o="http://omnifaces.org/ui"      
       xmlns:p="http://primefaces.org/ui">
-<f:view locale="#{dataverseLocaleBean.localeCode}">
     <h:head>
     </h:head>
 
@@ -34,5 +33,4 @@
             </ui:define>
         </ui:composition>
     </h:body>
-</f:view>
 </html>

src/main/webapp/404.xhtml

@@ -6,7 +6,6 @@
       xmlns:p="http://primefaces.org/ui"
       xmlns:o="http://omnifaces.org/ui"      
       xmlns:jsf="http://xmlns.jcp.org/jsf">
-<f:view locale="#{dataverseLocaleBean.localeCode}">
     <h:head>
     </h:head>
 
@@ -44,5 +43,4 @@
             </ui:define>
         </ui:composition>
     </h:body>
-</f:view>
 </html>

src/main/webapp/500.xhtml

@@ -4,7 +4,6 @@
       xmlns:f="http://java.sun.com/jsf/core"
       xmlns:ui="http://java.sun.com/jsf/facelets"
       xmlns:p="http://primefaces.org/ui">
-<f:view locale="#{dataverseLocaleBean.localeCode}">
     <h:head>
     </h:head>
 
@@ -21,5 +20,4 @@
             </ui:define>
         </ui:composition>
     </h:body>
-</f:view>
 </html>

src/main/webapp/ThemeAndWidgets.xhtml

@@ -6,7 +6,6 @@
       xmlns:p="http://primefaces.org/ui"
       xmlns:c="http://xmlns.jcp.org/jsp/jstl/core"
       xmlns:jsf="http://xmlns.jcp.org/jsf">
-<f:view locale="#{dataverseLocaleBean.localeCode}">
     <h:head>
     </h:head>
 
@@ -28,5 +27,4 @@
             </ui:define>
         </ui:composition>
     </h:body>
-</f:view>
 </html>

src/main/webapp/confirmemail.xhtml

@@ -5,7 +5,6 @@
       xmlns:ui="http://java.sun.com/jsf/facelets"
       xmlns:p="http://primefaces.org/ui"
       xmlns:jsf="http://xmlns.jcp.org/jsf">
-<f:view locale="#{dataverseLocaleBean.localeCode}">
     <h:head>
     </h:head>  
 
@@ -29,5 +28,4 @@
             </ui:define>
         </ui:composition>
     </h:body>
-</f:view>
 </html>

src/main/webapp/dashboard-users.xhtml

@@ -6,7 +6,6 @@
       xmlns:jsf="http://xmlns.jcp.org/jsf"
       xmlns:p="http://primefaces.org/ui"
       xmlns:c="http://xmlns.jcp.org/jsp/jstl/core">
-<f:view locale="#{dataverseLocaleBean.localeCode}">
     <h:head>
     </h:head>
 
@@ -115,5 +114,4 @@
         </ui:composition>
 
     </h:body>
-</f:view>
 </html>

src/main/webapp/dashboard.xhtml

@@ -5,7 +5,6 @@
       xmlns:ui="http://java.sun.com/jsf/facelets"
       xmlns:jsf="http://xmlns.jcp.org/jsf"
       xmlns:p="http://primefaces.org/ui">
-<f:view locale="#{dataverseLocaleBean.localeCode}">
     <h:head>
     </h:head>
 
@@ -136,5 +135,4 @@
             </ui:define>
         </ui:composition>
     </h:body>
-</f:view>
 </html>