Merge branch 'develop' into 10220-thumbnail-size-bug

docker-compose-dev.yml

@@ -60,6 +60,8 @@ services:
     volumes:
       - ./docker-dev-volumes/app/data:/dv
       - ./docker-dev-volumes/app/secrets:/secrets
+      # Uncomment to map the glassfish applications folder so that we can update webapp resources using scripts/intellij/cpwebapp.sh
+      # - ./docker-dev-volumes/glassfish/applications:/opt/payara/appserver/glassfish/domains/domain1/applications
       # Uncomment for changes to xhtml to be deployed immediately (if supported your IDE or toolchain).
       # Replace 6.0 with the current version.
       # - ./target/dataverse-6.0:/opt/payara/deployments/dataverse

scripts/intellij/cpwebapp.sh

@@ -0,0 +1,33 @@
+#!/usr/bin/env bash
+#
+# cpwebapp <project dir> <file in webapp>
+#
+# Usage:
+#
+# Add a File watcher by importing watchers.xml into IntelliJ IDEA, and let it do the copying whenever you save a
+# file under webapp.
+#
+#     https://www.jetbrains.com/help/idea/settings-tools-file-watchers.html
+#
+# Alternatively, you can add an External tool and trigger via menu or shortcut to do the copying manually:
+#
+#     https://www.jetbrains.com/help/idea/configuring-third-party-tools.html
+#
+
+PROJECT_DIR=$1
+FILE_TO_COPY=$2
+RELATIVE_PATH="${FILE_TO_COPY#$PROJECT_DIR/}"
+
+# Check if RELATIVE_PATH starts with 'src/main/webapp', otherwise ignore
+if [[ $RELATIVE_PATH == src/main/webapp* ]]; then
+    # Get current version. Any other way to do this? A simple VERSION file would help.
+    VERSION=`perl -ne 'print $1 if /<revision>(.*?)<\/revision>/' ./modules/dataverse-parent/pom.xml`
+    RELATIVE_PATH_WITHOUT_WEBAPP="${RELATIVE_PATH#src/main/webapp/}"
+    TARGET_DIR=./docker-dev-volumes/glassfish/applications/dataverse-$VERSION
+    TARGET_PATH="${TARGET_DIR}/${RELATIVE_PATH_WITHOUT_WEBAPP}"
+
+    mkdir -p "$(dirname "$TARGET_PATH")"
+    cp "$FILE_TO_COPY" "$TARGET_PATH"
+
+    echo "File $FILE_TO_COPY copied to $TARGET_PATH"
+fi

scripts/intellij/watchers.xml

@@ -0,0 +1,22 @@
+<TaskOptions>
+  <TaskOptions>
+    <option name="arguments" value="$ProjectFileDir$ $FilePath$" />
+    <option name="checkSyntaxErrors" value="false" />
+    <option name="description" />
+    <option name="exitCodeBehavior" value="ERROR" />
+    <option name="fileExtension" value="*" />
+    <option name="immediateSync" value="false" />
+    <option name="name" value="Dataverse webapp file copy on save" />
+    <option name="output" value="" />
+    <option name="outputFilters">
+      <array />
+    </option>
+    <option name="outputFromStdout" value="false" />
+    <option name="program" value="$ProjectFileDir$/scripts/intellij/cpwebapp.sh" />
+    <option name="runOnExternalChanges" value="true" />
+    <option name="scopeName" value="Current File" />
+    <option name="trackOnlyRoot" value="false" />
+    <option name="workingDir" value="$ProjectFileDir$" />
+    <envs />
+  </TaskOptions>
+</TaskOptions>

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

@@ -752,9 +752,21 @@ public void setDatasetExternalCitations(List<DatasetExternalCitations> datasetEx
         this.datasetExternalCitations = datasetExternalCitations;
     }
 
+    @ManyToOne
+    @JoinColumn(name="harvestingClient_id")
+    private  HarvestingClient harvestedFrom;
 
-
+    public HarvestingClient getHarvestedFrom() {
+        return this.harvestedFrom;
+    }
 
+    public void setHarvestedFrom(HarvestingClient harvestingClientConfig) {
+        this.harvestedFrom = harvestingClientConfig;
+    }
+
+    public boolean isHarvested() {
+        return this.harvestedFrom != null;
+    }
 
     private String harvestIdentifier;
 

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

@@ -583,6 +583,54 @@ public Long getDatasetVersionCardImage(Long versionId, User user) {
         return null;
     }
 
+    /**
+     * Used to identify and properly display Harvested objects on the dataverse page.
+     *
+     * @param datasetIds
+     * @return
+     */
+    public Map<Long, String> getArchiveDescriptionsForHarvestedDatasets(Set<Long> datasetIds){
+        if (datasetIds == null || datasetIds.size() < 1) {
+            return null;
+        }
+
+        String datasetIdStr = StringUtils.join(datasetIds, ", ");
+
+        String qstr = "SELECT d.id, h.archiveDescription FROM harvestingClient h, dataset d WHERE d.harvestingClient_id = h.id AND d.id IN (" + datasetIdStr + ")";
+        List<Object[]> searchResults;
+
+        try {
+            searchResults = em.createNativeQuery(qstr).getResultList();
+        } catch (Exception ex) {
+            searchResults = null;
+        }
+
+        if (searchResults == null) {
+            return null;
+        }
+
+        Map<Long, String> ret = new HashMap<>();
+
+        for (Object[] result : searchResults) {
+            Long dsId;
+            if (result[0] != null) {
+                try {
+                    dsId = (Long)result[0];
+                } catch (Exception ex) {
+                    dsId = null;
+                }
+                if (dsId == null) {
+                    continue;
+                }
+
+                ret.put(dsId, (String)result[1]);
+            }
+        }
+
+        return ret;
+    }
+
+
 
     public boolean isDatasetCardImageAvailable(DatasetVersion datasetVersion, User user) {
         if (datasetVersion == null) {

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

@@ -1,7 +1,6 @@
 package edu.harvard.iq.dataverse;
 
 import edu.harvard.iq.dataverse.authorization.users.AuthenticatedUser;
-import edu.harvard.iq.dataverse.harvest.client.HarvestingClient;
 import edu.harvard.iq.dataverse.pidproviders.PidUtil;
 import edu.harvard.iq.dataverse.storageuse.StorageQuota;
 
@@ -372,22 +371,6 @@ public GlobalId getGlobalId() {
         return globalId;
     }
 
-    @ManyToOne
-    @JoinColumn(name="harvestingClient_id")
-    private  HarvestingClient harvestedFrom;
-
-    public HarvestingClient getHarvestedFrom() {
-        return this.harvestedFrom;
-    }
-
-    public void setHarvestedFrom(HarvestingClient harvestingClientConfig) {
-        this.harvestedFrom = harvestingClientConfig;
-    }
-
-    public boolean isHarvested() {
-        return this.harvestedFrom != null;
-    }
-
     public abstract <T> T accept(Visitor<T> v);
 
     @Override

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

@@ -383,54 +383,6 @@ public Map<Long, String> getObjectPathsByIds(Set<Long> objectIds){
         return ret;        
     }
 
-    /**
-     * Used to identify and properly display Harvested objects on the dataverse page.
-     *
-     * @param dvObjectIds
-     * @return
-     */
-    public Map<Long, String> getArchiveDescriptionsForHarvestedDvObjects(Set<Long> dvObjectIds){
-
-        if (dvObjectIds == null || dvObjectIds.size() < 1) {
-            return null;
-        }
-
-        String dvObjectIsString = StringUtils.join(dvObjectIds, ", ");
-        String qstr = "SELECT d.id, h.archiveDescription FROM harvestingClient h, DvObject d WHERE d.harvestingClient_id = h.id AND d.id IN (" + dvObjectIsString + ")";
-        List<Object[]> searchResults;
-
-        try {
-            searchResults = em.createNativeQuery(qstr).getResultList();
-        } catch (Exception ex) {
-            searchResults = null;
-        }
-
-        if (searchResults == null) {
-            return null;
-        }
-
-        Map<Long, String> ret = new HashMap<>();
-
-        for (Object[] result : searchResults) {
-            Long dvObjId;
-            if (result[0] != null) {
-                try {
-                    Integer castResult = (Integer) result[0];
-                    dvObjId =  Long.valueOf(castResult);                    
-                } catch (Exception ex) {
-                    dvObjId = null;
-                }
-                if (dvObjId == null) {
-                    continue;
-                }
-                ret.put(dvObjId, (String)result[1]);
-            }
-        }
-
-        return ret;
-    }
-
-
     public String generateNewIdentifierByStoredProcedure() {
         StoredProcedureQuery query = this.em.createNamedStoredProcedureQuery("Dataset.generateIdentifierFromStoredProcedure");
         query.execute();

src/main/java/edu/harvard/iq/dataverse/api/imports/ImportServiceBean.java

@@ -332,11 +332,6 @@ public Dataset doImportHarvestedDataset(DataverseRequest dataverseRequest, Harve
 
             Dataset existingDs = datasetService.findByGlobalId(ds.getGlobalId().asString());
 
-            //adding the harvesting client id to harvested files #9686
-            for (DataFile df : ds.getFiles()){
-                df.setHarvestedFrom(harvestingClient);
-            }  
-
             if (existingDs != null) {
                 // If this dataset already exists IN ANOTHER DATAVERSE
                 // we are just going to skip it!

src/main/java/edu/harvard/iq/dataverse/harvest/client/HarvestingClientServiceBean.java

@@ -199,8 +199,8 @@ public void recordHarvestJobStatus(Long hcId, Date finishTime, int harvestedCoun
 
     public Long getNumberOfHarvestedDatasetsByAllClients() {
         try {
-            return (Long) em.createNativeQuery("SELECT count(d.id) FROM dvobject d "
-                    + " WHERE d.harvestingclient_id IS NOT NULL and d.dtype = 'Dataset'").getSingleResult();
+            return (Long) em.createNativeQuery("SELECT count(d.id) FROM dataset d "
+                    + " WHERE d.harvestingclient_id IS NOT NULL").getSingleResult();
 
         } catch (Exception ex) {
             logger.info("Warning: exception looking up the total number of harvested datasets: " + ex.getMessage());