Merge pull request IQSS#3408 from IQSS/file-metadata-provenance-2295

File metadata provenance 2295

src/main/java/Bundle.properties

@@ -1060,7 +1060,7 @@ dataset.cite.title.released=DRAFT VERSION will be replaced in the citation with
 dataset.cite.title.draft=DRAFT VERSION will be replaced in the citation with the selected version once the dataset has been published.
 dataset.cite.title.deassessioned=DEACCESSIONED VERSION has been added to the citation for this version since it is no longer available.
 dataset.cite.standards.tip=Learn about <a href="http://best-practices.dataverse.org/data-citation/" title="Get Recognition: Data Citation  - Dataverse Best Practices" target="_blank">Data Citation Standards</a>.
-dataset.cite.downloadBtn=Cite Data
+dataset.cite.downloadBtn=Cite Dataset
 dataset.cite.downloadBtn.xml=EndNote XML
 dataset.cite.downloadBtn.ris=RIS
 dataset.cite.downloadBtn.bib=BibTeX
@@ -1201,6 +1201,7 @@ file.spss-porExtraLabels=Variable Labels
 file.spss-porExtraLabels.title=Upload an additional text file with extra variable labels.
 file.spss-porExtraLabels.selectToAddBtn=Select File to Add
 file.ingestFailed=Tabular Data Ingest Failed
+file.explore.twoRavens=TwoRavens
 file.mapData=Map Data
 file.mapData.viewMap=WorldMap
 file.mapData.unpublished.header=Data Not Published
@@ -1218,7 +1219,7 @@ file.requestAccess.dialog.msg=You need to <a href="/loginpage.xhtml{0}" target="
 file.requestAccess.dialog.msg.signup=You need to <a href="/dataverseuser.xhtml{0}&amp;editMode=CREATE" target="{1}" title="Sign Up for a Dataverse Account">Sign Up</a> or <a href="/loginpage.xhtml{0}" target="{1}" title="Log into your Dataverse Account">Log In</a> to request access to this file.
 file.accessRequested=Access Requested
 
-file.ingestInproGress=Ingest in progress...
+file.ingestInProgress=Ingest in progress...
 
 file.dataFilesTab.metadata.header=Metadata
 file.dataFilesTab.metadata.addBtn=Add + Edit Metadata
@@ -1390,18 +1391,25 @@ dataset.widgets.advanced.success.message=Successfully updated your Personal Webs
 dataset.widgets.advanced.failure.message=The dataverse Personal Website URL has not been updated.
 
 # file.xhtml
+file.share.fileShare=Share File
+file.share.fileShare.tip=Share this file on your favorite social media networks.
+file.share.fileShare.shareText=View this file.
 file.title.label=Title
 file.citation.label=Citation
+file.cite.downloadBtn=Cite Data File
 file.general.metadata.label=General Metadata
 file.description.label=Description
 file.tags.label=Tags
+file.lastupdated.label=Last Updated
 
 file.metadataTab.fileMetadata.header=File Metadata
 file.metadataTab.fileMetadata.persistentid.label=Data File Persistent ID
 file.metadataTab.fileMetadata.unf.label=UNF
 file.metadataTab.fileMetadata.size.label=Size
 file.metadataTab.fileMetadata.type.label=Type
 file.metadataTab.fileMetadata.description.label=Description
+file.metadataTab.fileMetadata.publicationDate.label=Publication Date
+file.metadataTab.fileMetadata.depositDate.label=Deposit Date
 file.metadataTab.fitsMetadata.header=FITS Metadata
 file.metadataTab.provenance.header=File Provenance
 file.metadataTab.provenance.body=File Provenance information coming in a later release...

src/main/java/Bundle_zh_CN.properties

@@ -361,7 +361,7 @@ file.downloadBtn.format.original=\u539f\u59cb\u6587\u4ef6\u683c\u5f0f\uff08{0}\u
 file.downloadBtn.format.rdata=RDATA\u683c\u5f0f
 file.downloadBtn.format.var=\u53ef\u53d8\u5143
 file.downloadBtn.format.citation=\u6570\u636e\u6587\u4ef6\u5f15\u7528
-file.ingestInproGress=\u6444\u53d6\u4e2d...
+file.ingestInProgress=\u6444\u53d6\u4e2d...
 file.dataFilesTab.metadata.header=\u5143\u6570\u636e
 file.dataFilesTab.metadata.addBtn=\u6dfb\u52a0+\u7f16\u8f91\u5143\u6570\u636e
 file.dataFilesTab.terms.header=\u8bb8\u53ef+\u6761\u6b3e

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

@@ -172,7 +172,7 @@ public String toString(boolean html) {
 
         // append UNF
         if (!StringUtils.isEmpty(UNF)) {
-            citation.append(" [").append(UNF).append("]");
+            citation.append(", ").append(UNF);
         }
 
         for (DatasetField dsf : optionalValues) {

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

@@ -17,6 +17,7 @@
 import java.nio.file.Path;
 import java.nio.file.Paths;
 import java.nio.file.Files;
+import java.text.SimpleDateFormat;
 import java.util.Arrays;
 import javax.persistence.Entity;
 import javax.persistence.OneToMany;
@@ -693,4 +694,19 @@ public boolean hasGeospatialTag(){
         }
         return false;
     }
+
+    public String getPublicationDateFormattedYYYYMMDD() {
+        if (getPublicationDate() != null){
+                   return new SimpleDateFormat("yyyy-MM-dd").format(getPublicationDate()); 
+        }
+        return null;
+    }
+
+    public String getCreateDateFormattedYYYYMMDD() {
+        if (getCreateDate() != null){
+                   return new SimpleDateFormat("yyyy-MM-dd").format(getCreateDate()); 
+        }
+        return null;
+    }
+
 }

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

@@ -435,7 +435,7 @@ public void findFileMetadataOptimizedExperimental(Dataset owner, DatasetVersion
 
         int i = 0; 
 
-        List<Object[]> dataTableResults = em.createNativeQuery("SELECT t0.ID, t0.DATAFILE_ID, t0.UNF, t0.CASEQUANTITY, t0.VARQUANTITY, t0.ORIGINALFILEFORMAT FROM dataTable t0, dataFile t1, dvObject t2 WHERE ((t0.DATAFILE_ID = t1.ID) AND (t1.ID = t2.ID) AND (t2.OWNER_ID = " + owner.getId() + "))").getResultList();
+        List<Object[]> dataTableResults = em.createNativeQuery("SELECT t0.ID, t0.DATAFILE_ID, t0.UNF, t0.CASEQUANTITY, t0.VARQUANTITY, t0.ORIGINALFILEFORMAT FROM dataTable t0, dataFile t1, dvObject t2 WHERE ((t0.DATAFILE_ID = t1.ID) AND (t1.ID = t2.ID) AND (t2.OWNER_ID = " + owner.getId() + ")) ORDER BY t0.ID").getResultList();
 
         for (Object[] result : dataTableResults) {
             DataTable dataTable = new DataTable(); 
@@ -476,7 +476,7 @@ public void findFileMetadataOptimizedExperimental(Dataset owner, DatasetVersion
 
         i = 0; 
 
-        List<Object[]> fileResults = em.createNativeQuery("SELECT t0.ID, t0.CREATEDATE, t0.INDEXTIME, t0.MODIFICATIONTIME, t0.PERMISSIONINDEXTIME, t0.PERMISSIONMODIFICATIONTIME, t0.PUBLICATIONDATE, t0.CREATOR_ID, t0.RELEASEUSER_ID, t1.CONTENTTYPE, t1.FILESYSTEMNAME, t1.FILESIZE, t1.INGESTSTATUS, t1.CHECKSUMVALUE, t1.RESTRICTED, t1.CHECKSUMTYPE FROM DVOBJECT t0, DATAFILE t1 WHERE ((t0.OWNER_ID = " + owner.getId() + ") AND ((t1.ID = t0.ID) AND (t0.DTYPE = 'DataFile')))").getResultList(); 
+        List<Object[]> fileResults = em.createNativeQuery("SELECT t0.ID, t0.CREATEDATE, t0.INDEXTIME, t0.MODIFICATIONTIME, t0.PERMISSIONINDEXTIME, t0.PERMISSIONMODIFICATIONTIME, t0.PUBLICATIONDATE, t0.CREATOR_ID, t0.RELEASEUSER_ID, t1.CONTENTTYPE, t1.FILESYSTEMNAME, t1.FILESIZE, t1.INGESTSTATUS, t1.CHECKSUMVALUE, t1.RESTRICTED, t1.CHECKSUMTYPE FROM DVOBJECT t0, DATAFILE t1 WHERE ((t0.OWNER_ID = " + owner.getId() + ") AND ((t1.ID = t0.ID) AND (t0.DTYPE = 'DataFile'))) ORDER BY t0.ID").getResultList(); 
 
         for (Object[] result : fileResults) {
             Integer file_id = (Integer) result[0];
@@ -599,7 +599,6 @@ public void findFileMetadataOptimizedExperimental(Dataset owner, DatasetVersion
             filesMap.put(dataFile.getId(), i++);
         } 
 
-        owner.setFiles(dataFiles);
         fileResults = null; 
 
         logger.fine("Retrieved and cached "+i+" datafiles.");
@@ -613,13 +612,14 @@ public void findFileMetadataOptimizedExperimental(Dataset owner, DatasetVersion
         logger.fine("Retreived "+i+" file categories attached to the dataset.");
 
         if (requestedVersion != null) {
-            requestedVersion.setFileMetadatas(retrieveFileMetadataForVersion(owner, requestedVersion, filesMap, categoryMap));
+            requestedVersion.setFileMetadatas(retrieveFileMetadataForVersion(owner, requestedVersion, dataFiles, filesMap, categoryMap));
         } else {
             for (DatasetVersion version : owner.getVersions()) {
-                version.setFileMetadatas(retrieveFileMetadataForVersion(owner, version, filesMap, categoryMap));
+                version.setFileMetadatas(retrieveFileMetadataForVersion(owner, version, dataFiles, filesMap, categoryMap));
                 logger.fine("Retrieved "+version.getFileMetadatas().size()+" filemetadatas for the version "+version.getId());
             }
         }
+        owner.setFiles(dataFiles);
     }
 
      private List<AuthenticatedUser> retrieveFileAccessRequesters(DataFile fileIn){
@@ -638,7 +638,7 @@ private List<AuthenticatedUser> retrieveFileAccessRequesters(DataFile fileIn){
         return retList;
     }
 
-    private List<FileMetadata> retrieveFileMetadataForVersion(Dataset dataset, DatasetVersion version, Map<Long, Integer> filesMap, Map<Long, Integer> categoryMap) {
+    private List<FileMetadata> retrieveFileMetadataForVersion(Dataset dataset, DatasetVersion version, List<DataFile> dataFiles, Map<Long, Integer> filesMap, Map<Long, Integer> categoryMap) {
         List<FileMetadata> retList = new ArrayList<>();
         Map<Long, Set<Long>> categoryMetaMap = new HashMap<>();
 
@@ -656,7 +656,7 @@ private List<FileMetadata> retrieveFileMetadataForVersion(Dataset dataset, Datas
         logger.fine("Retrieved and mapped "+i+" file categories attached to files in the version "+version.getId());
         categoryResults = null;
 
-        List<Object[]> metadataResults = em.createNativeQuery("select id, datafile_id, DESCRIPTION, LABEL, RESTRICTED, DIRECTORYLABEL from FileMetadata where datasetversion_id = "+version.getId()).getResultList();
+        List<Object[]> metadataResults = em.createNativeQuery("select id, datafile_id, DESCRIPTION, LABEL, RESTRICTED, DIRECTORYLABEL from FileMetadata where datasetversion_id = "+version.getId() + " ORDER BY LABEL").getResultList();
 
         for (Object[] result : metadataResults) {
             Integer filemeta_id = (Integer) result[0];
@@ -688,7 +688,8 @@ private List<FileMetadata> retrieveFileMetadataForVersion(Dataset dataset, Datas
 
             fileMetadata.setDatasetVersion(version);
 
-            fileMetadata.setDataFile(dataset.getFiles().get(file_list_id));
+            //fileMetadata.setDataFile(dataset.getFiles().get(file_list_id));
+            fileMetadata.setDataFile(dataFiles.get(file_list_id));
 
             String description = (String) result[2]; 
 
@@ -720,7 +721,14 @@ private List<FileMetadata> retrieveFileMetadataForVersion(Dataset dataset, Datas
         logger.fine("Retrieved "+retList.size()+" file metadatas for version "+version.getId()+" (inside the retrieveFileMetadataForVersion method).");
 
 
-        Collections.sort(retList, FileMetadata.compareByLabel);
+        /* 
+            We no longer perform this sort here, just to keep this filemetadata
+            list as identical as possible to when it's produced by the "traditional"
+            EJB method. When it's necessary to have the filemetadatas sorted by 
+            FileMetadata.compareByLabel, the DatasetVersion.getFileMetadatasSorted()
+            method should be called. 
+        
+        Collections.sort(retList, FileMetadata.compareByLabel); */
 
         return retList; 
     }
@@ -1226,4 +1234,4 @@ public void populateFileSearchCard(SolrSearchResult solrSearchResult) {
         solrSearchResult.setEntity(this.findCheapAndEasy(solrSearchResult.getEntityId()));
     }
 
-}
+}

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

@@ -10,6 +10,7 @@
 import java.util.Date;
 import java.util.List;
 import java.util.Objects;
+import java.util.logging.Logger;
 import javax.persistence.CascadeType;
 import javax.persistence.Column;
 import javax.persistence.Entity;
@@ -41,6 +42,7 @@
     @Index(columnList = "thumbnailfile_id")},
         uniqueConstraints = @UniqueConstraint(columnNames = {"authority,protocol,identifier,doiseparator"}))
 public class Dataset extends DvObjectContainer {
+    private static final Logger logger = Logger.getLogger(Dataset.class.getCanonicalName());
 
 //    public static final String REDIRECT_URL = "/dataset.xhtml?persistentId=";
     public static final String TARGET_URL = "/citation?persistentId=";
@@ -185,10 +187,12 @@ public String getGlobalId() {
     }
 
     public List<DataFile> getFiles() {
+        logger.info("getFiles() on dataset "+this.getId());
         return files;
     }
 
     public void setFiles(List<DataFile> files) {
+        logger.info("setFiles() on dataset "+this.getId());
         this.files = files;
     }