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Merged
kcondon merged 2 commits into from
Oct 4, 2019
Merged

Force all edits to use command #6248

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b86843c
Drop dataupdate not needed path
qqmyers Oct 2, 2019
5f7155e
Merge remote-tracking branch 'IQSS/develop' into IQSS-alt6092
qqmyers Oct 4, 2019
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305 changes: 77 additions & 228 deletions src/main/java/edu/harvard/iq/dataverse/EditDatafilesPage.java
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Original file line number Diff line number Diff line change
Expand Up @@ -159,7 +159,6 @@ public enum FileEditMode {
private DatasetVersion clone;
private String dropBoxSelection = "";
private String displayCitation;
private boolean datasetUpdateRequired = false;
private boolean tabularDataTagsUpdated = false;

private String persistentId;
Expand Down Expand Up @@ -1004,10 +1003,6 @@ private void removeDataFileFromList(List<DataFile> dfs, DataFile dfToDelete) {

public String saveWithTermsOfUse() {
logger.fine("saving terms of use, and the dataset version");
//Set update required only if dataset already exists
if (dataset.getId() != null){
datasetUpdateRequired = true;
}
return save();
}

Expand Down Expand Up @@ -1149,239 +1144,102 @@ public String save() {
JsfHelper.addErrorMessage(getBundleString("file.metadataTab.provenance.error"));
Logger.getLogger(EditDatafilesPage.class.getName()).log(Level.SEVERE, null, ex);
}
//Always update the whole dataset if updating prov
//The flow that happens when datasetUpdateRequired is false has problems with doing saving actions after its merge
//This was the simplest way to work around this issue for prov. --MAD 4.8.6.
datasetUpdateRequired = datasetUpdateRequired || provFreeChanges || provJsonChanges;
}

if (workingVersion.getId() == null || datasetUpdateRequired) {
logger.fine("issuing the dataset update command");
// We are creating a new draft version;
// (OR, a full update of the dataset has been explicitly requested,
// because of the nature of the updates the user has made).
// We'll use an Update command for this:

//newDraftVersion = true;

if (datasetUpdateRequired) {
for (int i = 0; i < workingVersion.getFileMetadatas().size(); i++) {
for (FileMetadata fileMetadata : fileMetadatas) {
if (fileMetadata.getDataFile().getStorageIdentifier() != null) {
if (fileMetadata.getDataFile().getStorageIdentifier().equals(workingVersion.getFileMetadatas().get(i).getDataFile().getStorageIdentifier())) {
workingVersion.getFileMetadatas().set(i, fileMetadata);
}
}
}
}


//Moves DataFile updates from popupFragment to page for saving
//This does not seem to collide with the tags updating below
if(systemConfig.isProvCollectionEnabled() && provJsonChanges) {
HashMap<String,ProvPopupFragmentBean.UpdatesEntry> provenanceUpdates = provPopupFragmentBean.getProvenanceUpdates();
for (int i = 0; i < dataset.getFiles().size(); i++) {
for (ProvPopupFragmentBean.UpdatesEntry ue : provenanceUpdates.values()) {
if (ue.dataFile.getStorageIdentifier() != null ) {
if (ue.dataFile.getStorageIdentifier().equals(dataset.getFiles().get(i).getStorageIdentifier())) {
dataset.getFiles().set(i, ue.dataFile);
}
}
logger.fine("issuing the dataset update command");
// We are creating a new draft version or updating an existing draft;
// We'll use an Update command for this:
if (workingVersion.getId() != null) {
for (int i = 0; i < workingVersion.getFileMetadatas().size(); i++) {
for (FileMetadata fileMetadata : fileMetadatas) {
if (fileMetadata.getDataFile().getStorageIdentifier() != null) {
if (fileMetadata.getDataFile().getStorageIdentifier().equals(workingVersion.getFileMetadatas().get(i).getDataFile().getStorageIdentifier())) {
workingVersion.getFileMetadatas().set(i, fileMetadata);
}
}
}

// Tabular data tags are assigned to datafiles, not to
// version-specfic filemetadatas!
// So if tabular tags have been modified, we also need to
// refresh the list of datafiles, as found in dataset.getFiles(),
// similarly to what we've just done, above, for the filemetadatas.
// Otherwise, when we call UpdateDatasetCommand, it's not going
// to update the tags in the database (issue #2798).
// TODO: Is the above still true/is this still necessary?
// (and why?...)

if (tabularDataTagsUpdated) {
for (int i = 0; i < dataset.getFiles().size(); i++) {
for (FileMetadata fileMetadata : fileMetadatas) {
if (fileMetadata.getDataFile().getStorageIdentifier() != null) {
if (fileMetadata.getDataFile().getStorageIdentifier().equals(dataset.getFiles().get(i).getStorageIdentifier())) {
dataset.getFiles().set(i, fileMetadata.getDataFile());
}
}
}
}
// Moves DataFile updates from popupFragment to page for saving
// This does not seem to collide with the tags updating below
if (systemConfig.isProvCollectionEnabled() && provJsonChanges) {
HashMap<String, ProvPopupFragmentBean.UpdatesEntry> provenanceUpdates = provPopupFragmentBean.getProvenanceUpdates();
for (int i = 0; i < dataset.getFiles().size(); i++) {
for (ProvPopupFragmentBean.UpdatesEntry ue : provenanceUpdates.values()) {
if (ue.dataFile.getStorageIdentifier() != null) {
if (ue.dataFile.getStorageIdentifier().equals(dataset.getFiles().get(i).getStorageIdentifier())) {
dataset.getFiles().set(i, ue.dataFile);
}
}
tabularDataTagsUpdated = false;
}
}

Map<Long, String> deleteStorageLocations = null;

if (!filesToBeDeleted.isEmpty()) {
deleteStorageLocations = datafileService.getPhysicalFilesToDelete(filesToBeDeleted);
}

Command<Dataset> cmd;
try {
cmd = new UpdateDatasetVersionCommand(dataset, dvRequestService.getDataverseRequest(), filesToBeDeleted, clone);
((UpdateDatasetVersionCommand) cmd).setValidateLenient(true);
dataset = commandEngine.submit(cmd);

} catch (EJBException ex) {
StringBuilder error = new StringBuilder();
error.append(ex).append(" ");
error.append(ex.getMessage()).append(" ");
Throwable cause = ex;
while (cause.getCause()!= null) {
cause = cause.getCause();
error.append(cause).append(" ");
error.append(cause.getMessage()).append(" ");
}
logger.log(Level.INFO, "Couldn''t save dataset: {0}", error.toString());
populateDatasetUpdateFailureMessage();
return null;
} catch (CommandException ex) {
//FacesContext.getCurrentInstance().addMessage(null, new FacesMessage(FacesMessage.SEVERITY_ERROR, "Dataset Save Failed", " - " + ex.toString()));
logger.log(Level.INFO, "Couldn''t save dataset: {0}", ex.getMessage());
populateDatasetUpdateFailureMessage();
return null;
}

// Have we just deleted some draft datafiles (successfully)?
// finalize the physical file deletes:
// (DataFileService will double-check that the datafiles no
// longer exist in the database, before attempting to delete
// the physical files)
if (deleteStorageLocations != null) {
datafileService.finalizeFileDeletes(deleteStorageLocations);
}

datasetUpdateRequired = false;
saveEnabled = false;
} else {
String lockInfoMessage = "saving current edits";
DatasetLock lock = datasetService.addDatasetLock(getDataset().getId(), DatasetLock.Reason.EditInProgress, session.getUser() != null ? ((AuthenticatedUser)session.getUser()).getId() : null, lockInfoMessage);
if (lock != null) {
getDataset().addLock(lock);
} else {
logger.log(Level.WARNING, "Failed to lock the dataset (dataset id={0})", getDataset().getId());
}
try {
// This is an existing Draft version (and nobody has explicitly
// requested that the entire dataset is updated). So we'll try to update
// only the filemetadatas and/or files affected, and not the
// entire version.
Timestamp updateTime = new Timestamp(new Date().getTime());

workingVersion.setLastUpdateTime(updateTime);
dataset.setModificationTime(updateTime);
}

StringBuilder saveError = new StringBuilder();
// Tabular data tags are assigned to datafiles, not to
// version-specfic filemetadatas!
// So if tabular tags have been modified, we also need to
// refresh the list of datafiles, as found in dataset.getFiles(),
// similarly to what we've just done, above, for the filemetadatas.
// Otherwise, when we call UpdateDatasetCommand, it's not going
// to update the tags in the database (issue #2798).
// TODO: Is the above still true/is this still necessary?
// (and why?...)

if (tabularDataTagsUpdated) {
for (int i = 0; i < dataset.getFiles().size(); i++) {
for (FileMetadata fileMetadata : fileMetadatas) {

if (fileMetadata.getDataFile().getCreateDate() == null) {
fileMetadata.getDataFile().setCreateDate(updateTime);
fileMetadata.getDataFile().setCreator((AuthenticatedUser) session.getUser());
}
fileMetadata.getDataFile().setModificationTime(updateTime);
try {
// DataFile savedDatafile = datafileService.save(fileMetadata.getDataFile());
fileMetadata = datafileService.mergeFileMetadata(fileMetadata);
logger.fine("Successfully saved DataFile " + fileMetadata.getLabel() + " in the database.");
} catch (EJBException ex) {
saveError.append(ex).append(" ");
saveError.append(ex.getMessage()).append(" ");
Throwable cause = ex;
while (cause.getCause() != null) {
cause = cause.getCause();
saveError.append(cause).append(" ");
saveError.append(cause.getMessage()).append(" ");
if (fileMetadata.getDataFile().getStorageIdentifier() != null) {
if (fileMetadata.getDataFile().getStorageIdentifier().equals(dataset.getFiles().get(i).getStorageIdentifier())) {
dataset.getFiles().set(i, fileMetadata.getDataFile());
}
}
}
}
tabularDataTagsUpdated = false;
}

// Remove / delete any files that were removed
for (FileMetadata fmd : filesToBeDeleted) {
// check if this file is being used as the default thumbnail
if (fmd.getDataFile().equals(dataset.getThumbnailFile())) {
logger.fine("deleting the dataset thumbnail designation");
dataset.setThumbnailFile(null);
}
Map<Long, String> deleteStorageLocations = null;

if (!fmd.getDataFile().isReleased()) {
// if file is draft (ie. new to this version, delete; otherwise just remove
// filemetadata object)
boolean deleteCommandSuccess = false;
Long dataFileId = fmd.getDataFile().getId();
String deleteStorageLocation = null;

if (dataFileId != null) { // is this check necessary?

deleteStorageLocation = datafileService.getPhysicalFileToDelete(fmd.getDataFile());

try {
commandEngine.submit(new DeleteDataFileCommand(fmd.getDataFile(), dvRequestService.getDataverseRequest()));
dataset.getFiles().remove(fmd.getDataFile());
workingVersion.getFileMetadatas().remove(fmd);
// added this check to handle an issue where you could not delete a file that
// shared a category with a new file
// the relationship does not seem to cascade, yet somehow it was trying to merge
// the filemetadata
// todo: clean this up some when we clean the create / update dataset methods
for (DataFileCategory cat : dataset.getCategories()) {
cat.getFileMetadatas().remove(fmd);
}
deleteCommandSuccess = true;
} catch (CommandException cmde) {
// TODO:
// add diagnostics reporting for individual data files that
// we failed to delete.
logger.warning("Failed to delete DataFile id=" + dataFileId + " from the database; " + cmde.getMessage());
}
if (deleteCommandSuccess) {
if (deleteStorageLocation != null) {
// Finalize the delete of the physical file
// (File service will double-check that the datafile no
// longer exists in the database, before proceeding to
// delete the physical file)
try {
datafileService.finalizeFileDelete(dataFileId, deleteStorageLocation);
} catch (IOException ioex) {
logger.warning("Failed to delete the physical file associated with the deleted datafile id="
+ dataFileId + ", storage location: " + deleteStorageLocation);
}
}
}
}
} else {
datafileService.removeFileMetadata(fmd);
fmd.getDataFile().getFileMetadatas().remove(fmd);
workingVersion.getFileMetadatas().remove(fmd);
}
}
if (!filesToBeDeleted.isEmpty()) {
deleteStorageLocations = datafileService.getPhysicalFilesToDelete(filesToBeDeleted);
}

String saveErrorString = saveError.toString();
if (saveErrorString != null && !saveErrorString.isEmpty()) {
logger.log(Level.INFO, "Couldn''t save dataset: {0}", saveErrorString);
populateDatasetUpdateFailureMessage();
return null;
}
Command<Dataset> cmd;
try {
cmd = new UpdateDatasetVersionCommand(dataset, dvRequestService.getDataverseRequest(), filesToBeDeleted, clone);
((UpdateDatasetVersionCommand) cmd).setValidateLenient(true);
dataset = commandEngine.submit(cmd);

} catch (EJBException ex) {
StringBuilder error = new StringBuilder();
error.append(ex).append(" ");
error.append(ex.getMessage()).append(" ");
Throwable cause = ex;
while (cause.getCause() != null) {
cause = cause.getCause();
error.append(cause).append(" ");
error.append(cause.getMessage()).append(" ");
}
logger.log(Level.INFO, "Couldn''t save dataset: {0}", error.toString());
populateDatasetUpdateFailureMessage();
return null;
} catch (CommandException ex) {
// FacesContext.getCurrentInstance().addMessage(null, new
// FacesMessage(FacesMessage.SEVERITY_ERROR, "Dataset Save Failed", " - " +
// ex.toString()));
logger.log(Level.INFO, "Couldn''t save dataset: {0}", ex.getMessage());
populateDatasetUpdateFailureMessage();
return null;
}

// Refresh the instance of the dataset object:
// (being in the UPLOAD mode more or less guarantees that the
// dataset object already exists in the database, but we'll check
// the id for null, just in case)
if (mode == FileEditMode.UPLOAD) {
if (dataset.getId() != null) {
dataset = datasetService.find(dataset.getId());
}
}
} finally {
datasetService.removeDatasetLocks(dataset, DatasetLock.Reason.EditInProgress);
}
// Have we just deleted some draft datafiles (successfully)?
// finalize the physical file deletes:
// (DataFileService will double-check that the datafiles no
// longer exist in the database, before attempting to delete
// the physical files)
if (deleteStorageLocations != null) {
datafileService.finalizeFileDeletes(deleteStorageLocations);
}

saveEnabled = false;

if (newFiles.size() > 0) {
logger.fine("clearing newfiles list.");
Expand Down Expand Up @@ -1431,11 +1289,6 @@ public String save() {
return returnToFileLandingPage();
}

//if (newDraftVersion) {
// return returnToDraftVersionById();
//}
// indexService.indexDataset(dataset, true);
// indexing is handled by the commands
logger.fine("Redirecting to the dataset page, from the edit/upload page.");
return returnToDraftVersion();
}
Expand Down Expand Up @@ -2502,8 +2355,6 @@ public void saveAsDesignatedThumbnail() {
logger.fine(successMessage);
successMessage = successMessage.replace("{0}", fileMetadataSelectedForThumbnailPopup.getLabel());
JsfHelper.addFlashMessage(successMessage);

datasetUpdateRequired = true;
}

// And reset the selected fileMetadata:
Expand Down Expand Up @@ -2747,8 +2598,6 @@ public void saveFileTagsAndCategories() {
// ignore
}
}

datasetUpdateRequired = true;
}

fileMetadataSelectedForTagsPopup = null;
Expand Down