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Merge pull request #7312 from IQSS/7081-file-metadata-include
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Checksum truncation, click to copy + file metadata fragment code consolidation
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@kcondon
kcondon authored Feb 3, 2021
2 parents 1b18bfb + e9e99b4 commit 78a1044
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Showing 16 changed files with 432 additions and 487 deletions.
2 changes: 1 addition & 1 deletion src/main/java/edu/harvard/iq/dataverse/DataFileServiceBean.java
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Original file line number Diff line number Diff line change
Expand Up @@ -497,7 +497,7 @@ public DataFile findCheapAndEasy(Long id) {
// If content type indicates it's tabular data, spend 2 extra queries
// looking up the data table and tabular tags objects:

if (MIME_TYPE_TSV.equalsIgnoreCase(contentType)) {
if (MIME_TYPE_TSV.equalsIgnoreCase(contentType) || MIME_TYPE_TSV_ALT.equalsIgnoreCase(contentType)) {
Object[] dtResult;
try {
dtResult = (Object[]) em.createNativeQuery("SELECT ID, UNF, CASEQUANTITY, VARQUANTITY, ORIGINALFILEFORMAT, ORIGINALFILESIZE FROM dataTable WHERE DATAFILE_ID = " + id).getSingleResult();
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19 changes: 1 addition & 18 deletions src/main/java/edu/harvard/iq/dataverse/DatasetPage.java
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Original file line number Diff line number Diff line change
Expand Up @@ -1310,15 +1310,6 @@ public boolean isSuperUser(){
}
return false;
}
/*
TODO/OPTIMIZATION: This is still costing us N SELECT FROM GuestbookResponse queries,
where N is the number of files. This could of course be replaced by a query that'll
look up all N at once... Not sure if it's worth it; especially now that N
will always be 10, for the initial page load. -- L.A. 4.2.1
*/
public Long getGuestbookResponseCount(FileMetadata fileMetadata) {
return guestbookResponseService.getCountGuestbookResponsesByDataFileId(fileMetadata.getDataFile().getId());
}
/**
* Check Dataset related permissions
*
Expand Down Expand Up @@ -5107,15 +5098,7 @@ public String getPrivateUrlLink(PrivateUrl privateUrl) {
}


public FileDownloadHelper getFileDownloadHelper() {
return fileDownloadHelper;
}

public void setFileDownloadHelper(FileDownloadHelper fileDownloadHelper) {
this.fileDownloadHelper = fileDownloadHelper;
}


// todo: we should be able to remove - this is passed in the html pages to other fragments, but they could just access this service bean directly.
public FileDownloadServiceBean getFileDownloadService() {
return fileDownloadService;
}
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65 changes: 10 additions & 55 deletions src/main/java/edu/harvard/iq/dataverse/DatasetVersionDifference.java
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Original file line number Diff line number Diff line change
Expand Up @@ -36,7 +36,6 @@ public final class DatasetVersionDifference {
private List<String[]> changedTermsAccess = new ArrayList<>();
private List<Object[]> summaryDataForNote = new ArrayList<>();
private List<Object[]> blockDataForNote = new ArrayList<>();
String noFileDifferencesFoundLabel = "";

private VariableMetadataUtil variableMetadataUtil;

Expand Down Expand Up @@ -104,7 +103,6 @@ public DatasetVersionDifference(DatasetVersion newVersion, DatasetVersion origin
addToSummary(null, dsfn);
}
}


// TODO: ?
// It looks like we are going through the filemetadatas in both versions,
Expand Down Expand Up @@ -493,7 +491,6 @@ private void addToSummary(DatasetField dsfo, DatasetField dsfn) {
}

private void updateBlockSummary(DatasetField dsf, int added, int deleted, int changed) {

boolean addedToAll = false;
for (Object[] blockList : blockDataForNote) {
DatasetField dsft = (DatasetField) blockList[0];
Expand All @@ -512,7 +509,6 @@ private void updateBlockSummary(DatasetField dsf, int added, int deleted, int ch
newArray[3] = changed;
blockDataForNote.add(newArray);
}

}

private void addToNoteSummary(DatasetField dsfo, int added, int deleted, int changed) {
Expand Down Expand Up @@ -552,8 +548,6 @@ private boolean compareVarGroup(FileMetadata fmdo, FileMetadata fmdn) {
}
}



private boolean compareFileMetadatas(FileMetadata fmdo, FileMetadata fmdn) {

if (!StringUtils.equals(fmdo.getDescription(), fmdn.getDescription())) {
Expand Down Expand Up @@ -786,7 +780,6 @@ private void initDatasetFilesDifferencesList() {
datasetFilesDiffList = new ArrayList<>();
datasetFilesReplacementList = new ArrayList <>();


// Study Files themselves are version-less;
// In other words, 2 different versions can have different sets of
// study files, but the files themselves don't have versions.
Expand All @@ -798,13 +791,6 @@ private void initDatasetFilesDifferencesList() {
// same study file, the file metadatas ARE version-specific, so some of
// the fields there (filename, etc.) may be different. If this is the
// case, we want to display these differences as well.

if (originalVersion.getFileMetadatas().isEmpty() && newVersion.getFileMetadatas().isEmpty()) {
noFileDifferencesFoundLabel = "No data files in either version of the study";
return;
}



int i = 0;
int j = 0;
Expand All @@ -825,7 +811,6 @@ private void initDatasetFilesDifferencesList() {

if (!replacedFiles.isEmpty()) {


replacedFiles.stream().map((replacedPair) -> {
FileMetadata replacedFile = replacedPair[0];
FileMetadata newFile = replacedPair[1];
Expand All @@ -851,7 +836,6 @@ private void initDatasetFilesDifferencesList() {

}


Collections.sort(fileMetadatasOriginal, (FileMetadata l1, FileMetadata l2) -> {
FileMetadata fm3 = l1; //(DatasetField[]) l1.get(0);
FileMetadata fm4 = l2;
Expand All @@ -871,7 +855,6 @@ private void initDatasetFilesDifferencesList() {
// added file. Since we are only doing this for the purposes of generating
// version differences, this should be OK.
// -- L.A. Aug. 2014


Collections.sort(fileMetadatasNew, (FileMetadata l1, FileMetadata l2) -> {
FileMetadata fm3 = l1; //(DatasetField[]) l1.get(0);
Expand Down Expand Up @@ -964,14 +947,6 @@ private void initDatasetFilesDifferencesList() {

j++;
}





if (datasetFilesDiffList.isEmpty()) {
noFileDifferencesFoundLabel = "These study versions have identical sets of data files";
}
}

private boolean fileMetadataIsDifferent(FileMetadata fm1, FileMetadata fm2) {
Expand Down Expand Up @@ -1080,12 +1055,8 @@ private boolean fileMetadataIsDifferent(FileMetadata fm1, FileMetadata fm2) {
return true;
}

//File restrictions

value1 = fm1.isRestricted() ? "Restricted" : "Not Restricted";
value2 = fm2.isRestricted() ? "Restricted" : "Not Restricted";

return !value1.equals(value2);
// File restrictions
return fm1.isRestricted() != fm2.isRestricted();
}

private datasetFileDifferenceItem selectFileMetadataDiffs(FileMetadata fm1, FileMetadata fm2) {
Expand All @@ -1109,7 +1080,7 @@ private datasetFileDifferenceItem selectFileMetadataDiffs(FileMetadata fm1, File
}

fdi.setFileProvFree1(fm1.getProvFreeForm());
fdi.setFileRest1(fm1.isRestricted() ? "Restricted" : "Not Restricted");
fdi.setFileRest1(fm1.isRestricted() ? BundleUtil.getStringFromBundle("restricted") : BundleUtil.getStringFromBundle("public"));
fdi.setFile2Empty(true);

} else if (fm1 == null) {
Expand All @@ -1125,7 +1096,7 @@ private datasetFileDifferenceItem selectFileMetadataDiffs(FileMetadata fm1, File
fdi.setFileCat2(fm2.getCategoriesByName().toString());
}
fdi.setFileProvFree2(fm2.getProvFreeForm());
fdi.setFileRest2(fm2.isRestricted() ? "Restricted" : "Not Restricted");
fdi.setFileRest2(fm2.isRestricted() ? BundleUtil.getStringFromBundle("restricted") : BundleUtil.getStringFromBundle("public"));
} else {
// Both are non-null metadata objects.
// We simply go through the 5 metadata fields, if any are
Expand Down Expand Up @@ -1206,11 +1177,9 @@ private datasetFileDifferenceItem selectFileMetadataDiffs(FileMetadata fm1, File
}

// file restricted:
value1 = fm1.isRestricted() ? "Restricted" : "Not Restricted";
value2 = fm2.isRestricted() ? "Restricted" : "Not Restricted";
if (!value1.equals(value2)) {
fdi.setFileRest1(value1);
fdi.setFileRest2(value2);
if (fm1.isRestricted() != fm2.isRestricted() ) {
fdi.setFileRest1(fm1.isRestricted() ? BundleUtil.getStringFromBundle("restricted") : BundleUtil.getStringFromBundle("public"));
fdi.setFileRest2(fm2.isRestricted() ? BundleUtil.getStringFromBundle("restricted") : BundleUtil.getStringFromBundle("public"));
}
}
return fdi;
Expand Down Expand Up @@ -1314,7 +1283,7 @@ public String getEditSummaryForLog() {
}

if (item.fileRest1 != null || item.fileRest2 != null) {
itemDiff += System.lineSeparator() + " " + BundleUtil.getStringFromBundle("file.viewDiffDialog.restricted") + ": ";
itemDiff += System.lineSeparator() + " " + BundleUtil.getStringFromBundle("file.viewDiffDialog.fileAccess") + ": ";
itemDiff += item.fileRest1 != null ? item.fileRest1 : BundleUtil.getStringFromBundle("file.viewDiffDialog.notAvailable");
itemDiff += " : ";
itemDiff += item.fileRest2 != null ? item.fileRest2 : BundleUtil.getStringFromBundle("file.viewDiffDialog.notAvailable") + " ";
Expand Down Expand Up @@ -1356,7 +1325,7 @@ public String getEditSummaryForLog() {
itemDiff += item.fdi.fileProvFree1 != null ? item.fdi.fileProvFree1 : BundleUtil.getStringFromBundle("file.viewDiffDialog.notAvailable");
itemDiff += " : ";
itemDiff += item.fdi.fileProvFree2 != null ? item.fdi.fileProvFree2 : BundleUtil.getStringFromBundle("file.viewDiffDialog.notAvailable") + " ";
itemDiff += System.lineSeparator() + " " + BundleUtil.getStringFromBundle("file.viewDiffDialog.restricted") + ": ";
itemDiff += System.lineSeparator() + " " + BundleUtil.getStringFromBundle("file.viewDiffDialog.fileAccess") + ": ";
itemDiff += item.fdi.fileRest1 != null ? item.fdi.fileRest1 : BundleUtil.getStringFromBundle("file.viewDiffDialog.notAvailable");
itemDiff += " : ";
itemDiff += item.fdi.fileRest2 != null ? item.fdi.fileRest2 : BundleUtil.getStringFromBundle("file.viewDiffDialog.notAvailable") + " ";
Expand All @@ -1377,12 +1346,11 @@ public String getEditSummaryForLog() {
retVal +=termsOfUseDiff;
}


return retVal;
}


public class DifferenceSummaryGroup{
public class DifferenceSummaryGroup {

private String displayName;
private String type;
Expand Down Expand Up @@ -1411,8 +1379,6 @@ public List<DifferenceSummaryItem> getDifferenceSummaryItems() {
public void setDifferenceSummaryItems(List<DifferenceSummaryItem> differenceSummaryItems) {
this.differenceSummaryItems = differenceSummaryItems;
}


}

public class DifferenceSummaryItem {
Expand Down Expand Up @@ -1470,9 +1436,6 @@ public boolean isMultiple() {
public void setMultiple(boolean multiple) {
this.multiple = multiple;
}



}

public class datasetReplaceFileItem {
Expand Down Expand Up @@ -1733,7 +1696,6 @@ public String getFileChecksumValue() {
public void setFileChecksumValue(String fileChecksumValue) {
this.fileChecksumValue = fileChecksumValue;
}

}

public List<datasetFileDifferenceItem> getDatasetFilesDiffList() {
Expand All @@ -1744,11 +1706,4 @@ public void setDatasetFilesDiffList(List<datasetFileDifferenceItem> datasetFiles
this.datasetFilesDiffList = datasetFilesDiffList;
}

public String getNoFileDifferencesFoundLabel() {
return noFileDifferencesFoundLabel;
}

public void setNoFileDifferencesFoundLabel(String noFileDifferencesFoundLabel) {
this.noFileDifferencesFoundLabel = noFileDifferencesFoundLabel;
}
}
14 changes: 0 additions & 14 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 @@ -2453,20 +2453,6 @@ public boolean isLocked() {
return false;
}

public boolean isThumbnailAvailable(FileMetadata fileMetadata) {
// new and optimized logic:
// - check download permission here (should be cached - so it's free!)
// - only then ask the file service if the thumbnail is available/exists.
// the service itself no longer checks download permissions.
if (!fileDownloadHelper.canDownloadFile(fileMetadata)) {
return false;
}

return datafileService.isThumbnailAvailable(fileMetadata.getDataFile());
}



private Boolean lockedFromEditsVar;

public boolean isLockedFromEdits() {
Expand Down
37 changes: 18 additions & 19 deletions src/main/java/edu/harvard/iq/dataverse/search/SearchIncludeFragment.java
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Original file line number Diff line number Diff line change
Expand Up @@ -1201,53 +1201,52 @@ public SearchException getSearchException() {
}

public String tabularDataDisplayInfo(DataFile datafile) {
String ret = "";
String tabInfo = "";

if (datafile == null) {
return null;
return "";
}

if (datafile.isTabularData() && datafile.getDataTable() != null) {
DataTable datatable = datafile.getDataTable();
String unf = datatable.getUnf();
Long varNumber = datatable.getVarQuantity();
Long obsNumber = datatable.getCaseQuantity();
if (varNumber != null && varNumber.intValue() != 0) {
ret = ret.concat(varNumber + " Variables");
tabInfo = tabInfo.concat(varNumber + " " + BundleUtil.getStringFromBundle("file.metaData.dataFile.dataTab.variables"));
if (obsNumber != null && obsNumber.intValue() != 0) {
ret = ret.concat(", " + obsNumber + " Observations");
tabInfo = tabInfo.concat(", " + obsNumber + " " + BundleUtil.getStringFromBundle("file.metaData.dataFile.dataTab.observations"));
}
ret = ret.concat(" - ");
}
if (unf != null && !unf.equals("")) {
ret = ret.concat("UNF: " + unf);
}
}

return ret;
return tabInfo;
}

public String tabularDataUnfDisplay(DataFile datafile) {
String tabUnf = "";

public String dataFileSizeDisplay(DataFile datafile) {
if (datafile == null) {
return "";
}

return datafile.getFriendlySize();
if (datafile.isTabularData() && datafile.getDataTable() != null) {
DataTable datatable = datafile.getDataTable();
String unf = datatable.getUnf();
if (unf != null && !unf.equals("")) {
tabUnf = tabUnf.concat(unf);
}
}

return tabUnf;
}

public String dataFileChecksumDisplay(DataFile datafile) {
public String dataFileSizeDisplay(DataFile datafile) {
if (datafile == null) {
return "";
}

if (datafile.getChecksumValue() != null && !StringUtils.isEmpty(datafile.getChecksumValue())) {
if (datafile.getChecksumType() != null) {
return " " + datafile.getChecksumType() + ": " + datafile.getChecksumValue() + " ";
}
}
return datafile.getFriendlySize();

return "";
}

public void setDisplayCardValues() {
Expand Down
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