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CLARIN-DSpace v9/Restore the fork health checks taken wholesale from vanilla (23 of 26 report-diff mappings have no emitter) #1439

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57 changes: 39 additions & 18 deletions dspace-api/src/main/java/org/dspace/health/InfoCheck.java
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Original file line number Diff line number Diff line change
Expand Up @@ -8,13 +8,14 @@
package org.dspace.health;

import java.io.File;
import java.time.Instant;
import java.time.format.DateTimeFormatter;
import java.time.LocalDateTime;

import org.apache.commons.io.FileUtils;
import org.dspace.services.ConfigurationService;
import org.dspace.storage.bitstore.DSBitStoreService;
import org.dspace.utils.DSpace;
import org.json.JSONArray;
import org.json.JSONObject;

/**
* @author LINDAT/CLARIN dev team
Expand All @@ -26,51 +27,71 @@ public String run(ReportInfo ri) {
ConfigurationService configurationService
= new DSpace().getConfigurationService();
StringBuilder sb = new StringBuilder();
sb.append("Generated: ").append(
Instant.now().toString()
).append("\n");
JSONObject root = new JSONObject();

sb.append("From - Till: ").append(
DateTimeFormatter.ISO_LOCAL_DATE.format(ri.from())
).append(" - ").append(
DateTimeFormatter.ISO_LOCAL_DATE.format(ri.till())
).append("\n");
String generatedStr = LocalDateTime.now().format(DateFormatConstants.DATETIME_FORMATTER);
sb.append("Generated: ").append(generatedStr).append("\n");
root.put("generated", generatedStr);

sb.append("Url: ").append(
configurationService.getProperty("dspace.ui.url")
).append("\n");
String fromTill = "From - Till: "
+ ri.from().format(DateFormatConstants.DATE_FORMATTER)
+ " - " + ri.till().format(DateFormatConstants.DATE_FORMATTER);
sb.append(fromTill).append("\n");
root.put("fromTill", fromTill);

String urlValue = configurationService.getProperty("dspace.ui.url");
sb.append("Url: ").append(urlValue).append("\n");
sb.append("\n");
root.put("url", urlValue);

DSBitStoreService localStore = new DSpace().getServiceManager()
.getServicesByType(DSBitStoreService.class)
.get(0);

// Build the directory stats array. report-diff-fields.json addresses these positionally
// (directoryStats/0 = assetstore, directoryStats/1 = log dir), so an entry is appended for
// every directory even when it cannot be read - dropping one would shift the other's index.
JSONArray dirStatsArray = new JSONArray();
for (String[] ss : new String[][] {
new String[] {
localStore.getBaseDir().toString(),
"Assetstore size",},
new String[] {
configurationService.getProperty("log.report.dir"),
"Log dir size",},}) {
JSONObject oneStat = new JSONObject();
oneStat.put("label", ss[1]);

if (ss[0] != null) {
try {
File dir = new File(ss[0]);
if (dir.exists()) {
long dir_size = FileUtils.sizeOfDirectory(dir);
sb.append(String.format("%-20s: %s\n", ss[1],
FileUtils.byteCountToDisplaySize(dir_size))
String displaySize = FileUtils.byteCountToDisplaySize(dir_size);
sb.append(String.format("%-20s: %s\n", ss[1], displaySize)
);
oneStat.put("path", ss[0]);
oneStat.put("size_bytes", dir_size);
oneStat.put("size_display", displaySize);
} else {
sb.append(String.format("Directory [%s] does not exist!\n", ss[0]));
String msg = String.format("Directory %s does not exist!", ss[0]);
oneStat.put("path", ss[0]);
oneStat.put("notExist", msg);
sb.append(msg).append("\n");
}
} catch (Exception e) {
error(e, "directory - " + ss[0]);
}
} else { // cannot read property for some reason
sb.append(String.format("Could not get information for %s!\n", ss[1]));
String msg = String.format("Could not get information for %s!\n", ss[1]);
sb.append(msg);
oneStat.put("warning", msg);
}
dirStatsArray.put(oneStat);
}
root.put("directoryStats", dirStatsArray);

this.setReportJson(root);
return sb.toString();
}

}
161 changes: 110 additions & 51 deletions dspace-api/src/main/java/org/dspace/health/ItemCheck.java
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Original file line number Diff line number Diff line change
Expand Up @@ -35,6 +35,8 @@
import org.dspace.handle.service.HandleService;
import org.dspace.xmlworkflow.factory.XmlWorkflowServiceFactory;
import org.dspace.xmlworkflow.storedcomponents.service.XmlWorkflowItemService;
import org.json.JSONArray;
import org.json.JSONObject;

/**
* @author LINDAT/CLARIN dev team
Expand All @@ -57,88 +59,124 @@ public class ItemCheck extends Check {

@Override
public String run(ReportInfo ri) {
String ret = "";
StringBuilder sb = new StringBuilder();
JSONObject root = new JSONObject();
int tot_cnt = 0;
Context context = new Context();
try {
JSONArray communitiesArray = new JSONArray();
for (Map.Entry<String, Integer> name_count : getCommunities(context)) {
ret += String.format("Community [%s]: %d\n",
name_count.getKey(), name_count.getValue());
tot_cnt += name_count.getValue();
String comName = name_count.getKey();
int comSize = name_count.getValue();
sb.append(String.format("Community [%s]: %d\n", comName, comSize));
tot_cnt += comSize;
JSONObject oneCommunity = new JSONObject();
oneCommunity.put("name", comName);
oneCommunity.put("size", comSize);
communitiesArray.put(oneCommunity);
}
root.put("communities", communitiesArray);
} catch (SQLException e) {
error(e);
}

try {
ret += "\nCollection sizes:\n";
ret += getCollectionSizesInfo(context);
JSONObject colSizesInfo = new JSONObject();
sb.append("\nCollection sizes:\n");
sb.append(getCollectionSizesInfo(context, colSizesInfo));
root.put("collectionsSizesInfo", colSizesInfo);
} catch (SQLException e) {
error(e);
}

ret += String.format(
"\nPublished items (archived, not withdrawn): %d\n", tot_cnt);
sb.append(String.format("\nPublished items (archived, not withdrawn): %d\n", tot_cnt));
root.put("publishedItems", tot_cnt);
try {
ret += String.format(
"Withdrawn items: %d\n", itemService.countWithdrawnItems(context));
ret += String.format(
"Not published items (in workspace or workflow mode): %d\n",
itemService.countNotArchivedItems(context));
int withdrawnItems = itemService.countWithdrawnItems(context);
sb.append(String.format("Withdrawn items: %d\n", withdrawnItems));
root.put("withdrawnItems", withdrawnItems);

int notPublishedItems = itemService.countNotArchivedItems(context);
sb.append(String.format("Not published items (in workspace or workflow mode): %d\n", notPublishedItems));
root.put("notPublishedItems", notPublishedItems);

JSONArray stagesCountArray = new JSONArray();
for (Map.Entry<Integer, Long> row : workspaceItemService.getStageReachedCounts(context)) {
ret += String.format("\tIn Stage %s: %s\n",
row.getKey(), //"stage_reached"
row.getValue() //"cnt"
);
sb.append(String.format("\tIn Stage %s: %s\n",
row.getKey(), //"stage_reached"
row.getValue() //"cnt"
));
JSONObject oneStage = new JSONObject();
oneStage.put("stage", row.getKey());
oneStage.put("count", row.getValue());
stagesCountArray.put(oneStage);
}
root.put("stagesCounts", stagesCountArray);

ret += String.format(
"\tWaiting for approval (workflow items): %d\n",
workflowItemService.countAll(context));
int waitingForApprovalCount = workflowItemService.countAll(context);
sb.append(String.format("\tWaiting for approval (workflow items): %d\n", waitingForApprovalCount));
root.put("waitingForApproval", waitingForApprovalCount);

} catch (SQLException e) {
error(e);
}

try {
ret += getObjectSizesInfo(context);
sb.append(getObjectSizesInfo(context, root));
context.complete();
} catch (SQLException e) {
error(e);
}
return ret;

this.setReportJson(root);
return sb.toString();
}


public String getObjectSizesInfo(Context context) throws SQLException {
/**
* Appends the entity counts to the human-readable report and puts each of them into {@code jo} under
* the key {@code report-diff-fields.json} addresses it by.
*
* @param context current DSpace session
* @param jo the check's JSON report, extended in place
* @return the human-readable section of the report
* @throws SQLException passed through so that {@link #run(ReportInfo)} records it with
* {@link Check#error(Throwable)} and still finishes the rest of the report
*/
public String getObjectSizesInfo(Context context, JSONObject jo) throws SQLException {
StringBuilder sb = new StringBuilder();
sb.append(String.format("Count %-14s: %s\n", "Bitstream",
String.valueOf(bitstreamService.countTotal(context))));
sb.append(String.format("Count %-14s: %s\n", "Bundle",
String.valueOf(bundleService.countTotal(context))));
sb.append(String.format("Count %-14s: %s\n", "Collection",
String.valueOf(collectionService.countTotal(context))));
sb.append(String.format("Count %-14s: %s\n", "Community",
String.valueOf(communityService.countTotal(context))));
sb.append(String.format("Count %-14s: %s\n", "MetadataValue",
String.valueOf(metadataValueService.countTotal(context))));
sb.append(String.format("Count %-14s: %s\n", "EPerson",
String.valueOf(ePersonService.countTotal(context))));
sb.append(String.format("Count %-14s: %s\n", "Item",
String.valueOf(itemService.countTotal(context))));
sb.append(String.format("Count %-14s: %s\n", "Handle",
String.valueOf(handleService.countTotal(context))));
sb.append(String.format("Count %-14s: %s\n", "Group",
String.valueOf(groupService.countTotal(context))));
sb.append(String.format("Count %-14s: %s\n", "BasicWorkflowItem",
String.valueOf(workflowItemService.countAll(context))));
sb.append(String.format("Count %-14s: %s\n", "WorkspaceItem",
String.valueOf(workspaceItemService.countTotal(context))));
sb.append(countLine(jo, "Bitstream", "bitstreamsCount", bitstreamService.countTotal(context)));
sb.append(countLine(jo, "Bundle", "bundlesCount", bundleService.countTotal(context)));
sb.append(countLine(jo, "Collection", "collectionsCount", collectionService.countTotal(context)));
sb.append(countLine(jo, "Community", "communitiesCount", communityService.countTotal(context)));
sb.append(countLine(jo, "MetadataValue", "metadataValuesCount", metadataValueService.countTotal(context)));
sb.append(countLine(jo, "EPerson", "ePersonsCount", ePersonService.countTotal(context)));
sb.append(countLine(jo, "Item", "itemsCount", itemService.countTotal(context)));
sb.append(countLine(jo, "Handle", "handlesCount", handleService.countTotal(context)));
sb.append(countLine(jo, "Group", "groupsCount", groupService.countTotal(context)));
sb.append(countLine(jo, "BasicWorkflowItem", "basicWorkflowItemsCount", workflowItemService.countAll(context)));
sb.append(countLine(jo, "WorkspaceItem", "workspaceItemsCount", workspaceItemService.countTotal(context)));
return sb.toString();
}

public String getCollectionSizesInfo(final Context context) throws SQLException {
/**
* Emits one count into both halves of the report: the formatted text line and the JSON key.
*/
private String countLine(JSONObject jo, String displayName, String jsonKey, int count) {
jo.put(jsonKey, count);
return String.format("Count %-20s: %s\n", displayName, String.valueOf(count));
}

/**
* Appends the per-collection sizes to the human-readable report and puts the aggregate numbers into
* {@code jo}, which {@link #run(ReportInfo)} stores under {@code collectionsSizesInfo}.
*
* @param context current DSpace session
* @param jo the {@code collectionsSizesInfo} object, extended in place
* @return the human-readable section of the report
* @throws SQLException passed through, see {@link #getObjectSizesInfo(Context, JSONObject)}
*/
public String getCollectionSizesInfo(final Context context, JSONObject jo) throws SQLException {
final StringBuffer ret = new StringBuffer();
List<Map.Entry<Collection, Long>> colBitSizes = collectionService
.getCollectionsWithBitstreamSizesTotal(context);
Expand All @@ -157,31 +195,52 @@ public int compare(Map.Entry<Collection, Long> o1, Map.Entry<Collection, Long> o
return 0;
}
});

JSONArray collectionsSizesArray = new JSONArray();
for (Map.Entry<Collection, Long> row : colBitSizes) {
Long size = row.getValue();
total_size += size;
Collection col = row.getKey();
String colPath = CollectionDropDown.collectionPath(context, col);
String colSize = FileUtils.byteCountToDisplaySize((long) size);
ret.append(String.format(
"\t%s: %s\n", CollectionDropDown.collectionPath(context, col),
FileUtils.byteCountToDisplaySize((long) size)));
"\t%s: %s\n", colPath, colSize));
JSONObject oneColSize = new JSONObject();
oneColSize.put("path", colPath);
oneColSize.put("size", colSize);
collectionsSizesArray.put(oneColSize);
}
jo.put("collectionSizes", collectionsSizesArray);

String totalSizeToDisplay = FileUtils.byteCountToDisplaySize(total_size);
ret.append(String.format(
"Total size: %s\n", FileUtils.byteCountToDisplaySize(total_size)));
"Total size: %s\n", totalSizeToDisplay));
jo.put("totalSize", totalSizeToDisplay);

int resourceWOPolicyCount = bitstreamService.countBitstreamsWithoutPolicy(context);
ret.append(String.format(
"Resource without policy: %d\n", bitstreamService.countBitstreamsWithoutPolicy(context)));
"Resource without policy: %d\n", resourceWOPolicyCount));
jo.put("resourceWOPolicy", resourceWOPolicyCount);

int deletedBitstreamsCount = bitstreamService.countDeletedBitstreams(context);
ret.append(String.format(
"Deleted bitstreams: %d\n", bitstreamService.countDeletedBitstreams(context)));
"Deleted bitstreams: %d\n", deletedBitstreamsCount));
jo.put("deletedBitstreams", deletedBitstreamsCount);

String list_str = "";
JSONArray orphanBitstreamsArray = new JSONArray();
List<Bitstream> bitstreamOrphans = bitstreamService.getNotReferencedBitstreams(context);
for (Bitstream orphan : bitstreamOrphans) {
UUID id = orphan.getID();
JSONObject oneOrphanBitstream = new JSONObject();
oneOrphanBitstream.put("uuid", id.toString());
orphanBitstreamsArray.put(oneOrphanBitstream);
list_str += String.format("%s, ", id);
}
ret.append(String.format(
"Orphan bitstreams: %d [%s]\n", bitstreamOrphans.size(), list_str));
jo.put("orphanBitstreamsCount", bitstreamOrphans.size());
jo.put("orphanBitstreams", orphanBitstreamsArray);

return ret.toString();
}
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