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WIP editing new healthchecks
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Matus Kasak committed Dec 19, 2024
1 parent b1f0978 commit abc6c39
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Showing 24 changed files with 9,938 additions and 14 deletions.
4 changes: 4 additions & 0 deletions dspace-api/src/main/java/org/dspace/health/AdditionalInfoCheck.java
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Expand Up @@ -7,12 +7,16 @@
*/
package org.dspace.health;

import org.dspace.health.additionalUtilities.Info;

public class AdditionalInfoCheck extends Check {

@Override
protected String run(ReportInfo ri) {
String output = "";

output += String.format(
"Server uptime: %s\n", Info.get_proc_uptime());
output += String.format(
"JVM uptime: %s\n", Info.get_jvm_uptime());
output += String.format(
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14 changes: 9 additions & 5 deletions dspace-api/src/main/java/org/dspace/health/OAIPMHCheck.java
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Expand Up @@ -7,9 +7,12 @@
*/
package org.dspace.health;

import org.dspace.health.additionalUtilities.IOUtils;
import org.dspace.services.ConfigurationService;
import org.dspace.services.factory.DSpaceServicesFactory;

import java.io.File;

public class OAIPMHCheck extends Check {
protected static final ConfigurationService configurationService
= DSpaceServicesFactory.getInstance().getConfigurationService();
Expand All @@ -18,14 +21,15 @@ public class OAIPMHCheck extends Check {
protected String run(ReportInfo ri) {
String output = "";
String dspace_dir = configurationService.getProperty("dspace.dir");
System.out.println("Dspace dir " + dspace_dir);
String dspace_url = configurationService.getProperty("dspace.server.url");
System.out.println("Dspace url " + dspace_url);
String oaiurl = dspace_url + "/oai/request";
System.out.println("Dspace oai " + oaiurl);
output += String.format("Trying [%s]\n", oaiurl);
//output += IOUtils.run(new File(dspace_dir + "/bin/"), new String[]{
// "python", "./validators/oai_pmh/validate.py", oaiurl});

File scriptDir = new File(
"C:\\WorkSpace\\DSpace\\dspace-api\\src\\main\\java\\org\\dspace\\health\\additionalUtilities\\");

output += IOUtils.runScript(scriptDir, new String[]{
"python", "validate.py", oaiurl});
return output;
}
}
117 changes: 116 additions & 1 deletion dspace-api/src/main/java/org/dspace/health/PIDCheck.java
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*/
package org.dspace.health;

import org.apache.commons.lang.NotImplementedException;
import org.dspace.handle.PIDService;
import org.dspace.health.additionalUtilities.PIDLogMiner;
import org.dspace.health.additionalUtilities.PIDLogStatistics;
import org.dspace.health.additionalUtilities.PIDLogStatisticsEntry;
import org.dspace.services.ConfigurationService;
import org.dspace.services.factory.DSpaceServicesFactory;

import java.text.SimpleDateFormat;
import java.util.Calendar;
import java.util.List;
import java.util.Map;

public class PIDCheck extends Check {
protected static final ConfigurationService configurationService
= DSpaceServicesFactory.getInstance().getConfigurationService();

@Override
protected String run(ReportInfo ri) {
return "";
String output = "";
output += "This is space for PID Check output";
try {
String whoami = PIDService.who_am_i("encoding=xml");
output += String.format("Who am I\n\t%s\n",
whoami.replaceAll("\n", "\n\t"));
String test_pid = configurationService.getProperty("lr.pid.service.testPid");
output += "Testing PID server\n\t";
if (test_pid != null) {
output += PIDService.test_pid(test_pid);
} else {
output += "Testing PID server not done! Test pid not in dspace.cfg!";
}
} catch (IllegalArgumentException e) {
error(e, "Warning: PID service type is not defined or wrong");
} catch (NotImplementedException e) {
error(e, "Testing PID server - method who_am_i not implemented");
} catch (Exception e) {
error(e, "Testing PID server failed - exception occurred: %s");
}

// try {
// long total_count = Core.getHandlesTotalCount();
// output += "\n";
// output += String.format("Total count: %d\n", total_count);
// List<TableRow> invalid_handles = Core.getHandlesInvalidRows();
// output += String.format("Invalid handles count: %d\n",
// invalid_handles.size());
// if (invalid_handles.size() > 0) {
// output += "\n";
// output += "Invalid handles:\n";
// output += "----------------\n";
// output += String.format("%-6s\t%-32s\t%-10s\t%-10s\t%s\n",
// "Handle ID", "Handle", "Res. type ID", "Resource ID",
// "URL");
// for (TableRow row : invalid_handles) {
// int handle_id = row.getIntColumn("handle_id");
// String handle = row.getStringColumn("handle");
//
// Integer resource_type_id = row.getIntColumn("resource_type_id");
// if (resource_type_id < 0)
// resource_type_id = null;
//
// Integer resource_id = row.getIntColumn("resource_id");
// if (resource_id < 0)
// resource_id = null;
//
// String url = row.getStringColumn("url");
// output += String.format("%-10d\t%-32s\t%-10d\t%-10d\t%s\n",
// handle_id, handle, resource_type_id, resource_id,
// url);
// }
// }
// } catch (SQLException e) {
// error(e);
// }

SimpleDateFormat dateFormat = new SimpleDateFormat("yyyy-MM-dd");
Calendar realEndDate = Calendar.getInstance();
realEndDate.setTime(ri.till());
realEndDate.add(Calendar.DATE, -1);

final int topN = 10;
StringBuffer buf = new StringBuffer();
buf.append("============================================================\n");
buf.append(String.format("PID resolution statistics\n"));
buf.append("============================================================\n");
buf.append("\n\n");
PIDLogMiner logMiner = new PIDLogMiner();
PIDLogStatistics statistics = logMiner.computeStatistics(
ri.from(), realEndDate.getTime());
Map<String, List<PIDLogStatisticsEntry>> topNEntries = statistics
.getTopN(topN);
String eventsToDisplay[] = { PIDLogMiner.FAILURE_EVENT,
PIDLogMiner.REQUEST_EVENT, PIDLogMiner.SUCCESS_EVENT,
PIDLogMiner.UNKNOWN_EVENT };
SimpleDateFormat dateTimeFormat = new SimpleDateFormat(
"yyyy-MM-dd HH:mm:ss.SSS");
for (String event : eventsToDisplay) {
if (topNEntries.containsKey(event)) {
buf.append(String.format(
"Top %d events of type %s between %s and %s\n", topN,
event, dateFormat.format(ri.from()),
dateFormat.format(realEndDate.getTime())));
buf.append(String
.format("---------------------------------------------------------------\n"));
buf.append(String.format("%-10s%-40s%-25s%-25s\n", "Count",
"PID", "First occurence", "Last occurence"));
buf.append(String
.format("--------------------------------------------------------------------------------------------------\n"));
for (PIDLogStatisticsEntry entry : topNEntries.get(event)) {
buf.append(String.format("%-10d%-40s%-25s%-25s\n",
entry.getCount(), entry.getPID(),
dateTimeFormat.format(entry.getFirstOccurence()),
dateTimeFormat.format(entry.getLastOccurence())));
}
buf.append("\n");
}
}
return output + buf.toString();
}
}
114 changes: 113 additions & 1 deletion dspace-api/src/main/java/org/dspace/health/ShibbolethCheck.java
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Expand Up @@ -7,9 +7,121 @@
*/
package org.dspace.health;

import org.dspace.services.ConfigurationService;
import org.dspace.services.factory.DSpaceServicesFactory;
//import java.io.BufferedReader;
//import java.io.File;
//import java.io.InputStreamReader;
//import java.io.StringWriter;
//import java.net.URL;
//import java.text.SimpleDateFormat;
//import java.util.Date;
//import java.util.HashSet;
//import java.util.Iterator;
//import java.util.Set;

public class ShibbolethCheck extends Check {

protected static final ConfigurationService configurationService
= DSpaceServicesFactory.getInstance().getConfigurationService();

@Override
protected String run(ReportInfo ri) {
return "";
// StringBuilder ret = new StringBuilder();
// final String input_dir = configurationService.getProperty("lr",
// "lr.shibboleth.log.path");
// final String default_log = configurationService.getProperty("lr",
// "lr.shibboleth.log.defaultName");
//
// String input_file = new File(input_dir, default_log).toString();
//
// ret.append(String.format("Parsing %s:\n", input_file));
// BufferedReader safe_reader = null;
// try {
// safe_reader = IOUtils.safe_reader(input_file);
// // output warnings
// ShibUserLogins user_logins = new ShibUserLogins(safe_reader);
// if (0 < user_logins.warnings().size()) {
// for (String warning : user_logins.warnings()) {
// ret.append(warning + "\n");
// }
// } else {
// ret.append("No shibboleth warnings have been found.\n");
// }
// } catch (Exception e) {
// error(e, String.format("Problematic file [%s]", default_log));
// return ret.toString();
// }
//
// // > WARN from shibd_warn in the last week
// ret.append("\nParsing shibd_warn.*:\n");
// File dir = new File(input_dir);
// String[] files = dir.list(new java.io.FilenameFilter() {
// @Override
// public boolean accept(File dir, String name) {
// return name.contains("shibd_warn");
// }
// });
// Long nowMillis = System.currentTimeMillis();
// String weekAgo = new SimpleDateFormat("yyyy-MM-dd").format(new Date(
// nowMillis - 604800000));
// String[] cmd = new String[] { "awk", "-v", "from=" + weekAgo,
// "BEGIN{FS=\" \"} {if($1>=from) print $0}" };
// String[] cmdWithFiles = new String[cmd.length + files.length];
// System.arraycopy(cmd, 0, cmdWithFiles, 0, cmd.length);
// System.arraycopy(files, 0, cmdWithFiles, cmd.length, files.length);
// try {
// Process child = Runtime.getRuntime().exec(cmdWithFiles, null, dir);
// BufferedReader[] outputs = new BufferedReader[] {
// new BufferedReader(new InputStreamReader(
// child.getInputStream())),
// new BufferedReader(new InputStreamReader(
// child.getErrorStream())) };
// for (BufferedReader out : outputs) {
// String s = null;
// while ((s = out.readLine()) != null) {
// ret.append(s);
// ret.append("\n");
// }
// }
// } catch (java.io.IOException e) {
// error(e);
// }
//
//
// try {
// String feedsConfig = configurationService.getProperty("discojuice", "feeds");
// ret.append(String.format( "Using these static discojuice feeds [%s] as source.\n",
// feedsConfig ));
// // Try to download our feeds file, so the proper action is triggered
// StringWriter writer = new StringWriter();
// org.apache.commons.io.IOUtils.copy(
// new URL(configurationService.getProperty("dspace.url")
// + "/discojuice/feeds").openStream(), writer);
// String json = writer.toString();
// // end download
// Set<String> entities = new HashSet<String>();
// JSONParser parser = new JSONParser();
// JSONArray entityArray = (JSONArray) parser.parse(json);
// Iterator<JSONObject> i = entityArray.iterator();
// int counter = 0;
// while (i.hasNext()) {
// counter++;
// JSONObject entity = i.next();
// String entityID = (String) entity.get("entityID");
// entities.add(entityID);
// }
// int idCount = entities.size();
// ret.append(String.format(
// "Our feeds file contains %d entities out of which %d are unique.\n"
// + "This number should be around 1200?? (20.11.2014).",
// counter, idCount)
// );
// } catch (Exception e) {
// error(e);
// }
//
// return ret.toString();
return "Space for shibboleth output.";
}
}
48 changes: 48 additions & 0 deletions dspace-api/src/main/java/org/dspace/health/additionalUtilities/IOUtils.java
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/**
* The contents of this file are subject to the license and copyright
* detailed in the LICENSE and NOTICE files at the root of the source
* tree and available online at
*
* http://www.dspace.org/license/
*/
package org.dspace.health.additionalUtilities;

import org.apache.logging.log4j.Logger;

import java.io.BufferedReader;
import java.io.File;
import java.io.InputStreamReader;

public class IOUtils {
private static Logger log = org.apache.logging.log4j.LogManager.getLogger(IOUtils.class);

public static String runScript(File where, String[] cmd) {
String message = null;
try {
ProcessBuilder pb = new ProcessBuilder(cmd);
pb.directory( where );
Process p = pb.start();
BufferedReader std_out = new BufferedReader(new InputStreamReader(p.getInputStream()) );
BufferedReader std_err = new BufferedReader(new InputStreamReader(p.getErrorStream()) );

String s = null;
message = "Returned stdout:\n";
while ((s = std_out.readLine()) != null) {
message += s + "\n ";
}
message += "Returned stderr:\n";
while ((s = std_err.readLine()) != null) {
message += s + "\n ";
}

//Wait to get exit value
int exitValue = p.waitFor();
message += "Exit code: [" + String.valueOf( exitValue ) + "]\n";

} catch (Exception e) {
message += "\nException:" + e.toString();
log.error( e );
}
return message;
}
}
11 changes: 5 additions & 6 deletions ...src/main/java/org/dspace/health/Info.java → ...pace/health/additionalUtilities/Info.java
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Expand Up @@ -5,18 +5,17 @@
*
* http://www.dspace.org/license/
*/
package org.dspace.health;

import org.dspace.services.ConfigurationService;
import org.dspace.services.factory.DSpaceServicesFactory;
//import src.main.java.org.dspace.xoai.services.impl.config.DSpaceConfigurationService;

package org.dspace.health.additionalUtilities;

import java.io.FileInputStream;
import java.lang.management.ManagementFactory;
import java.lang.management.RuntimeMXBean;
import java.util.Scanner;

import org.dspace.services.ConfigurationService;
import org.dspace.services.factory.DSpaceServicesFactory;
//import src.main.java.org.dspace.xoai.services.impl.config.DSpaceConfigurationService;

public class Info {

protected static final ConfigurationService configurationService
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