Ufal/Regulart reports for health check

dspace-api/pom.xml

@@ -858,7 +858,12 @@
                 </exclusion>
             </exclusions>
         </dependency>
-
+        <dependency>
+            <groupId>com.flipkart.zjsonpatch</groupId>
+            <artifactId>zjsonpatch</artifactId>
+            <version>0.4.6</version>
+        </dependency>
+
     </dependencies>
 
     <dependencyManagement>

dspace-api/src/main/java/org/dspace/app/healthreport/HealthReport.java

@@ -19,9 +19,13 @@
 import java.util.Map;
 import javax.mail.MessagingException;
 
+import org.apache.commons.cli.Option;
 import org.apache.commons.cli.ParseException;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
+import org.dspace.content.ReportResult;
+import org.dspace.content.factory.ContentServiceFactory;
+import org.dspace.content.service.ReportResultService;
 import org.dspace.core.Context;
 import org.dspace.core.Email;
 import org.dspace.core.I18nUtil;
@@ -34,6 +38,8 @@
 import org.dspace.services.ConfigurationService;
 import org.dspace.services.factory.DSpaceServicesFactory;
 import org.dspace.utils.DSpace;
+import org.json.JSONArray;
+import org.json.JSONObject;
 
 /**
  * This class is used to generate a health report of the DSpace instance.
@@ -44,6 +50,7 @@ public class HealthReport extends DSpaceRunnable<HealthReportScriptConfiguration
     private static final Logger log = LogManager.getLogger(HealthReport.class);
 
     private ConfigurationService configurationService = DSpaceServicesFactory.getInstance().getConfigurationService();
+    private ReportResultService reportResultService = ContentServiceFactory.getInstance().getReportResultService();
     private EPersonService ePersonService;
 
     /**
@@ -136,56 +143,82 @@ public void internalRun() throws Exception {
             return;
         }
 
-        ReportInfo ri = new ReportInfo(this.forLastNDays);
+        try (Context context = new Context()) {
+            context.setCurrentUser(ePersonService.find(context, this.getEpersonIdentifier()));
 
-        StringBuilder sbReport = new StringBuilder();
-        sbReport.append("\n\nHEALTH REPORT:\n");
+            ReportInfo ri = new ReportInfo(this.forLastNDays);
 
-        int position = -1;
-        for (Map.Entry<String, Check> check_entry : Report.checks().entrySet()) {
-            ++position;
-            if (specificCheck != -1 && specificCheck != position) {
-                continue;
-            }
+            StringBuilder sbReport = new StringBuilder();
+            sbReport.append("\n\nHEALTH REPORT:\n");
 
-            String name = check_entry.getKey();
-            Check check = check_entry.getValue();
+            int position = -1;
+            JSONObject root = new JSONObject();
+            // Create the array
+            JSONArray checksArray = new JSONArray();
+            for (Map.Entry<String, Check> check_entry : Report.checks().entrySet()) {
+                ++position;
+                if (specificCheck != -1 && specificCheck != position) {
+                    continue;
+                }
 
-            log.info("#{}. Processing [{}] at [{}]", position, name, new SimpleDateFormat(
-                    "yyyy-MM-dd HH:mm:ss.SSS").format(new Date()));
+                String name = check_entry.getKey();
+                Check check = check_entry.getValue();
 
-            sbReport.append("\n######################\n\n").append(name).append(":\n");
-            check.report(ri);
-            sbReport.append(check.getReport());
-        }
+                log.info("#{}. Processing [{}] at [{}]", position, name, new SimpleDateFormat(
+                        "yyyy-MM-dd HH:mm:ss.SSS").format(new Date()));
 
-        // save output to file
-        if (fileName != null) {
-            Context context = new Context();
-            context.setCurrentUser(ePersonService.find(context, this.getEpersonIdentifier()));
+                sbReport.append("\n######################\n\n").append(name).append(":\n");
+                check.report(ri);
+                sbReport.append(check.getReport());
 
-            InputStream inputStream = toInputStream(sbReport.toString(), StandardCharsets.UTF_8);
-            handler.writeFilestream(context, fileName, inputStream, "export");
+                // JSON:
+                // Check name: {Report}
+                JSONObject report = check.getReportJson();  // assume check is already defined
 
-            context.restoreAuthSystemState();
-            context.complete();
-        }
+                JSONObject checkJson = new JSONObject();
+                checkJson.put("name", name);
+                checkJson.put("report", report);
+                // Add items to array
+                checksArray.put(checkJson);
+            }
 
-        // send email to email address from argument
-        if (emails != null && emails.length > 0) {
-            try {
-                Email e = Email.getEmail(I18nUtil.getEmailFilename(Locale.getDefault(), "healthcheck"));
-                for (String recipient : emails) {
-                    e.addRecipient(recipient);
+            // Add array to root object under a key "checks"
+            root.put("checks", checksArray);
+
+            // Add health report summary to the ReportResult object
+            ReportResult reportResult = reportResultService.create(context);
+            reportResult.setArgs(printCommandlineOptions());
+            reportResult.setExecutor(context.getCurrentUser());
+            reportResult.setType("healthcheck");
+            reportResult.setValue(root.toString());
+            reportResultService.update(context, reportResult);
+            context.commit();
+
+            // save output to file
+            if (fileName != null) {
+                InputStream inputStream = toInputStream(sbReport.toString(), StandardCharsets.UTF_8);
+                handler.writeFilestream(context, fileName, inputStream, "export");
+
+                context.restoreAuthSystemState();
+
+            }
+
+            // send email to email address from argument
+            if (emails != null && emails.length > 0) {
+                try {
+                    Email e = Email.getEmail(I18nUtil.getEmailFilename(Locale.getDefault(), "healthcheck"));
+                    for (String recipient : emails) {
+                        e.addRecipient(recipient);
+                    }
+                    e.addArgument(sbReport.toString());
+                    e.send();
+                } catch (IOException | MessagingException e) {
+                    log.error("Error sending email:", e);
                 }
-                e.addArgument(sbReport.toString());
-                e.send();
-            } catch (IOException | MessagingException e) {
-                log.error("Error sending email:", e);
             }
-        }
 
-        handler.logInfo(sbReport.toString());
+            handler.logInfo(sbReport.toString());
+        }
     }
 
     @Override
@@ -201,6 +234,25 @@ public void printHelp() {
         );
     }
 
+    /**
+     * Print command line options in a readable format.
+     * This method is used to print the options used for the report.
+     */
+    private String printCommandlineOptions() {
+        // Return key-value pairs of options
+        StringBuilder options = new StringBuilder();
+        for (Option option : commandLine.getOptions()) {
+            String key = option.getOpt();
+            String value = commandLine.getOptionValue(key);
+            if (value != null) {
+                options.append(String.format("  -%s: %s\n", key, value));
+            } else {
+                options.append(String.format("  -%s\n", key));
+            }
+        }
+        return options.toString();
+    }
+
     /**
      * Convert checks names to string.
      */
@@ -219,4 +271,25 @@ private String checksNamesToString() {
     public static int getNumberOfChecks() {
         return checks.size();
     }
+
+    /**
+     * Get the name of a specific check by its index.
+     * This is used for the `-c` option.
+     *
+     * @param specificCheck the index of the check
+     * @return the name of the check, or null if the index is invalid
+     */
+    public static String getCheckName(int specificCheck) {
+        if (specificCheck < 0 || specificCheck >= getNumberOfChecks()) {
+            return null;
+        }
+        int pos = 0;
+        for (String name : checks.keySet()) {
+            if (pos == specificCheck) {
+                return name;
+            }
+            pos++;
+        }
+        return null; // should not happen
+    }
 }