BITMAG-1181: RepairMissingFiles workflow not working in quickstart - and other small fixes

bitrepository-core/src/main/java/org/bitrepository/protocol/ProtocolComponentFactory.java

@@ -31,11 +31,14 @@
 import org.bitrepository.protocol.messagebus.MessageBusManager;
 import org.bitrepository.protocol.security.SecurityManager;
 import org.bitrepository.settings.referencesettings.ProtocolType;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 /**
  * Provides access to the different component in the org.bitrepository.org.bitrepository.protocol module (Spring/IOC wannabe)
  */
 public final class ProtocolComponentFactory {
+    private static final Logger log = LoggerFactory.getLogger(ProtocolComponentFactory.class);
     private static ProtocolComponentFactory instance;
 
     public static synchronized ProtocolComponentFactory getInstance() {
@@ -84,7 +87,8 @@ public FileExchange getFileExchange(Settings settings) {
                 } else if (protocolType == ProtocolType.HTTPS) {
                     fileExchange = new HttpsFileExchange(settings);
                 } else if (protocolType == ProtocolType.FILE) {
-                    fileExchange = new LocalFileExchange(settings.getReferenceSettings().getFileExchangeSettings().getPath());
+                    fileExchange = new LocalFileExchange(
+                            settings.getReferenceSettings().getFileExchangeSettings().getPath());
                 }
             } else {
                 fileExchange = new HttpFileExchange(settings);

bitrepository-integration/src/main/resources/quickstart/conf/integrityservice/ReferenceSettings.xml

@@ -126,4 +126,10 @@
       </PillarDetails>
     </PillarIntegrityDetails>
   </IntegrityServiceSettings>
+  <FileExchangeSettings>
+    <ProtocolType>HTTP</ProtocolType>
+    <ServerName>localhost</ServerName>
+    <Port>80</Port>
+    <Path>/dav</Path>
+  </FileExchangeSettings>
 </ReferenceSettings>

bitrepository-integrity-service/src/main/java/org/bitrepository/integrityservice/reports/BasicIntegrityReporter.java

@@ -107,7 +107,7 @@ public void generateReport() throws IOException {
     private String generateSummary() {
         StringBuilder report = new StringBuilder();
         if (deletedFilesCount != 0L) {
-            report.append("Detected ").append(deletedFilesCount).append(" files as removed from the collection.");
+            report.append("\n").append("Detected ").append(deletedFilesCount).append(" file(s) as removed from the collection.");
         }
         for (String pillar : missingFiles.keySet()) {
             if (missingFiles.get(pillar) != 0) {

bitrepository-integrity-service/src/main/java/org/bitrepository/integrityservice/workflow/step/CreateStatisticsEntryStep.java

@@ -31,8 +31,7 @@
 import java.util.Map;
 
 /**
- * A workflow step for finding missing checksums.
- * Uses the IntegrityChecker to perform the actual check.
+ * A workflow step for creating pillar statistics.
  */
 public class CreateStatisticsEntryStep extends AbstractWorkFlowStep {
     private final IntegrityModel store;
@@ -51,8 +50,7 @@ public String getName() {
     }
 
     /**
-     * Uses IntegrityChecker to validate whether any checksums are missing.
-     * Dispatches an alarm if any checksums were missing.
+     * Collects pillar metrics for the given collection and creates from them a statistics entry in the store.
      */
     @Override
     public synchronized void performStep() {

bitrepository-reference-pillar/src/main/java/org/bitrepository/pillar/messagehandler/GetChecksumsRequestHandler.java

@@ -213,12 +213,12 @@ private File makeTemporaryChecksumFile(GetChecksumsRequest request,
         }
 
         // Print all the checksums safely (close the streams!)
-        try (OutputStream is = new FileOutputStream(checksumResultFile)) {
+        try (OutputStream os = new FileOutputStream(checksumResultFile)) {
             JaxbHelper jaxb = new JaxbHelper(XSD_CLASSPATH, XSD_BR_DATA);
             String xmlMessage = jaxb.serializeToXml(results);
             jaxb.validate(new ByteArrayInputStream(xmlMessage.getBytes(StandardCharsets.UTF_8)));
-            is.write(xmlMessage.getBytes(StandardCharsets.UTF_8));
-            is.flush();
+            os.write(xmlMessage.getBytes(StandardCharsets.UTF_8));
+            os.flush();
         }
 
         return checksumResultFile;

bitrepository-service/src/main/java/org/bitrepository/service/contributor/handler/GetAuditTrailsRequestHandler.java

@@ -202,12 +202,12 @@ protected File createAuditTrailFile(GetAuditTrailsRequest request, AuditTrailDat
         results.setCollectionID(request.getCollectionID());
         results.getAuditTrailEvents().add(extractedAuditTrails.getAuditTrailEvents());
 
-        try (OutputStream is = new FileOutputStream(checksumResultFile)) {
+        try (OutputStream os = new FileOutputStream(checksumResultFile)) {
             JaxbHelper jaxb = new JaxbHelper(XSD_CLASSPATH, XSD_BR_DATA);
             String xmlMessage = jaxb.serializeToXml(results);
             jaxb.validate(new ByteArrayInputStream(xmlMessage.getBytes(StandardCharsets.UTF_8)));
-            is.write(xmlMessage.getBytes(StandardCharsets.UTF_8));
-            is.flush();
+            os.write(xmlMessage.getBytes(StandardCharsets.UTF_8));
+            os.flush();
         }
 
         return checksumResultFile;

bitrepository-webclient/src/main/webapp/alarm-service.html

@@ -42,7 +42,9 @@
   <div class="row-fluid">
     <div class="span11">
       <div class="span11" style="height:0px; min-height:0px"></div>
-      <div class="span11"><h2>Alarm service</h2></div>
+      <div class="span11">
+        <h2>Alarm service</h2>
+      </div>
       <div class="span11">
         <form class="form-inline">
           <legend>Alarm display filters</legend>
@@ -133,7 +135,7 @@
 
 <script>
     let nameMapper;
-    let descriptionMapper;
+    let descriptionExpandedMapper;
     let autoGetAlarmsInterval;
     let alarmServiceUrl;
 
@@ -151,7 +153,7 @@
         let collectionIDStr = $("#collectionIDFilter").val();
         let url = alarmServiceUrl + '/alarm/AlarmService/queryAlarms/';
 
-        getDescriptionState();
+        getDescriptionExpandedState();
 
         $.post(url,
             {
@@ -163,65 +165,51 @@
                 maxAlarms: maxAlarmStr,
                 collectionID: collectionIDStr,
                 oldestAlarmFirst: false
-            }, function (j) {
+            }, function (json) {
                 let htmlTableBody = "";
-                if (j != null) {
-                    for (let i = 0; i < j.length; i++) {
+                if (json != null) {
+                    for (let i = 0; i < json.length; i++) {
                         htmlTableBody += `<tr>
-                          <td>${j[i].origDateTime}</td>
-                          <td>${j[i].alarmRaiser}</td>
-                          <td>${nameMapper.getName(j[i].collectionID)}</td>
-                          <td>${j[i].fileID}</td>
-                          <td>${j[i].alarmCode}</td>
-                          <td class="description"><p class="teaser">${nl2br(j[i].alarmText)}</p></td>
+                          <td>${json[i].origDateTime}</td>
+                          <td>${json[i].alarmRaiser}</td>
+                          <td>${nameMapper.getName(json[i].collectionID)}</td>
+                          <td>${json[i].fileID}</td>
+                          <td>${json[i].alarmCode}</td>
+                          <td class="description">${renderAlarmDescription(i, json[i].alarmText).prop('outerHTML')}</td>
                         </tr>`;
                     }
                 }
                 $("#alarms-table-body").html(htmlTableBody);
-                compressDescription();
                 enableDescriptionExpansionOnClick();
             });
     }
 
-    function init() {
-        $.get('repo/urlservice/alarmService/', {}, function (url) {
-            alarmServiceUrl = url;
-        }, 'html').done(function () {
-            $.getJSON('repo/reposervice/getCollections/', {}, function (collections) {
-                nameMapper = new CollectionNameMapper(collections);
-                let cols = nameMapper.getCollectionIDs();
-                for (let i in cols) {
-                    $("#collectionIDFilter").append(
-                        `<option value="${cols[i]}">${nameMapper.getName(cols[i])}</option>`
-                    );
-                }
-                updateAlarms();
-                autoGetAlarmsInterval = setInterval(function () {
-                    updateAlarms();
-                }, 2500);
-            });
+    function getDescriptionExpandedState() {
+        descriptionExpandedMapper = {};
+        $("#alarms-table-body tr").each(function (index) {
+            // Grab the
+            descriptionExpandedMapper[index] = $(this).find("td:eq(5)").find(".complete").css("display");
         });
     }
 
-    function compressDescription() {
+    function renderAlarmDescription(index, alarmDescription) {
         const maxLength = 80;
-        $(".teaser").each(function () {
-            let index = $(this).closest("tr").find("td:eq(0)").text() + $(this).text();
-            let string = $(this).html();
+        let descriptionHtml = $('<p class="teaser">').css("margin", 0);
+        let isExpandedDesc = descriptionExpandedMapper.hasOwnProperty(index) &&
+            descriptionExpandedMapper[index] !== "none";
 
-            if (descriptionMapper.hasOwnProperty(index) && descriptionMapper[index] !== "none") {
-                $(this).empty().html(`<span class="complete" style="display: inline">${string}</span>`);
-            } else {
-                if (string.length > maxLength) {
-                    let newString = string.substring(0, maxLength);
-                    let removedString = string.substring(maxLength, string.length);
-                    $(this).empty().html(newString);
-                    $(this).append(`<span class="dots">... </span>`)
-                    $(this).append(`<span class="complete">${removedString}</span>`);
-                    $(this).append('<a href="javascript:void(0);" class="show-more">show more</a>');
-                }
-            }
-        });
+        if (alarmDescription.length <= maxLength || isExpandedDesc) {
+            let fullDescSpan = `<span class="complete" style="display: inline">${nl2br(alarmDescription)}</span>`
+            descriptionHtml.empty().html(fullDescSpan);
+        } else { // Alarm description is too long and is not expanded
+            let shortenedDesc = alarmDescription.substring(0, maxLength);
+            let remainingDesc = alarmDescription.substring(maxLength, alarmDescription.length);
+            descriptionHtml.empty().html(nl2br(shortenedDesc));
+            descriptionHtml.append(`<span class="dots">... </span>`)
+            descriptionHtml.append(`<span class="complete">${nl2br(remainingDesc)}</span>`);
+            descriptionHtml.append('<a href="javascript:void(0);" class="show-more">show more</a>');
+        }
+        return descriptionHtml;
     }
 
     function enableDescriptionExpansionOnClick() {
@@ -234,11 +222,23 @@
         });
     }
 
-    function getDescriptionState() {
-        descriptionMapper = {};
-        $("#alarms-table-body tr").each(function () {
-            let identifier = $(this).find("td:eq(0)").text() + $(this).find("td:eq(5)").text();
-            descriptionMapper[identifier] = $(this).find("td:eq(5)").find(".complete").css("display");
+    function init() {
+        $.get('repo/urlservice/alarmService/', {}, function (url) {
+            alarmServiceUrl = url;
+        }, 'html').done(function () {
+            $.getJSON('repo/reposervice/getCollections/', {}, function (collections) {
+                nameMapper = new CollectionNameMapper(collections);
+                let cols = nameMapper.getCollectionIDs();
+                for (let i in cols) {
+                    $("#collectionIDFilter").append(
+                        `<option value="${cols[i]}">${nameMapper.getName(cols[i])}</option>`
+                    );
+                }
+                updateAlarms();
+                autoGetAlarmsInterval = setInterval(function () {
+                    updateAlarms();
+                }, 2500);
+            });
         });
     }