PN-252: Run local matches search only for patients updated/created si…

…nce last search

matching-notification-api/src/main/java/org/phenotips/matchingnotification/finder/MatchFinder.java

@@ -43,4 +43,13 @@ public interface MatchFinder
      */
     List<PatientMatch> findMatches(Patient patient);
 
+    /**
+     * Record start time for running matches search.
+     */
+    void recordStartMatchesSearch();
+
+    /**
+     * Record completed time for running matches search.
+     */
+    void recordEndMatchesSearch();
 }

matching-notification-api/src/main/java/org/phenotips/matchingnotification/finder/MatchFinderManager.java

@@ -37,4 +37,14 @@ public interface MatchFinderManager
      * @return list of matches
      */
     List<PatientMatch> findMatches(Patient patient);
+
+    /**
+     * For every match finder record start time for running matches search.
+     */
+    void recordStartMatchesSearch();
+
+    /**
+     * For every match finder record completed time for running matches search.
+     */
+    void recordEndMatchesSearch();
 }

matching-notification-api/src/main/java/org/phenotips/matchingnotification/finder/internal/DefaultMatchFinderManager.java

@@ -75,4 +75,20 @@ public List<PatientMatch> findMatches(Patient patient)
 
         return matches;
     }
+
+    @Override
+    public void recordStartMatchesSearch()
+    {
+        for (MatchFinder service : this.matchFinderProvider.get()) {
+            service.recordStartMatchesSearch();
+        }
+    }
+
+    @Override
+    public void recordEndMatchesSearch()
+    {
+        for (MatchFinder service : this.matchFinderProvider.get()) {
+            service.recordEndMatchesSearch();
+        }
+    }
 }

matching-notification-api/src/main/java/org/phenotips/matchingnotification/finder/internal/LocalMatchFinder.java

@@ -18,6 +18,7 @@
 package org.phenotips.matchingnotification.finder.internal;
 
 import org.phenotips.data.Patient;
+import org.phenotips.data.PatientData;
 import org.phenotips.data.similarity.PatientSimilarityView;
 import org.phenotips.matchingnotification.finder.MatchFinder;
 import org.phenotips.matchingnotification.match.PatientMatch;
@@ -26,25 +27,48 @@
 import org.phenotips.similarity.SimilarPatientsFinder;
 
 import org.xwiki.component.annotation.Component;
+import org.xwiki.component.phase.Initializable;
+import org.xwiki.component.phase.InitializationException;
+import org.xwiki.model.EntityType;
+import org.xwiki.model.reference.EntityReference;
 
+import java.util.Date;
 import java.util.LinkedList;
 import java.util.List;
 
 import javax.inject.Inject;
 import javax.inject.Named;
+import javax.inject.Provider;
 import javax.inject.Singleton;
 
+import org.joda.time.DateTime;
+import org.joda.time.DateTimeZone;
+import org.joda.time.format.DateTimeFormatter;
+import org.joda.time.format.ISODateTimeFormat;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import com.xpn.xwiki.XWikiContext;
+import com.xpn.xwiki.XWikiException;
+import com.xpn.xwiki.doc.XWikiDocument;
+import com.xpn.xwiki.objects.BaseObject;
+
 /**
  * @version $Id$
  */
 @Component
 @Named("local")
 @Singleton
-public class LocalMatchFinder implements MatchFinder
+public class LocalMatchFinder implements MatchFinder, Initializable
 {
+    private static final EntityReference PHENOMECENTRAL_SPACE = new EntityReference("PhenomeCentral", EntityType.SPACE);
+
+    private static final EntityReference MATCHING_RUN_INFO_CLASS = new EntityReference(
+        "MatchingRunInfoClass", EntityType.DOCUMENT, PHENOMECENTRAL_SPACE);
+
+    private static final EntityReference MATCHING_RUN_INFO_DOCUMENT =
+        new EntityReference("MatchingRunInfo", EntityType.DOCUMENT, PHENOMECENTRAL_SPACE);
+
     private Logger logger = LoggerFactory.getLogger(LocalMatchFinder.class);
 
     @Inject
@@ -53,6 +77,38 @@ public class LocalMatchFinder implements MatchFinder
     @Inject
     private MatchStorageManager matchStorageManager;
 
+    @Inject
+    private Provider<XWikiContext> provider;
+
+    private DateTimeFormatter dateFormatter = ISODateTimeFormat.dateTime().withZone(DateTimeZone.UTC);
+
+    private Date previousStartedTime;
+
+    private XWikiDocument prefsDoc;
+
+    @Override
+    public void initialize() throws InitializationException
+    {
+        XWikiContext context = this.provider.get();
+        this.previousStartedTime = null;
+        this.prefsDoc = null;
+
+        try {
+            this.prefsDoc = context.getWiki().getDocument(MATCHING_RUN_INFO_DOCUMENT, context);
+
+            if (this.prefsDoc != null && !this.prefsDoc.isNew()) {
+                BaseObject object = this.prefsDoc.getXObject(MATCHING_RUN_INFO_CLASS, "serverName", "localhost", false);
+                if (object == null) {
+                    object = this.prefsDoc.newXObject(MATCHING_RUN_INFO_CLASS, context);
+                    object.setStringValue("serverName", "localhost");
+                    context.getWiki().saveDocument(this.prefsDoc, context);
+                }
+            }
+        } catch (XWikiException e) {
+            this.logger.error("Failed to modify matching run info document: {}", e.getMessage(), e);
+        }
+    }
+
     @Override
     public int getPriority()
     {
@@ -62,10 +118,18 @@ public int getPriority()
     @Override
     public List<PatientMatch> findMatches(Patient patient)
     {
+        List<PatientMatch> matches = new LinkedList<>();
+
+        PatientData<String> patientData = patient.<String>getData("metadata");
+        String date = patientData.get("date");
+        DateTime lastModificationDate = this.dateFormatter.parseDateTime(date);
+
+        if (this.previousStartedTime != null && lastModificationDate.isBefore(new DateTime(this.previousStartedTime))) {
+            return matches;
+        }
 
         this.logger.debug("Finding local matches for patient {}.", patient.getId());
 
-        List<PatientMatch> matches = new LinkedList<>();
         List<PatientSimilarityView> similarPatients = this.finder.findSimilarPatients(patient);
         for (PatientSimilarityView similarityView : similarPatients) {
             PatientMatch match = new DefaultPatientMatch(similarityView, null, null);
@@ -76,4 +140,44 @@ public List<PatientMatch> findMatches(Patient patient)
 
         return matches;
     }
+
+    @Override
+    public void recordStartMatchesSearch()
+    {
+        if (this.prefsDoc == null) {
+            return;
+        }
+
+        BaseObject object = this.prefsDoc.getXObject(MATCHING_RUN_INFO_CLASS, "serverName", "localhost", false);
+
+        // cash last started search date to compare with last modification date for patient
+        this.previousStartedTime = object.getDateValue("startedTime");
+        // set new started time
+        object.setDateValue("startedTime", new Date());
+
+        try {
+            XWikiContext context = this.provider.get();
+            context.getWiki().saveDocument(this.prefsDoc, context);
+        } catch (XWikiException e) {
+            this.logger.error("Failed to save matching run start time for localhost {}.");
+        }
+    }
+
+    @Override
+    public void recordEndMatchesSearch()
+    {
+        if (this.prefsDoc == null) {
+            return;
+        }
+
+        BaseObject object = this.prefsDoc.getXObject(MATCHING_RUN_INFO_CLASS, "serverName", "localhost", false);
+        object.setDateValue("completedTime", new Date());
+
+        try {
+            XWikiContext context = this.provider.get();
+            context.getWiki().saveDocument(this.prefsDoc, context);
+        } catch (XWikiException e) {
+            this.logger.error("Failed to save matching run start time for localhost {}.");
+        }
+    }
 }

matching-notification-api/src/main/java/org/phenotips/matchingnotification/internal/DefaultMatchingNotificationManager.java

@@ -91,12 +91,15 @@ public class DefaultMatchingNotificationManager implements MatchingNotificationM
     @Override
     public void findAndSaveMatches()
     {
+        this.matchFinderManager.recordStartMatchesSearch();
+
         List<Patient> patients = this.getPatientsList();
         for (Patient patient : patients) {
             this.logger.debug("Finding matches for patient {}.", patient.getId());
-
             this.matchFinderManager.findMatches(patient);
         }
+
+        this.matchFinderManager.recordEndMatchesSearch();
     }
 
     /*

pom.xml

@@ -486,6 +486,30 @@
               <to>void</to>
               <justification>Removed unused return.</justification>
             </difference>
+            <difference>
+              <className>org/phenotips/matchingnotification/finder/MatchFinder</className>
+              <differenceType>7012</differenceType>
+              <method>void recordStartMatchesSearch()</method>
+              <justification>Record the beginning time of matches search for each server</justification>
+            </difference>
+            <difference>
+              <className>org/phenotips/matchingnotification/finder/MatchFinder</className>
+              <differenceType>7012</differenceType>
+              <method>void recordEndMatchesSearch()</method>
+              <justification>Record the completion time of matches search for each server</justification>
+            </difference>
+            <difference>
+              <className>org/phenotips/matchingnotification/finder/MatchFinderManager</className>
+              <differenceType>7012</differenceType>
+              <method>void recordStartMatchesSearch()</method>
+              <justification>Record the beginning time of matches search for each match finder</justification>
+            </difference>
+            <difference>
+              <className>org/phenotips/matchingnotification/finder/MatchFinderManager</className>
+              <differenceType>7012</differenceType>
+              <method>void recordEndMatchesSearch()</method>
+              <justification>Record the completion time of matches search for each match finder</justification>
+            </difference>
           </ignored>
           <excludes>
             <exclude>**/internal/**</exclude>