PN-239: Allow filtering matches separately by phenotipic and genotipi…

…c score Removed score parameter from find all matches
phenotips · Jan 16, 2018 · 9e543ca · 9e543ca
1 parent 8502f6f
commit 9e543ca
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Showing 6 changed files with 39 additions and 50 deletions.
diff --git a/...ion-api/src/main/java/org/phenotips/matchingnotification/MatchingNotificationManager.java b/...ion-api/src/main/java/org/phenotips/matchingnotification/MatchingNotificationManager.java
@@ -18,7 +18,6 @@
 package org.phenotips.matchingnotification;
 
 import org.phenotips.data.similarity.PatientSimilarityView;
-import org.phenotips.matchingnotification.match.PatientMatch;
 import org.phenotips.matchingnotification.notification.PatientMatchNotificationResponse;
 
 import org.xwiki.component.annotation.Role;
@@ -34,11 +33,8 @@ public interface MatchingNotificationManager
 {
     /**
      * Find and save matches to all local patients.
-     *
-     * @param score save matches with score higher or equals to this value
-     * @return true if successful
      */
-    List<PatientMatch> findAndSaveMatches(double score);
+    void findAndSaveMatches();
 
     /**
      * Sends notification to the owner of every match with id in {@code matchesId}, then marks match as notified.

diff --git a/.../java/org/phenotips/matchingnotification/internal/DefaultMatchingNotificationManager.java b/.../java/org/phenotips/matchingnotification/internal/DefaultMatchingNotificationManager.java
@@ -89,29 +89,14 @@ public class DefaultMatchingNotificationManager implements MatchingNotificationM
     private MatchStorageManager matchStorageManager;
 
     @Override
-    public List<PatientMatch> findAndSaveMatches(double score)
+    public void findAndSaveMatches()
     {
-        List<PatientMatch> addedMatches = new LinkedList<>();
-
         List<Patient> patients = this.getPatientsList();
         for (Patient patient : patients) {
-
             this.logger.debug("Finding matches for patient {}.", patient.getId());
 
-            List<PatientMatch> matchesForPatient = this.matchFinderManager.findMatches(patient);
-            if (matchesForPatient.isEmpty()) {
-                continue;
-            }
-
-            this.filterMatchesByScore(matchesForPatient, score);
-            if (matchesForPatient.isEmpty()) {
-                continue;
-            }
-
-            addedMatches.addAll(matchesForPatient);
+            this.matchFinderManager.findMatches(patient);
         }
-
-        return addedMatches;
     }
 
     /*
@@ -193,20 +178,6 @@ private List<PatientMatch> getSuccessfulNotifications(List<PatientMatchNotificat
         return successfulMatches;
     }
 
-    /*
-     * Removes all matches from list with score lower than score.
-     */
-    private void filterMatchesByScore(List<PatientMatch> matches, double score)
-    {
-        List<PatientMatch> toRemove = new LinkedList<>();
-        for (PatientMatch match : matches) {
-            if (match.getScore() < score) {
-                toRemove.add(match);
-            }
-        }
-        matches.removeAll(toRemove);
-    }
-
     @Override
     public boolean saveLocalMatchesViews(List<PatientSimilarityView> similarityViews, String patientId)
     {

diff --git a/...ain/java/org/phenotips/matchingnotification/script/MatchingNotificationScriptService.java b/...ain/java/org/phenotips/matchingnotification/script/MatchingNotificationScriptService.java
@@ -90,19 +90,11 @@ public class MatchingNotificationScriptService implements ScriptService
     private Logger logger = LoggerFactory.getLogger(MatchingNotificationScriptService.class);
 
     /**
-     * Find patient matches and saves only those with score higher or equals to {@code score}.
-     *
-     * @param score only matches with score higher or equal to this value are saved
-     * @return JSON with the saved matches (after filtering)
+     * Find and save matches to all local patients.
      */
-    public String findAndSaveMatches(double score)
+    public void findAndSaveMatches()
     {
-        List<PatientMatch> matches = this.matchingNotificationManager.findAndSaveMatches(score);
-        if (!isAdmin()) {
-            filterNonUsersMatches(matches);
-        }
-        JSONObject json = this.patientMatchExport.toJSON(matches);
-        return json.toString();
+        this.matchingNotificationManager.findAndSaveMatches();
     }
 
     /**

diff --git a/matching-notification-ui/src/main/resources/MatchingNotification/RequestHandler.xml b/matching-notification-ui/src/main/resources/MatchingNotification/RequestHandler.xml
@@ -40,8 +40,7 @@
   <content>{{velocity}}
 #set ($discard = $response.setContentType('application/json'))
 #if ($request.action == 'find-matches')
-   #set ($score = $request.score)
-   $services.matchingNotification.findAndSaveMatches($score)
+   $services.matchingNotification.findAndSaveMatches()
 #elseif ($request.action == 'show-matches')
    #set ($score = $request.score)
    #set ($phenScore = $request.phenScore)

diff --git a/matching-notification-ui/src/main/resources/MatchingNotification/UnnotifiedTable.xml b/matching-notification-ui/src/main/resources/MatchingNotification/UnnotifiedTable.xml
@@ -46,7 +46,6 @@ $xwiki.jsfx.use('uicomponents/matchingNotification/unnotifiedMatchesTable.js', t
 {{html}}
 &lt;div&gt;
   &lt;label&gt;$escapetool.xml($services.localization.render('phenotips.matchingNotifications.table.findMatches.label')) &lt;/label&gt;
-  &lt;input id="find-matches-score" type="text" style="width: 5em;"/&gt;
   &lt;button id="find-matches-button" type="button"&gt;$escapetool.xml($services.localization.render('phenotips.matchingNotifications.table.go.label'))&lt;/button&gt;
   &lt;div id="find-matches-messages"/&gt;
 &lt;/div&gt;

diff --git a/pom.xml b/pom.xml
@@ -448,6 +448,38 @@
               <method>java.util.List loadMatches(double, boolean)</method>
               <justification>Added phenotypical and genotypical score parameters.</justification>
             </difference>
+            <difference>
+              <className>org/phenotips/matchingnotification/MatchingNotificationManager</className>
+              <differenceType>7004</differenceType>
+              <method>java.util.List findAndSaveMatches(double)</method>
+              <justification>Removed score parameter.</justification>
+            </difference>
+            <difference>
+              <className>org/phenotips/matchingnotification/script/MatchingNotificationScriptService</className>
+              <differenceType>7004</differenceType>
+              <method>java.lang.String findAndSaveMatches(double)</method>
+              <justification>Removed score parameter.</justification>
+            </difference>
+            <difference>
+              <className>org/phenotips/matchingnotification/script/MatchingNotificationScriptService</className>
+              <differenceType>7004</differenceType>
+              <method>java.lang.String getMatches(double, boolean)</method>
+              <justification>Added phenotypical and genotypical score parameters.</justification>
+            </difference>
+            <difference>
+              <className>org/phenotips/matchingnotification/MatchingNotificationManager</className>
+              <differenceType>7006</differenceType>
+              <method>java.util.List findAndSaveMatches(double)</method>
+              <to>void</to>
+              <justification>Removed unused return.</justification>
+            </difference>
+            <difference>
+              <className>org/phenotips/matchingnotification/script/MatchingNotificationScriptService</className>
+              <differenceType>7006</differenceType>
+              <method>java.lang.String findAndSaveMatches(double)</method>
+              <to>void</to>
+              <justification>Removed unused return.</justification>
+            </difference>
           </ignored>
           <excludes>
             <exclude>**/internal/**</exclude>