From 55712ace9e7372d77fa1290fb7ef46339587e348 Mon Sep 17 00:00:00 2001
From: JacobsonMT <JacobsonMT+github@gmail.com>
Date: Mon, 23 Apr 2018 18:17:32 -0700
Subject: [PATCH 1/7] update for next development version

---
 gotrack/pom.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gotrack/pom.xml b/gotrack/pom.xml
index 6e03716..9ee4630 100644
--- a/gotrack/pom.xml
+++ b/gotrack/pom.xml
@@ -4,7 +4,7 @@
     <groupId>ubc.pavlab</groupId>
     <artifactId>gotrack</artifactId>
     <packaging>war</packaging>
-    <version>1.4</version>
+    <version>1.5-SNAPSHOT</version>
     <name>gotrack</name>
     <url>http://maven.apache.org</url>
 

From c1b998be75f91f51c6546251d9ba17e301fc803b Mon Sep 17 00:00:00 2001
From: JacobsonMT <JacobsonMT+github@gmail.com>
Date: Tue, 24 Apr 2018 10:55:13 -0700
Subject: [PATCH 2/7] Fix bug in GeneView annotation history

---
 .../ubc/pavlab/gotrack/beans/GeneView.java     | 18 ++++++++++++------
 1 file changed, 12 insertions(+), 6 deletions(-)

diff --git a/gotrack/src/main/java/ubc/pavlab/gotrack/beans/GeneView.java b/gotrack/src/main/java/ubc/pavlab/gotrack/beans/GeneView.java
index a081d2d..702b165 100644
--- a/gotrack/src/main/java/ubc/pavlab/gotrack/beans/GeneView.java
+++ b/gotrack/src/main/java/ubc/pavlab/gotrack/beans/GeneView.java
@@ -542,17 +542,23 @@ public void fetchTimeline() {
 
         for ( Edition ed : allEditions ) {
 
+            Map<String, Long> categoryCounts = Maps.newHashMap();
+
             Map<GeneOntologyTerm, Set<FullAnnotation>> editionData = annotationData.get( ed );
 
-            Stream<Entry<GeneOntologyTerm, Set<FullAnnotation>>> dataStream = editionData.entrySet().stream();
+            if (editionData != null) {
+                Stream<Entry<GeneOntologyTerm, Set<FullAnnotation>>> dataStream = editionData.entrySet().stream();
+
+                if ( !filterTerms.isEmpty() ) {
+                    dataStream = dataStream.filter( e -> filterTerms.contains( e.getKey() ) );
+                }
+
+                // Group by annotation.evidence.category
+                categoryCounts = dataStream.flatMap( e -> e.getValue().stream() )
+                        .collect( Collectors.groupingBy( o -> o.getAnnotation().getEvidence().getCategory(), Collectors.counting() ) );
 
-            if ( !filterTerms.isEmpty() ) {
-                dataStream = dataStream.filter( e -> filterTerms.contains( e.getKey() ) );
             }
 
-            // Group by annotation.evidence.category
-            Map<String, Long> categoryCounts = dataStream.flatMap( e -> e.getValue().stream() )
-                    .collect( Collectors.groupingBy( o -> o.getAnnotation().getEvidence().getCategory(), Collectors.counting() ) );
             for (String category : cache.getEvidenceCategories().keySet() ) {
                 seriesMap.computeIfAbsent( category, Series::new ).addDataPoint( ed.getDate(), categoryCounts.getOrDefault( category, 0L ) );
             }

From 2c56e1f6737602951403ba2ef70256ab636d15b6 Mon Sep 17 00:00:00 2001
From: JacobsonMT <JacobsonMT+github@gmail.com>
Date: Tue, 24 Apr 2018 11:42:04 -0700
Subject: [PATCH 3/7] Center align and add margin to about page

---
 gotrack/src/main/webapp/about.xhtml | 39 ++++++++++++++++-------------
 1 file changed, 22 insertions(+), 17 deletions(-)

diff --git a/gotrack/src/main/webapp/about.xhtml b/gotrack/src/main/webapp/about.xhtml
index 3994c9f..015c7ae 100644
--- a/gotrack/src/main/webapp/about.xhtml
+++ b/gotrack/src/main/webapp/about.xhtml
@@ -40,8 +40,13 @@
 
         .section {
             margin-bottom: 40px;
-            width: 80%;
-            max-width: 1000px;
+            /*width: 80%;*/
+            /*max-width: 1000px;*/
+        }
+
+        .section-separator {
+            height: 1px;
+            max-width: 150px;
         }
     </h:outputStylesheet>
 
@@ -76,21 +81,21 @@
             </div>
         </div>
 
-        <div id="content-wrapper" class="center" style="width:100%; max-width:1600px; min-width:900px;">
+        <div id="content-wrapper" class="center" style="width:100%; max-width:1000px; min-width:900px;">
 
-            <p:outputPanel styleClass="text-left">
+            <p:outputPanel>
 
                 <h:form id="titleForm">
                     <div class="page-title">
                         <h1>About GOTrack</h1>
                     </div>
                 </h:form>
-                <p:separator style="max-width:400px; margin-bottom:25px;"/>
+                <p:separator style="max-width:400px; margin-bottom:45px;"/>
 
 
-                <div class="text-left section-title">
+                <div class="section-title">
                     <h2 style="margin-bottom: 5px;">Citing</h2>
-                    <p:separator style="max-width:150px; margin:0;"/>
+                    <p:separator class="section-separator"/>
                 </div>
 
                 <div class="section">
@@ -102,9 +107,9 @@
                     </p>
                 </div>
 
-                <div class="text-left section-title">
+                <div class="section-title">
                     <h2 style="margin-bottom: 5px;">Contact</h2>
-                    <p:separator style="max-width:150px; margin:0;"/>
+                    <p:separator class="section-separator"/>
                 </div>
 
                 <div class="section">
@@ -114,9 +119,9 @@
                     </p>
                 </div>
 
-                <div class="text-left section-title">
+                <div class="section-title">
                     <h2 style="margin-bottom: 5px;">License</h2>
-                    <p:separator style="max-width:150px; margin:0;"/>
+                    <p:separator class="section-separator"/>
                 </div>
 
                 <div class="section">
@@ -131,16 +136,16 @@
                     <p>Fork it on <a href="https://github.com/PavlidisLab/gotrack">Github</a></p>
                 </div>
 
-                <div class="text-left section-title">
+                <div class="section-title">
                     <h2 style="margin-bottom: 5px;">Disclaimer</h2>
-                    <p:separator style="max-width:150px; margin:0;"/>
+                    <p:separator class="section-separator"/>
                 </div>
                 <div class="section">
                     <p>Use at your own risk. GOTrack is provided "AS-IS" without any warranty, expressed or implied.</p>
                 </div>
-                <div class="text-left section-title">
+                <div class="section-title">
                     <h2 style="margin-bottom: 5px;">Credits and acknowledgments</h2>
-                    <p:separator style="max-width:250px; margin:0;"/>
+                    <p:separator class="section-separator" style="max-width:250px;"/>
                 </div>
                 <div class="section">
                     <p>
@@ -157,9 +162,9 @@
                     </p>
                 </div>
 
-                <div class="text-left section-title">
+                <div class="section-title">
                     <h2 style="margin-bottom: 5px;">Financial support</h2>
-                    <p:separator style="max-width:150px; margin:0;"/>
+                    <p:separator class="section-separator"/>
                 </div>
                 <div class="section">
                     <div style="display: inline-block;position: relative;height:120px;width:150px;">

From 4772c2af1d1e3bcf4ac21a9e92da09d59927084d Mon Sep 17 00:00:00 2001
From: JacobsonMT <JacobsonMT+github@gmail.com>
Date: Tue, 24 Apr 2018 12:05:54 -0700
Subject: [PATCH 4/7] EnrichmentView clear genes also clears input forms

---
 .../src/main/java/ubc/pavlab/gotrack/beans/EnrichmentView.java  | 2 ++
 gotrack/src/main/webapp/enrichment.xhtml                        | 2 +-
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/gotrack/src/main/java/ubc/pavlab/gotrack/beans/EnrichmentView.java b/gotrack/src/main/java/ubc/pavlab/gotrack/beans/EnrichmentView.java
index 0d1bacd..b743000 100644
--- a/gotrack/src/main/java/ubc/pavlab/gotrack/beans/EnrichmentView.java
+++ b/gotrack/src/main/java/ubc/pavlab/gotrack/beans/EnrichmentView.java
@@ -896,6 +896,8 @@ public void removeAllGenes() {
         if ( selectGenes != null ) {
             selectGenes.clear();
         }
+        bulkQuery = "";
+        queryGene = null;
     }
 
     /**
diff --git a/gotrack/src/main/webapp/enrichment.xhtml b/gotrack/src/main/webapp/enrichment.xhtml
index a40b5d1..534dc9b 100644
--- a/gotrack/src/main/webapp/enrichment.xhtml
+++ b/gotrack/src/main/webapp/enrichment.xhtml
@@ -109,7 +109,7 @@
                                          oncomplete="PF('addMultipleGenesDlg').show()"/>
                         <p:commandButton icon="fa fa-trash" value="Clear"
                                          action="#{enrichmentView.removeAllGenes()}"
-                                         update=":formSelect:geneList :formSelect:runEnrichmentBtn"/>
+                                         update=":formSelect:geneList :formSelect:runEnrichmentBtn :formAddGenes"/>
                     </f:facet>
                 </p:dataList>
 

From e361993181a912b0141371f8f112934029945c57 Mon Sep 17 00:00:00 2001
From: JacobsonMT <JacobsonMT+github@gmail.com>
Date: Tue, 24 Apr 2018 12:26:27 -0700
Subject: [PATCH 5/7] GeneView: Remove inferred root level terms

---
 .../ubc/pavlab/gotrack/beans/GeneView.java    | 19 ++++++++++++++++++-
 1 file changed, 18 insertions(+), 1 deletion(-)

diff --git a/gotrack/src/main/java/ubc/pavlab/gotrack/beans/GeneView.java b/gotrack/src/main/java/ubc/pavlab/gotrack/beans/GeneView.java
index 702b165..04859df 100644
--- a/gotrack/src/main/java/ubc/pavlab/gotrack/beans/GeneView.java
+++ b/gotrack/src/main/java/ubc/pavlab/gotrack/beans/GeneView.java
@@ -19,7 +19,10 @@
 
 package ubc.pavlab.gotrack.beans;
 
-import com.google.common.collect.*;
+import com.google.common.collect.ImmutableMap;
+import com.google.common.collect.Lists;
+import com.google.common.collect.Maps;
+import com.google.common.collect.Sets;
 import com.google.gson.Gson;
 import lombok.Getter;
 import lombok.Setter;
@@ -277,6 +280,20 @@ public void fetchData() {
         // retrieve data
         annotationData = fetchAnnotationData();
 
+        // Prune inferred root terms
+        Set<GeneOntologyTerm> rootGOTerms = Sets.newHashSet( "GO:0003674", "GO:0008150", "GO:0005575" ).stream()
+                .map( s -> cache.getCurrentTerm( s ) )
+                .collect( Collectors.toSet() );
+
+        annotationData.values().forEach( editionData -> {
+            for ( GeneOntologyTerm term : rootGOTerms ) {
+                Set<FullAnnotation> annotations = editionData.get( term );
+                if ( annotations != null && annotations.stream().noneMatch( FullAnnotation::isDirect ) ) {
+                    editionData.remove( term );
+                }
+            }
+        } );
+
         // A map that will be needed in the front end for drilling down
         Map<Long, Integer> dateToEdition = new HashMap<>();
 

From 3e70e50af6e2d836b6041bd60bee85224032ee50 Mon Sep 17 00:00:00 2001
From: JacobsonMT <JacobsonMT+github@gmail.com>
Date: Tue, 24 Apr 2018 12:37:13 -0700
Subject: [PATCH 6/7] Fix bug with livescroll datatables and max-height

using max-height instead of scrollHeight prevented
livescroll from loading more rows.
---
 .../resources/composites/enrichmentResultsTable.xhtml     | 3 ++-
 .../src/main/webapp/resources/composites/geneTable.xhtml  | 8 +++++++-
 2 files changed, 9 insertions(+), 2 deletions(-)

diff --git a/gotrack/src/main/webapp/resources/composites/enrichmentResultsTable.xhtml b/gotrack/src/main/webapp/resources/composites/enrichmentResultsTable.xhtml
index e29349d..eb9c40d 100644
--- a/gotrack/src/main/webapp/resources/composites/enrichmentResultsTable.xhtml
+++ b/gotrack/src/main/webapp/resources/composites/enrichmentResultsTable.xhtml
@@ -22,7 +22,7 @@
 <composite:implementation>
     <p:dataTable id="enrichmentTable" widgetVar="tableEnrichmentWdg"
                  var="entry" value="#{cc.attrs.value}"
-                 sortMode="multiple" style="margin-bottom:0;max-height: 225px;"
+                 sortMode="multiple" style="margin-bottom:0;"
                  emptyMessage="No enrichment data found for selected edition"
                  filteredValue="#{cc.attrs.filteredValue}"
                  rowStyleClass="#{entry.result.significant == true ? 'significant' : 'not-significant'}"
@@ -33,6 +33,7 @@
                  rowKey="#{entry.term.goId}"
                  liveScroll="true"
                  scrollRows="25"
+                 scrollHeight="225"
                  resizableColumns="true">
         <p:ajax event="filter"
                 oncomplete="postAjaxSortTable(PF('tableEnrichmentWdg'))"/>
diff --git a/gotrack/src/main/webapp/resources/composites/geneTable.xhtml b/gotrack/src/main/webapp/resources/composites/geneTable.xhtml
index ae7c48a..8d9d6b5 100644
--- a/gotrack/src/main/webapp/resources/composites/geneTable.xhtml
+++ b/gotrack/src/main/webapp/resources/composites/geneTable.xhtml
@@ -17,7 +17,13 @@
 
 <composite:implementation>
 
-    <p:dataTable var="gene" value="#{cc.attrs.value}" emptyMessage="No genes found." style="width:100%;max-height: 200px;" scrollable="true" scrollRows="25">
+    <p:dataTable var="gene"
+                 value="#{cc.attrs.value}"
+                 emptyMessage="No genes found."
+                 style="width:100%;"
+                 scrollHeight="150"
+                 scrollable="true"
+                 scrollRows="25">
         <p:column headerText="Symbol" style="width:120px;">
             <a href="http://www.uniprot.org/uniprot/#{gene.accession.accession}"
                target="_blank" style="margin-right: 5px; text-decoration: none;">

From 3eb6caef2119e378d3b2dc7b0482fbd4a82202dc Mon Sep 17 00:00:00 2001
From: JacobsonMT <JacobsonMT+github@gmail.com>
Date: Tue, 24 Apr 2018 13:34:46 -0700
Subject: [PATCH 7/7] update versions for release

---
 gotrack/pom.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gotrack/pom.xml b/gotrack/pom.xml
index 9ee4630..638e176 100644
--- a/gotrack/pom.xml
+++ b/gotrack/pom.xml
@@ -4,7 +4,7 @@
     <groupId>ubc.pavlab</groupId>
     <artifactId>gotrack</artifactId>
     <packaging>war</packaging>
-    <version>1.5-SNAPSHOT</version>
+    <version>1.5</version>
     <name>gotrack</name>
     <url>http://maven.apache.org</url>