From d48be0ad6fc0889eacc43e0a71043d5ca89ecc76 Mon Sep 17 00:00:00 2001
From: Ino de Bruijn <ino@ino.pm>
Date: Wed, 9 May 2018 18:20:33 -0400
Subject: [PATCH 1/2] E2E test remove uniprot from mutations tab

The timing here is flaky so remove instead.


Former-commit-id: 65d40c0dd9f27b68710078ba615cd546e19355ed
---
 src/pages/resultsView/mutation/MutationMapper.tsx | 15 ++++++++-------
 1 file changed, 8 insertions(+), 7 deletions(-)

diff --git a/src/pages/resultsView/mutation/MutationMapper.tsx b/src/pages/resultsView/mutation/MutationMapper.tsx
index 95c35958c1c..9f67e4131f7 100644
--- a/src/pages/resultsView/mutation/MutationMapper.tsx
+++ b/src/pages/resultsView/mutation/MutationMapper.tsx
@@ -78,13 +78,14 @@ export default class MutationMapper extends React.Component<IMutationMapperProps
             <div style={{'paddingBottom':10}}>
                 <h4>{hugoGeneSymbol}</h4>
                 <div className={this.props.store.uniprotId.result ? '' : 'invisible'}>
-                    <span data-test="GeneSummaryUniProt">UniProt: </span>
-                    <a
-                        href={`http://www.uniprot.org/uniprot/${uniprotId}`}
-                        target="_blank"
-                    >
-                        {uniprotId}
-                    </a>
+                    <span data-test="GeneSummaryUniProt">{'UniProt: '}
+                        <a
+                            href={`http://www.uniprot.org/uniprot/${uniprotId}`}
+                            target="_blank"
+                        >
+                            {uniprotId}
+                        </a>
+                    </span>
                 </div>
                 <div className={this.props.store.canonicalTranscript.result ? '' : 'invisible'}>
                     <span>Transcript: </span>

From 1939922583912b6a4f2cb12dad3e3a2e33fdcfdc Mon Sep 17 00:00:00 2001
From: Ersin Ciftci <arseniusthegreat@gmail.com>
Date: Thu, 10 May 2018 11:19:54 -0400
Subject: [PATCH 2/2] Fix mutex filtering bug

Fixes https://github.com/cBioPortal/cbioportal/issues/4202


Former-commit-id: d3e497f8ab708b5863bcbeb80ef7f0ba2893c184
---
 .../MutualExclusivityUtil.spec.tsx            | 32 +++++++++----------
 .../MutualExclusivityUtil.tsx                 |  7 ++--
 2 files changed, 20 insertions(+), 19 deletions(-)

diff --git a/src/pages/resultsView/mutualExclusivity/MutualExclusivityUtil.spec.tsx b/src/pages/resultsView/mutualExclusivity/MutualExclusivityUtil.spec.tsx
index 15489b829f6..bb0ba1b973d 100644
--- a/src/pages/resultsView/mutualExclusivity/MutualExclusivityUtil.spec.tsx
+++ b/src/pages/resultsView/mutualExclusivity/MutualExclusivityUtil.spec.tsx
@@ -26,6 +26,18 @@ const exampleData = [
         "adjustedPValue": 0.023809523809523704,
         "association": "Mutual exclusivity"
     },
+    {
+        "geneA": "TP53",
+        "geneB": "BRAF",
+        "neitherCount": 6,
+        "aNotBCount": 0,
+        "bNotACount": 1,
+        "bothCount": 3,
+        "logOddsRatio": Infinity,
+        "pValue": 0.03333333333333314,
+        "adjustedPValue": 0.19999999999999885,
+        "association": "Co-occurrence"
+    },
     {
         "geneA": "EGFR",
         "geneB": "TP53",
@@ -73,18 +85,6 @@ const exampleData = [
         "pValue": 0.2619047619047609,
         "adjustedPValue": 1,
         "association": "Co-occurrence"
-    },
-    {
-        "geneA": "TP53",
-        "geneB": "BRAF",
-        "neitherCount": 6,
-        "aNotBCount": 0,
-        "bNotACount": 1,
-        "bothCount": 3,
-        "logOddsRatio": Infinity,
-        "pValue": 0.03333333333333314,
-        "adjustedPValue": 0.19999999999999885,
-        "association": "Co-occurrence"
     }
 ];
 
@@ -242,8 +242,8 @@ describe("MutualExclusivityUtil", () => {
                         "bNotACount": 5,
                         "bothCount": 0,
                         "logOddsRatio": -6.51,
-                        "pValue": 0.04,
-                        "adjustedPValue": 0.08,
+                        "pValue": 0.02,
+                        "adjustedPValue": 0.04,
                         "association": "Mutual exclusivity"
                     },
                     {
@@ -277,8 +277,8 @@ describe("MutualExclusivityUtil", () => {
                     "bNotACount": 5,
                     "bothCount": 0,
                     "logOddsRatio": -6.51,
-                    "pValue": 0.04,
-                    "adjustedPValue": 0.08,
+                    "pValue": 0.02,
+                    "adjustedPValue": 0.04,
                     "association": "Mutual exclusivity"
                 },
                 {
diff --git a/src/pages/resultsView/mutualExclusivity/MutualExclusivityUtil.tsx b/src/pages/resultsView/mutualExclusivity/MutualExclusivityUtil.tsx
index 47c5b5ba6f4..dafbf5123ee 100644
--- a/src/pages/resultsView/mutualExclusivity/MutualExclusivityUtil.tsx
+++ b/src/pages/resultsView/mutualExclusivity/MutualExclusivityUtil.tsx
@@ -3,6 +3,7 @@ import { getCumulativePValue } from "../../../shared/lib/FisherExactTestCalculat
 import { MutualExclusivity } from "../../../shared/model/MutualExclusivity";
 import Combinatorics from 'js-combinatorics';
 import Dictionary = _.Dictionary;
+import * as _ from 'lodash';
 
 export function calculateAssociation(logOddsRatio: number): string {
     return logOddsRatio > 0 ? "Co-occurrence" : "Mutual exclusivity";
@@ -55,7 +56,7 @@ export function getMutuallyExclusiveCounts(data: MutualExclusivity[],
     let significantCount = null;
 
     const exclusiveData = data.filter(mutualExclusivity => exclusive(mutualExclusivity.logOddsRatio));
-    const significantData = exclusiveData.filter(mutualExclusivity => mutualExclusivity.pValue < 0.05);
+    const significantData = exclusiveData.filter(mutualExclusivity => mutualExclusivity.adjustedPValue < 0.05);
 
     const exclusiveLength = exclusiveData.length;
     const significantLength = significantData.length;
@@ -105,7 +106,7 @@ export function getData(isSampleAlteredMap: Dictionary<boolean[]>): MutualExclus
             bothCount: counts[3], logOddsRatio, pValue, 
             adjustedPValue: calculateAdjustedPValue(pValue, combinations.length), association });
     });
-    return data;
+    return _.sortBy(data, ["pValue"]);
 }
 
 export function getFilteredData(data: MutualExclusivity[], mutualExclusivityFilter: boolean, coOccurenceFilter: boolean,
@@ -120,7 +121,7 @@ export function getFilteredData(data: MutualExclusivity[], mutualExclusivityFilt
             result = result || mutualExclusivity.logOddsRatio > 0;
         }
         if (significantPairsFilter) {
-            result = result && mutualExclusivity.pValue < 0.05;
+            result = result && mutualExclusivity.adjustedPValue < 0.05;
         }
         return result;
     });