From 045e5bedb98cb202d34b241927474b0925e9d78f Mon Sep 17 00:00:00 2001
From: kshefchek <kshefchek@gmail.com>
Date: Fri, 16 Mar 2018 15:58:15 -0700
Subject: [PATCH 1/3] switch travis back to dev

---
 .travis.yml        |  2 +-
 lib/monarch/api.js | 10 +---------
 2 files changed, 2 insertions(+), 10 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 54d05e8d..ecdb6883 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -61,7 +61,7 @@ install:
 before_script:
   - "export DISPLAY=:99.0"
   - "ls -lhS dist/"
-  - "USE_LOG_FETCH=1 npm run startprod &"
+  - "USE_LOG_FETCH=1 npm run startbeta &"
   - "sleep 20"
 
 after_success:
diff --git a/lib/monarch/api.js b/lib/monarch/api.js
index a05da898..75615547 100644
--- a/lib/monarch/api.js
+++ b/lib/monarch/api.js
@@ -667,7 +667,6 @@ bbop.monarch.Engine.prototype.fetchOrthologList = function(ids) {
 
     ids.forEach(function(id) {
         var orthoObj = engine.fetchGeneOrthologFromSciGraph(id,'label',true);
-        //results.orthologs = results.orthologs.concat(orthoObj);
         orthoObj.forEach(function(homolog) {
             if (homolog.orthology_class === 'Paralog'){
                 results.paralogs = results.paralogs.concat(homolog.ortholog.id);
@@ -679,7 +678,7 @@ bbop.monarch.Engine.prototype.fetchOrthologList = function(ids) {
         });
     });
 
-    var filter = "^OMIM|NCBI|MGI|ZFIN|ENSEMBL:ENSG\\d+|ENSEMBL:ENSDARG\\d+|ENSEMBL\:ENSMUSG\\d+";
+    var filter = "^OMIM|HGNC|NCBI|MGI|ZFIN|ENSEMBL:ENSG\\d+|ENSEMBL:ENSDARG\\d+|ENSEMBL\:ENSMUSG\\d+";
     var filtered_regex = new RegExp(filter);
 
     results.paralogs = results.paralogs.filter(function(d){
@@ -2304,13 +2303,6 @@ bbop.monarch.Engine.prototype.getPhenotypeGenotypeDistro = function(id,levels,is
 
     var taxMap = {};
 
-    /*var taxMap = {
-            10090 : "Mouse",
-            7955  : "Zebrafish",
-            6239  : "Nematode",
-            9606  : "Human",
-            7227  : "Fruit Fly"
-    };*/
     if (countFn == 'fetchGenoPhenoAsAssociationsBySpecies'){
         taxMap = {
                 10090 : "Mouse"

From 231d7abd28677aa1486f098911c0d73fa3cd5a09 Mon Sep 17 00:00:00 2001
From: kshefchek <kshefchek@gmail.com>
Date: Fri, 23 Mar 2018 10:33:33 -0700
Subject: [PATCH 2/3] fix hyper-beta test

---
 tests/behave/maui_autocomplete.feature | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/behave/maui_autocomplete.feature b/tests/behave/maui_autocomplete.feature
index b3560f1a..d9bd1606 100644
--- a/tests/behave/maui_autocomplete.feature
+++ b/tests/behave/maui_autocomplete.feature
@@ -37,7 +37,7 @@ Scenario: "ZRS" in the navbar search with a click goes to a gene page
 Scenario: "hyper-be" in the navbar search with a click goes to a disease page
    Given I go to page "/"
     and I type "Hyper-bet" into the navbar search
-    and I wait until "HYPER-BETA-ALANINEMIA" appears in the autocomplete
-    and I click the autocomplete item "HYPER-BETA-ALANINEMIA"
+    and I wait until "Hyper-beta-alaninemia" appears in the autocomplete
+    and I click the autocomplete item "Hyper-beta-alaninemia"
     when I wait for id "monarch-node"
     then the title should be "Monarch Disease: hyper-beta-alaninemia (MONDO:0009378)"

From 4300033342b33dda7414e7334022bccfb54a6925 Mon Sep 17 00:00:00 2001
From: kshefchek <kshefchek@gmail.com>
Date: Fri, 23 Mar 2018 11:19:05 -0700
Subject: [PATCH 3/3] reintroduce clinical modifier hack

---
 lib/monarch/web/webapp.js | 33 ++++++++++++++++++++++++++++++++-
 1 file changed, 32 insertions(+), 1 deletion(-)

diff --git a/lib/monarch/web/webapp.js b/lib/monarch/web/webapp.js
index 35b1f730..cd182bb5 100644
--- a/lib/monarch/web/webapp.js
+++ b/lib/monarch/web/webapp.js
@@ -3421,6 +3421,37 @@ function diseaseByIdHandler(request, id, fmt) {
         }
     }
 
+    const inheritanceClasses = [
+        'HP:0001444',
+        'HP:0001423',
+        'HP:0001417',
+        'HP:0010983',
+        'HP:0010982',
+        'HP:0003743',
+        'HP:0001475',
+        'HP:0001470',
+        'HP:0025352',
+        'HP:0001442',
+        'HP:0012275',
+        'HP:0001419',
+        'HP:0001466',
+        'HP:0000005',
+        'HP:0000006',
+        'HP:0000007',
+        'HP:0012274',
+        'HP:0010985',
+        'HP:0010984',
+        'HP:0003744',
+        'HP:0003745',
+        'HP:0001472',
+        'HP:0001450',
+        'HP:0001452',
+        'HP:0001425',
+        'HP:0001426',
+        'HP:0001427',
+        'HP:0001428',
+    ];
+
     if (inheritanceList.length > 0) {
         info.inheritance = inheritanceList
             .filter(node => node.metadata().types.indexOf('inheritance') > -1)
@@ -3428,7 +3459,7 @@ function diseaseByIdHandler(request, id, fmt) {
             .join(', ');
 
         info.modifier = inheritanceList
-            .filter(node => node.metadata().types.indexOf('clinical modifier') > -1)
+            .filter(node => inheritanceClasses.indexOf(node.id()) === -1)
             .map(node => node.label())
             .join(', ');
     }