Merge 96126f7 into 2ffa36d

varfish-org · May 23, 2022 · 173db0b · 173db0b
2 parents 2ffa36d + 96126f7
commit 173db0b
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Showing 3 changed files with 22 additions and 6 deletions.
diff --git a/HISTORY.rst b/HISTORY.rst
@@ -23,6 +23,7 @@ End-User Summary
 - Properly display the clinvar annotations that we have in the database (#464).
 - Adjusting default frequency filters for "clinvar pathogenic" filter: remove all threshold (#464).
 - Adding note about difference with upstream Clinvar (#464).
+- Switching scoring to MutationTaster 85 interface, added back MT 85 link-out alongside MT 2021 link-out (#509).
 
 Full Change List
 ================
@@ -41,6 +42,7 @@ Full Change List
 - Properly display the clinvar annotations that we have in the database (#464).
 - Adjusting default frequency filters for "clinvar pathogenic" filter: remove all threshold (#464).
 - Adding note about difference with upstream Clinvar (#464).
+- Switching scoring to MutationTaster 85 interface, added back MT 85 link-out alongside MT 2021 link-out (#509).
 
 ------
 v1.2.0

diff --git a/config/settings/base.py b/config/settings/base.py
@@ -540,7 +540,7 @@ def set_logging(level=None):
 
 # Varfish: MutationTaster URL
 VARFISH_MUTATIONTASTER_REST_API_URL = env.str(
-    "VARFISH_MUTATIONTASTER_REST_API_URL", "https://www.genecascade.org/MT2021/MT_API102.cgi",
+    "VARFISH_MUTATIONTASTER_REST_API_URL", "https://www.genecascade.org/MTc85/MT_API.cgi",
 )
 VARFISH_MUTATIONTASTER_BATCH_VARS = env.int("VARFISH_MUTATIONTASTER_BATCH_VARS", 50)
 VARFISH_MUTATIONTASTER_MAX_VARS = env.int("VARFISH_MUTATIONTASTER_MAX_VARS", 500)

diff --git a/variants/templates/variants/filter_result/row.html b/variants/templates/variants/filter_result/row.html
@@ -458,13 +458,27 @@
         <span class="iconify" data-icon="mdi:binoculars"></span>
       </button>
       {% if entry.release == "GRCh37" %}
-        <a
-          href="https://www.genecascade.org/MTc2021/ChrPos102.cgi?chromosome={{ entry.chromosome }}&position={{ entry.start }}&ref={{ entry.reference }}&alt={{ entry.alternative }}"
-          data-toggle="tooltip"
-          title="Open variant in MutationTaster"
-          class="btn btn-primary sodar-list-btn">
+        <a class="btn btn-primary dropdown-toggle sodar-list-dropdown" role="button" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">
           MT
         </a>
+        <div class="dropdown-menu dropdown-menu-right">
+          <a
+            href="https://www.genecascade.org/MTc2021/ChrPos102.cgi?chromosome={{ entry.chromosome }}&position={{ entry.start }}&ref={{ entry.reference }}&alt={{ entry.alternative }}"
+            data-toggle="tooltip"
+            target="_blank"
+            title="Open variant in MutationTaster 2021"
+            class="btn btn-primary dropdown-item">
+            MT 2021
+          </a>
+          <a
+            href="https://www.genecascade.org/MT85/ChrPos85.cgi?chromosome={{ entry.chromosome }}&position={{ entry.start }}&ref={{ entry.reference }}&alt={{ entry.alternative }}"
+            data-toggle="tooltip"
+            target="_blank"
+            title="Open variant in MutationTaster 85"
+            class="btn btn-primary dropdown-item">
+            MT 85
+          </a>
+        </div>
       {% else %}
         <span
           class="btn btn-disabled sodar-list-btn btn-outline-secondary"