bugfixes & disabled automatic classification algorithm

GC-HBOC · Jan 10, 2024 · c14a688 · c14a688
1 parent c810027
commit c14a688
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Showing 5 changed files with 47 additions and 27 deletions.
diff --git a/resources/classification_schemes/ClinGen_BRCA1_v1.0.0.json b/resources/classification_schemes/ClinGen_BRCA1_v1.0.0.json
@@ -409,7 +409,7 @@
                 "PP1_Very Strong - LR>350:1",
                 "PP1_Strong - LR>18.7:1",
                 "PP1_Moderate - LR>4.3:1",
-                "PP1 - LR >2.08:1",
+                "PP1 - LR>2.08:1",
                 "",
                 "Instructions:",
                 "Recommend use of online tool: https://fengbj-laboratory.org/cool3/analysis.html ",
@@ -419,6 +419,24 @@
             "is_selectable": "1",
             "relevant_info": "",
             "strengths": [
+                {
+                    "name": "pvs",
+                    "display_name":"vstr",
+                    "description": "very strong pathogenic",
+                    "is_default": "0"
+                },
+                {
+                    "name": "ps",
+                    "display_name":"str",
+                    "description": "strong pathogenic",
+                    "is_default": "0"
+                },
+                {
+                    "name": "pm",
+                    "display_name":"mod",
+                    "description": "medium pathogenic",
+                    "is_default": "0"
+                },
                 {
                     "name": "pp",
                     "display_name":"sup",
@@ -442,24 +460,6 @@
             "is_selectable": "0",
             "relevant_info": "",
             "strengths": [
-                {
-                    "name": "pvs",
-                    "display_name":"vstr",
-                    "description": "very strong pathogenic",
-                    "is_default": "0"
-                },
-                {
-                    "name": "ps",
-                    "display_name":"str",
-                    "description": "strong pathogenic",
-                    "is_default": "0"
-                },
-                {
-                    "name": "pm",
-                    "display_name":"mod",
-                    "description": "medium pathogenic",
-                    "is_default": "0"
-                },
                 {
                     "name": "pp",
                     "display_name":"sup",
@@ -514,7 +514,7 @@
                 "PP4_Very Strong - LR>350:1",
                 "PP4_Strong - LR>18.7:1",
                 "PP4_Moderate - LR>4.3:1",
-                "PP4 - LR >2.08:1 ",
+                "PP4 - LR>2.08:1 ",
                 "Combined LR 1.00-2.08 is not informative (PP4 not applicable).",
                 "See Specifications Table7 and Appendix B for details.",
                 "",
@@ -525,6 +525,12 @@
             "is_selectable": "1",
             "relevant_info": "",
             "strengths": [
+                {
+                    "name": "pvs",
+                    "display_name":"vstr",
+                    "description": "very strong pathogenic",
+                    "is_default": "0"
+                },
                 {
                     "name": "ps",
                     "display_name":"str",

diff --git a/resources/classification_schemes/ClinGen_BRCA2_v1.0.0.json b/resources/classification_schemes/ClinGen_BRCA2_v1.0.0.json
@@ -410,7 +410,7 @@
                 "PP1_Very Strong - LR>350:1",
                 "PP1_Strong - LR>18.7:1",
                 "PP1_Moderate - LR>4.3:1",
-                "PP1 - LR >2.08:1",
+                "PP1 - LR>2.08:1",
                 "",
                 "Instructions:",
                 "Recommend use of online tool: https://fengbj-laboratory.org/cool3/analysis.html ",
@@ -420,6 +420,12 @@
             "is_selectable": "1",
             "relevant_info": "",
             "strengths": [
+                {
+                    "name": "pvs",
+                    "display_name":"vstr",
+                    "description": "very strong pathogenic",
+                    "is_default": "0"
+                },
                 {
                     "name": "ps",
                     "display_name":"str",
@@ -506,10 +512,10 @@
                 "Gene-specific modifications:",
                 "Breast cancer is very common and has a high degree of genetic heterogeneity (caused by pathogenic variants in numerous genes). Use ONLY to capture combined LR towards pathogenicity, based on multifactorial likelihood clinical data.",
                 "",
-                "PP4_Strong - LR>18.7:1",
                 "PP4_Very Strong - LR>350:1",
+                "PP4_Strong - LR>18.7:1",
                 "PP4_Moderate - LR>4.3:1",
-                "PP4 - LR >2.08:1",
+                "PP4 - LR>2.08:1",
                 "",
                 "Combined LR 1.00-2.08 is not informative (PP4 not applicable).",
                 "See Specifications Table7 and Appendix B for details.",
@@ -521,6 +527,12 @@
             "is_selectable": "1",
             "relevant_info": "",
             "strengths": [
+                {
+                    "name": "pvs",
+                    "display_name":"vstr",
+                    "description": "very strong pathogenic",
+                    "is_default": "0"
+                },
                 {
                     "name": "ps",
                     "display_name":"str",

diff --git a/src/annotation_service/main.py b/src/annotation_service/main.py
@@ -19,7 +19,7 @@
 def get_default_job_config():
     job_config = {
         # heredicare annotations
-        'do_heredicare': False,
+        'do_heredicare': True,
 
         # external programs
         'do_phylop': True,
@@ -50,7 +50,7 @@ def get_default_job_config():
         # additional annotations
         'do_taskforce_domains': True,
         'do_litvar': True,
-        'do_auto_class': True
+        'do_auto_class': False
     }
     return job_config
 

diff --git a/src/frontend_celery/webapp/templates/index.html b/src/frontend_celery/webapp/templates/index.html
@@ -92,7 +92,7 @@ <h4>Overview</h4>
 
 <div class="bst bsb">
     <h4>Changelog</h4>
-    <div class="underline">v 1.6 ()</div>
+    <div class="underline">v 1.6 (10.01.2024)</div>
     <div>
         General changes:
         <ul>
@@ -132,6 +132,8 @@ <h4>Changelog</h4>
             <li>Fixed a bug when trying to add all variants from a search to a list</li>
             <li>In BRCA2 v1.0.0 criteria supporting strength was not selectable</li>
             <li>Sometimes, the classification scheme was not changeable in consensus classifications</li>
+            <li>BRCA1 v1.0.0 PP1 criterium was missing strength selection and PP4 criterium was missing very strong strength</li>
+            <li>BRCA2 v1.0.0 PP1 and PP4 criteria were missing very strong strength</li>
         </ul>
         Known issues:
         <ul>

diff --git a/src/frontend_celery/webapp/templates/user/admin_dashboard.html b/src/frontend_celery/webapp/templates/user/admin_dashboard.html
@@ -118,7 +118,7 @@ <h4>Warnings</h4>
                 <div class="d-flex flex-wrap">
                     {% for job in job_config %}
                     <div class="mb-3 form-check bsr width_very_medium">
-                        <input type="checkbox" class="form-check-input ssr" id="{{ job }}" name="job" value="{{ job }}">
+                        <input type="checkbox" class="form-check-input ssr" id="{{ job }}" name="job" value="{{ job }}" {% if not job_config[job] %} disabled {% endif %}>
                         <label class="form-check-label" for="{{ job }}">{{ job }}</label>
                     </div>
                     {% endfor %}