Made flag filter and flag form nomenclature consistent

varfish-org · Jun 10, 2022 · 6cf25be · 6cf25be
1 parent 68e6c22
commit 6cf25be
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Showing 3 changed files with 34 additions and 32 deletions.
diff --git a/HISTORY.rst b/HISTORY.rst
@@ -24,6 +24,7 @@ End-User Summary
 - 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).
+- Made flag filter and flag form nomenclature consistent (#297)
 
 Full Change List
 ================
@@ -43,6 +44,7 @@ Full Change List
 - 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).
+- Made flag filter and flag form nomenclature consistent (#297)
 
 ------
 v1.2.0

diff --git a/variants/templates/variants/_multi_variant_flag_form_tpl.html b/variants/templates/variants/_multi_variant_flag_form_tpl.html
@@ -57,19 +57,19 @@
           Visual
         </label>
         <div class="ml-auto">
-          <div class="form-check form-check-inline" data-toggle="tooltip" title="true variant">
+          <div class="form-check form-check-inline" data-toggle="tooltip" title="positive">
             <input class="form-check-input" id="comment-radio-visual-positive" type="radio" name="flag_visual" value="positive" {{if flag_visual == "positive"}}checked{{/if}}/>
             <label for="comment-radio-visual-positive" class="m-0"><i class="iconify text-danger" data-icon="fa-solid:exclamation-circle"></i></label>
           </div>
           <div class="form-check form-check-inline" data-toggle="tooltip" title="uncertain">
             <input class="form-check-input" id="comment-radio-visual-uncertain" type="radio" name="flag_visual" value="uncertain" {{if flag_visual == "uncertain"}}checked{{/if}} />
             <label for="comment-radio-visual-uncertain" class="m-0"><i class="iconify text-warning" data-icon="fa-solid:question"></i></label>
           </div>
-          <div class="form-check form-check-inline" data-toggle="tooltip" title="artifact">
+          <div class="form-check form-check-inline" data-toggle="tooltip" title="negative">
             <input class="form-check-input" id="comment-radio-visual-negative" type="radio" name="flag_visual" value="negative" {{if flag_visual == "negative"}}checked{{/if}}/>
             <label for="comment-radio-visual-negative" class="m-0"><i class="iconify text-success" data-icon="fa-solid:minus-circle"></i></label>
           </div>
-          <div class="form-check form-check-inline" data-toggle="tooltip" title="not considered">
+          <div class="form-check form-check-inline" data-toggle="tooltip" title="empty">
             <input class="form-check-input" id="comment-radio-visual-empty" type="radio" name="flag_visual" value="empty" {{if flag_visual == "empty"}}checked{{/if}} />
             <label for="comment-radio-visual-empty" class="m-0"><i class="iconify text-secondary" data-icon="fa-solid:times"></i></label>
           </div>
@@ -81,19 +81,19 @@
           Molecular
         </label>
         <div class="ml-auto">
-          <div class="form-check form-check-inline" data-toggle="tooltip" title="strong evidence for missense variant">
+          <div class="form-check form-check-inline" data-toggle="tooltip" title="positive">
             <input class="form-check-input" id="comment-radio-molecular-positive" type="radio" name="flag_molecular" value="positive" {{if flag_molecular == "positive"}}checked{{/if}}/>
             <label for="comment-radio-molecular-positive" class="m-0"><i class="iconify text-danger" data-icon="fa-solid:exclamation-circle"></i></label>
           </div>
-          <div class="form-check form-check-inline" data-toggle="tooltip" title="medium evidence for missense variant">
+          <div class="form-check form-check-inline" data-toggle="tooltip" title="uncertain">
             <input class="form-check-input" id="comment-radio-molecular-uncertain" type="radio" name="flag_molecular" value="uncertain" {{if flag_molecular == "uncertain"}}checked{{/if}} />
             <label for="comment-radio-molecular-uncertain" class="m-0"><i class="iconify text-warning" data-icon="fa-solid:question"></i></label>
           </div>
-          <div class="form-check form-check-inline" data-toggle="tooltip" title="weak evidence for missense variant">
+          <div class="form-check form-check-inline" data-toggle="tooltip" title="negative">
             <input class="form-check-input" id="comment-radio-molecular-negative" type="radio" name="flag_molecular" value="negative" {{if flag_molecular == "negative"}}checked{{/if}}/>
             <label for="comment-radio-molecular-negative" class="m-0"><i class="iconify text-success" data-icon="fa-solid:minus-circle"></i></label>
           </div>
-          <div class="form-check form-check-inline" data-toggle="tooltip" title="not considered">
+          <div class="form-check form-check-inline" data-toggle="tooltip" title="empty">
             <input class="form-check-input" id="comment-radio-molecular-empty" type="radio" name="flag_molecular" value="empty" {{if flag_molecular == "empty"}}checked{{/if}} />
             <label for="comment-radio-molecular-empty" class="m-0"><i class="iconify text-secondary" data-icon="fa-solid:times"></i></label>
           </div>
@@ -105,19 +105,19 @@
           Validation
         </label>
         <div class="ml-auto">
-          <div class="form-check form-check-inline" data-toggle="tooltip" title="confirmed / true variant">
+          <div class="form-check form-check-inline" data-toggle="tooltip" title="positive">
             <input class="form-check-input" id="comment-radio-validation-positive" type="radio" name="flag_validation" value="positive" {{if flag_validation == "positive"}}checked{{/if}} />
             <label for="comment-radio-validation-positive" class="m-0"><i class="iconify text-danger" data-icon="fa-solid:exclamation-circle"></i></label>
           </div>
           <div class="form-check form-check-inline" data-toggle="tooltip" title="uncertain">
             <input class="form-check-input" id="comment-radio-validation-uncertain" type="radio" name="flag_validation" value="uncertain" {{if flag_validation == "uncertain"}}checked{{/if}} />
             <label for="comment-radio-validation-uncertain" class="m-0"><i class="iconify text-warning" data-icon="fa-solid:question"></i></label>
           </div>
-          <div class="form-check form-check-inline" data-toggle="tooltip" title="not confirmed / artifact">
+          <div class="form-check form-check-inline" data-toggle="tooltip" title="negative">
             <input class="form-check-input" id="comment-radio-validation-negative" type="radio" name="flag_validation" value="negative" {{if flag_validation == "negative"}}checked{{/if}} />
             <label for="comment-radio-validation-negative" class="m-0"><i class="iconify text-success" data-icon="fa-solid:minus-circle"></i></label>
           </div>
-          <div class="form-check form-check-inline" data-toggle="tooltip" title="assign no rating">
+          <div class="form-check form-check-inline" data-toggle="tooltip" title="empty">
             <input class="form-check-input" id="comment-radio-validation-empty" type="radio" name="flag_validation" value="empty" {{if flag_validation == "empty"}}checked{{/if}} />
             <label for="comment-radio-validation-empty" class="m-0"><i class="iconify text-secondary" data-icon="fa-solid:times"></i></label>
           </div>
@@ -129,19 +129,19 @@
           Pheno./Clinic
         </label>
         <div class="ml-auto">
-          <div class="form-check form-check-inline" data-toggle="tooltip" title="good match">
+          <div class="form-check form-check-inline" data-toggle="tooltip" title="positive">
             <input class="form-check-input" id="comment-radio-clinic-positive" type="radio" name="flag_phenotype_match" value="positive" {{if flag_phenotype_match == "positive"}}checked{{/if}} />
             <label for="comment-radio-clinic-positive" class="m-0"><i class="iconify text-danger" data-icon="fa-solid:exclamation-circle"></i></label>
           </div>
           <div class="form-check form-check-inline" data-toggle="tooltip" title="uncertain">
             <input class="form-check-input" id="comment-radio-clinic-uncertain" type="radio" name="flag_phenotype_match" value="uncertain" {{if flag_phenotype_match == "uncertain"}}checked{{/if}} />
             <label for="comment-radio-clinic-uncertain" class="m-0"><i class="iconify text-warning" data-icon="fa-solid:question"></i></label>
           </div>
-          <div class="form-check form-check-inline" data-toggle="tooltip" title="no match">
+          <div class="form-check form-check-inline" data-toggle="tooltip" title="negative">
             <input class="form-check-input" id="comment-radio-clinic-negative" type="radio" name="flag_phenotype_match" value="negative" {{if flag_phenotype_match == "negative"}}checked{{/if}} />
             <label for="comment-radio-clinic-negative" class="m-0"><i class="iconify text-success" data-icon="fa-solid:minus-circle"></i></label>
           </div>
-          <div class="form-check form-check-inline" data-toggle="tooltip" title="assign no rating">
+          <div class="form-check form-check-inline" data-toggle="tooltip" title="empty">
             <input class="form-check-input" id="comment-radio-clinic-empty" type="radio" name="flag_phenotype_match" value="empty" {{if flag_phenotype_match == "empty"}}checked{{/if}} />
             <label for="comment-radio-clinic-empty" class="m-0"><i class="iconify text-secondary" data-icon="fa-solid:times"></i></label>
           </div>
@@ -153,19 +153,19 @@
           Summary
         </label>
         <div class="ml-auto">
-          <div class="form-check form-check-inline" data-toggle="tooltip" title="pathogenic">
+          <div class="form-check form-check-inline" data-toggle="tooltip" title="positive">
             <input class="form-check-input" id="comment-radio-summary-positive" type="radio" name="flag_summary" value="positive" {{if flag_summary == "positive"}}checked{{/if}} />
             <label for="comment-radio-summary-positive" class="m-0"><i class="iconify text-danger" data-icon="fa-solid:exclamation-circle"></i></label>
           </div>
           <div class="form-check form-check-inline" data-toggle="tooltip" title="uncertain">
             <input class="form-check-input" id="comment-radio-summary-uncertain" type="radio" name="flag_summary" value="uncertain" {{if flag_summary == "uncertain"}}checked{{/if}} />
             <label for="comment-radio-summary-uncertain" class="m-0"><i class="iconify text-warning" data-icon="fa-solid:question"></i></label>
           </div>
-          <div class="form-check form-check-inline" data-toggle="tooltip" title="benign or artifact">
+          <div class="form-check form-check-inline" data-toggle="tooltip" title="negative">
             <input class="form-check-input" id="comment-radio-summary-negative" type="radio" name="flag_summary" value="negative" {{if flag_summary == "negative"}}checked{{/if}} />
             <label for="comment-radio-summary-negative" class="m-0"><i class="iconify text-success" data-icon="fa-solid:minus-circle"></i></label>
           </div>
-          <div class="form-check form-check-inline" data-toggle="tooltip" title="assign no rating">
+          <div class="form-check form-check-inline" data-toggle="tooltip" title="empty">
             <input class="form-check-input" id="comment-radio-summary-empty" type="radio" name="flag_summary" value="empty" {{if flag_summary == "empty"}}checked{{/if}} />
             <label for="comment-radio-summary-empty" class="m-0"><i class="iconify text-secondary" data-icon="fa-solid:times"></i></label>
           </div>