Make gene panel manual inheritance models more clear (#3046)

* Made some improvements but custom models stringfield is still displaying an empoty array

* modify field name

* update changelog

* Rename the gene panels inheritance models in constants

* rename the 2 cols

* fix genetic models parsing in panels

CHANGELOG.md

@@ -8,6 +8,7 @@ About changelog [here](https://keepachangelog.com/en/1.0.0/)
 ### Added
 ### Changed
 - Start Scout also when loqusdbapi is not reachable
+- Clearer definition of manual standard and custom inheritance models in gene panels
 ### Fixed
 - Gene panel crashing on edit action
 

scout/constants/__init__.py

@@ -29,7 +29,7 @@
 from .file_types import FILE_TYPE_MAP
 from .filters import CLINICAL_FILTER_BASE, CLINICAL_FILTER_BASE_CANCER, CLINICAL_FILTER_BASE_SV
 from .gene_tags import (
-    GENE_CUSTOM_INHERITANCE_MODELS,
+    GENE_PANELS_INHERITANCE_MODELS,
     INCOMPLETE_PENETRANCE_MAP,
     MODELS_MAP,
     PANEL_GENE_INFO_MODELS,

scout/constants/gene_tags.py

@@ -2,17 +2,17 @@
 # which are specified by GENETIC_MODELS (in variant_tags.py).
 # The following models are used while describing inheritance of genes in gene panels
 # It's a custom-compiled list of values
-GENE_CUSTOM_INHERITANCE_MODELS = (
-    ("AD", "Autosomal Dominant"),
-    ("AR", "Autosomal recessive"),
-    ("XL", "X Linked"),
-    ("XD", "X Linked Dominant"),
-    ("XR", "X Linked Recessive"),
-    ("NA", "not available"),
-    ("AD (imprinting)", "Autosomal Dominant (imprinting)"),
-    ("digenic", "Digenic"),
-    ("AEI", "Allelic expression imbalance"),
-    ("other", "Other"),
+GENE_PANELS_INHERITANCE_MODELS = (
+    ("AD", "AD - Autosomal Dominant"),
+    ("AR", "AR - Autosomal recessive"),
+    ("XL", "XL - X Linked"),
+    ("XD", "XD - X Linked Dominant"),
+    ("XR", "XR - X Linked Recessive"),
+    ("NA", "NA - not available"),
+    ("AD (imprinting)", "AD (imprinting) - Autosomal Dominant (imprinting)"),
+    ("digenic", "digenic - Digenic"),
+    ("AEI", "AEI - Allelic expression imbalance"),
+    ("other", "other - Other"),
 )
 
 VALID_MODELS = ("AR", "AD", "MT", "XD", "XR", "X", "Y")

scout/parse/panel.py

@@ -138,7 +138,7 @@ def parse_gene(gene_info):
 
     # Collect whichever model provided by the user.
     # Then populate inheritance_models and custom_inheritance_models on gene build step
-    gene["inheritance_models"] = [model.strip() for model in models.split(",")]
+    gene["inheritance_models"] = [model.strip() for model in models.split(",") if model != ""]
 
     # If a gene is known to be associated with mosaicism this is annotated
     gene["mosaicism"] = bool(gene_info.get("mosaicism"))

scout/server/blueprints/panels/forms.py

@@ -2,18 +2,19 @@
 from flask_wtf import FlaskForm
 from wtforms import BooleanField, SelectMultipleField, StringField
 
-from scout.constants import GENE_CUSTOM_INHERITANCE_MODELS
+from scout.constants import GENE_PANELS_INHERITANCE_MODELS
 
 
 class PanelGeneForm(FlaskForm):
     disease_associated_transcripts = SelectMultipleField("Disease transcripts", choices=[])
     reduced_penetrance = BooleanField()
     mosaicism = BooleanField()
     database_entry_version = StringField()
+
     inheritance_models = SelectMultipleField(
-        "Standard inheritance models", choices=GENE_CUSTOM_INHERITANCE_MODELS
+        "Manual inheritance (pre-set terms)", choices=GENE_PANELS_INHERITANCE_MODELS
     )
     custom_inheritance_models = StringField(
-        "Other non-standard inheritance models (free text, comma separated)"
+        "Manual inheritance (free text terms)",
     )
     comment = StringField()

scout/server/blueprints/panels/templates/panels/gene-edit.html

@@ -43,13 +43,13 @@
             <div class="row">
               <div class="col-md-4">
                 {{ form.inheritance_models.label(class="control-label") }}<br>
-                {{ form.inheritance_models(class="selectpicker") }}
+                {{ form.inheritance_models(class="selectpicker", data_width="100%") }}
               </div>
               <div class="col-md-4">
                 {{ form.custom_inheritance_models.label(class="control-label") }}
-                {{ form.custom_inheritance_models(class="form-control") }}
+                {{ form.custom_inheritance_models(class="form-control", placeholder="free text, comma separated") }}
               </div>
-              <div class="col-md-4">
+              <div class="col-md-2">
                 {{ form.database_entry_version.label(class="control-label") }}
                 (ex: 1.2)
                 {{ form.database_entry_version(class="form-control") }}

scout/server/blueprints/panels/templates/panels/panel.html

@@ -121,8 +121,8 @@
             <th>Reduced penetrance</th>
             <th>Mosaicism</th>
             <th>Entry version</th>
-            <th>Standard inheritance models</th>
-            <th>Custom inheritance models</th>
+            <th>Manual inheritance (pre-set terms)</th>
+            <th>Manual inheritance (free text terms)</th>
             <th>Comment</th>
             <th>Action</th>
           </tr>

scout/server/blueprints/panels/views.py

@@ -235,7 +235,6 @@ def tx_choices(hgnc_id, panel_obj):
 @templated("panels/gene-edit.html")
 def gene_edit(panel_id, hgnc_id):
     """Edit additional information about a panel gene."""
-
     panel_obj = store.panel(panel_id)
     hgnc_gene = store.hgnc_gene(hgnc_identifier=hgnc_id, build="37") or store.hgnc_gene(
         hgnc_identifier=hgnc_id, build="38"
@@ -254,14 +253,17 @@ def gene_edit(panel_id, hgnc_id):
             info_data["custom_inheritance_models"] = info_data["custom_inheritance_models"].split(
                 ","
             )
-
         store.add_pending(panel_obj, hgnc_gene, action=action, info=info_data)
         return redirect(url_for(".panel", panel_id=panel_id))
 
     if panel_gene:
-        form.custom_inheritance_models.data = ", ".join(
-            panel_gene.get("custom_inheritance_models", [])
-        )
+        custom_models = [
+            model for model in panel_gene.get("custom_inheritance_models", []) if model != ""
+        ]
+        if custom_models:
+            form.custom_inheritance_models.data = ", ".join(
+                panel_gene.get("custom_inheritance_models")
+            )
         for field_key in [
             "disease_associated_transcripts",
             "reduced_penetrance",