scout-browser 4.82.1__tar.gz → 4.82.2__tar.gz

{scout-browser-4.82.1 → scout-browser-4.82.2}/CHANGELOG.md

@@ -4,7 +4,12 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 
 About changelog [here](https://keepachangelog.com/en/1.0.0/)
 
-# [4.82.1]
+## [4.82.2]
+### Fixed
+- Warning icon in case pages for individuals where `confirmed_sex` is false
+- Show allele sizes form ExpansionHunter on STR variantS page again
+
+## [4.82.1]
 ### Fixed
 - Revert the installation of flask-ldapconn to use the version available on PyPI to be able to push new scout releases to PyPI
 

{scout-browser-4.82.1/scout_browser.egg-info → scout-browser-4.82.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: scout-browser
-Version: 4.82.1
+Version: 4.82.2
 Summary: Clinical DNA variant visualizer and browser.
 Home-page: https://github.com/Clinical-Genomics/scout
 Author: Måns Magnusson

scout-browser-4.82.2/scout/__version__.py

@@ -0,0 +1 @@
+__version__ = "4.82.2"

{scout-browser-4.82.1 → scout-browser-4.82.2}/scout/server/blueprints/cases/templates/cases/case_bionano.html

@@ -1,5 +1,6 @@
 {% extends "cases/case_tabular_view.html" %}
 {% from "utils.html" import comments_panel, activity_panel %}
+{% from "cases/utils.html" import sex_table_cell_content %}
 
 {% block title %}
   {{ super() }}
@@ -96,18 +97,7 @@
                   {% if loop.index == 1 %}
                     <td> {{ ind.display_name }}</td>
                     <td style="font-weight: bold;">
-                    {% if ind.sex_human in ['female','male'] %}
-                      {% if ind.sex_human == 'female' %}
-                        F
-                      {% elif ind.sex_human == 'male' %}
-                        M
-                      {% else %}
-                        {{ind.sex_human}}
-                      {% endif %}
-                    {% endif %}
-                    {% if ind.confirmed_sex %}
-                      <i class="fa fa-check"></i>
-                    {% endif %}
+                      {{ sex_table_cell_content(ind) }}
                     </td>
                     <td>{{ ind.phenotype_human }}</td>
                   {% else %}
@@ -130,18 +120,7 @@
               <tr class="bg-secondary text-white">
                 <td> {{ ind.display_name }}</td>
                     <td style="font-weight: bold;">
-                    {% if ind.sex_human in ['female','male'] %}
-                      {% if ind.sex_human == 'female' %}
-                        F
-                      {% elif ind.sex_human == 'male' %}
-                        M
-                      {% else %}
-                        {{ind.sex_human}}
-                      {% endif %}
-                    {% endif %}
-                    {% if ind.confirmed_sex %}
-                      <i class="fa fa-check"></i>
-                    {% endif %}
+                      {{ sex_table_cell_content(ind) }}
                     </td>
                     <td>{{ ind.phenotype_human }}</td>
                   <td colspan="4">N/A</td>

{scout-browser-4.82.1 → scout-browser-4.82.2}/scout/server/blueprints/cases/templates/cases/case_report.html

@@ -124,9 +124,11 @@
                       {% else %}
                         n.a.
                       {% endif %}
-	                    {% if ind.confirmed_sex %}
-	                      <span class="badge rounded-pill py-1 bg-secondary">V</span>
-	                    {% endif %}
+                      {% if ind.confirmed_sex %}
+                        <span class="badge rounded-pill py-1 bg-secondary">V</span>
+                      {% else %}
+                        <span class="fa fa-exclamation-circle text-danger" data-bs-toggle='tooltip' title="Sex is not confirmed."></span>
+                      {% endif %}
 	                  </td>
 	                  <td>
 	                  {% if ind.phenotype==2 %} <!--for later use-->

{scout-browser-4.82.1 → scout-browser-4.82.2}/scout/server/blueprints/cases/templates/cases/case_sma.html

@@ -1,6 +1,6 @@
 {% extends "cases/case_tabular_view.html" %}
 {% from "utils.html" import comments_panel, activity_panel %}
-{% from "cases/utils.html" import individuals_table %}
+{% from "cases/utils.html" import individuals_table, sex_table_cell_content %}
 
 {% block title %}
   {{ super() }}
@@ -100,18 +100,7 @@
                 {% endif %}>
               <td>{{ ind.display_name }}</td>
               <td style="font-weight: bold;">
-                {% if ind.sex_human in ['female','male'] %}
-                    {% if ind.sex_human == 'female' %}
-                      F
-                    {% elif ind.sex_human == 'male' %}
-                      M
-                    {% else %}
-                      {{ind.sex_human}}
-                    {% endif %}
-                  {% endif %}
-                {% if ind.confirmed_sex %}
-                  <i class="fa fa-check"></i>
-                {% endif %}
+                {{ sex_table_cell_content(ind) }}
               </td>
               <td>{{ ind.phenotype_human }}</td>
               <td>{{ ind.is_sma }}</td>

{scout-browser-4.82.1 → scout-browser-4.82.2}/scout/server/blueprints/cases/templates/cases/individuals_table.html

@@ -1,3 +1,4 @@
+{% from "cases/utils.html" import sex_table_cell_content %}
 
 {% macro cancer_individuals_table(case, institute, tissues, gens_info=None) %}
 <form method="POST" action="{{ url_for('cases.update_cancer_sample', institute_id=institute._id, case_name=case.display_name) }}">
@@ -138,18 +139,7 @@
                   <option {% if not ind.sex_human in ["female", "male"] %} selected= {% endif %} value="unknown">Unknown</option>
                 </select>
                 <div class="sex-display fw-bold">
-                  {% if ind.sex_human in ['female','male'] %}
-                    {% if ind.sex_human == 'female' %}
-                      F
-                    {% elif ind.sex_human == 'male' %}
-                      M
-                    {% else %}
-                      {{ind.sex_human}}
-                    {% endif %}
-                  {% endif %}
-                  {% if ind.confirmed_sex %}
-                    <i class="fa fa-check"></i>
-                  {% endif %}
+                  {{ sex_table_cell_content(ind) }}
                 </div>
               </td>
               <td><input name="age_{{ind.individual_id}}" type="number" step="0.1" min="0"

{scout-browser-4.82.1 → scout-browser-4.82.2}/scout/server/blueprints/cases/templates/cases/utils.html

@@ -681,3 +681,20 @@
     </div>
   </form>
 {% endmacro %}
+
+{% macro sex_table_cell_content(ind) %}
+  {% if ind.sex_human in ['female','male'] %}
+    {% if ind.sex_human == 'female' %}
+      F
+    {% elif ind.sex_human == 'male' %}
+      M
+    {% else %}
+      {{ind.sex_human}}
+    {% endif %}
+  {% endif %}
+  {% if ind.confirmed_sex %}
+    <i class="fa fa-check"></i>
+  {% else %}
+    <span class="fa fa-exclamation-circle text-danger" data-bs-toggle='tooltip' title="Sex is not confirmed."></span>
+  {% endif %}
+{% endmacro %}

{scout-browser-4.82.1 → scout-browser-4.82.2}/scout/server/blueprints/variants/controllers.py

@@ -941,7 +941,6 @@ def parse_variant(
         variant_obj["end_chrom"] = variant_obj["chromosome"]
 
     # common motif count for STR variants
-
     variant_obj["str_mc"] = get_str_mc(variant_obj)
 
     # variant level links shown on variants page
@@ -970,7 +969,6 @@ def get_str_mc(variant_obj: dict) -> Optional[int]:
     from the variant FORMAT field, or as a number given in the ALT on the form
     '<STR123>'.
     """
-
     alt_mc = None
     if variant_obj["alternative"] == ".":
         return alt_mc
@@ -982,9 +980,9 @@ def get_str_mc(variant_obj: dict) -> Optional[int]:
     if alt_mc:
         return alt_mc
 
-    alt_num = NUM.match(variant_obj["alternative"])
+    alt_num = NUM.search(variant_obj["alternative"])
     if alt_num:
-        alt_mc = int(alt_num)
+        alt_mc = int(alt_num.group())
         return alt_mc
 
     return None

{scout-browser-4.82.1 → scout-browser-4.82.2}/scout/server/blueprints/variants/templates/variants/str-variants.html

@@ -93,7 +93,7 @@
             <td class="str-link">{{ str_locus_info(variant) }}</td>
 	          <td class="text-end">{{ variant.str_display_ru or variant.str_ru or variant.reference }}</td>
             <td class="text-end"><b><span data-bs-toggle="tooltip" title="{{ variant.alternative }}">{{ variant.str_mc }}</span></b></td>
-        <td class="text-end"><span data-bs-toggle="tooltip" title="{{ variant.reference }}">{{ variant.str_ref or "." }}</span></td>
+            <td class="text-end"><span data-bs-toggle="tooltip" title="{{ variant.reference }}">{{ variant.str_ref or "." }}</span></td>
             <td>{{ str_status(variant) }}</td>
             <td>{% for sample in variant.samples %}
                   {% if sample.genotype_call != "./." %}

{scout-browser-4.82.1 → scout-browser-4.82.2/scout_browser.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: scout-browser
-Version: 4.82.1
+Version: 4.82.2
 Summary: Clinical DNA variant visualizer and browser.
 Home-page: https://github.com/Clinical-Genomics/scout
 Author: Måns Magnusson

scout-browser-4.82.1/scout/__version__.py

@@ -1 +0,0 @@
-__version__ = "4.82.1"