scout-browser 4.82.1__py3-none-any.whl → 4.82.2__py3-none-any.whl

scout/__version__.py

@@ -1 +1 @@
-__version__ = "4.82.1"
+__version__ = "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/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/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/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/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/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/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.dist-info → scout_browser-4.82.2.dist-info}/METADATA

@@ -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.dist-info → scout_browser-4.82.2.dist-info}/RECORD

@@ -1,5 +1,5 @@
 scout/__init__.py,sha256=Z4liXvmEcLkC67ElsWvYHfemPKdWgWI5O6MB6XlDM8M,232
-scout/__version__.py,sha256=IIT6NV0FftHz0d-F_BFcONgDpXbfT_OzWph7we8o1qg,23
+scout/__version__.py,sha256=-tAuS8cIDLp6AGxFKcTo19IOq_e24ShlFdKfJzggGj0,23
 scout/adapter/__init__.py,sha256=-iX_hx2NI1EMAqX0pMd5_90Nnd9uvIMxv9EbefYBzsc,86
 scout/adapter/client.py,sha256=0VR5LRPEqZg_bAxQte1RGMxV8BSiQordbPs57PaZTlI,1512
 scout/adapter/mongo/__init__.py,sha256=NdHYCUXWUAuX5cUS3-6HCws2hW9uoGep8i0SC-oJd3k,31
@@ -454,20 +454,20 @@ scout/server/blueprints/cases/static/case_styles.css,sha256=2Pgc8pFf9DR5HM1sTdAj
 scout/server/blueprints/cases/static/edit_pedigree.js,sha256=ntC5fie7SsOYJau8qkke1UHxjiYWY_gBzWcIkGpdJUA,2978
 scout/server/blueprints/cases/static/madeline.js,sha256=KHxKMBVlYVJODNu5QkY9hhsGkDJNoaCoCZZ0DRu0YN0,1175
 scout/server/blueprints/cases/templates/cases/case.html,sha256=4u3XfrgcV1cZFWxQ5vmKJdWV-gEmnCr9SdP_rrUNt6o,35110
-scout/server/blueprints/cases/templates/cases/case_bionano.html,sha256=kRnhlflW80f4dXZeWh0CM9eM7Azmst64vvljxoLLozw,6774
-scout/server/blueprints/cases/templates/cases/case_report.html,sha256=PyO3EhRFYTdUybXXYNnd2r0jpFKIFRWnrRDEAEOJuN0,63461
-scout/server/blueprints/cases/templates/cases/case_sma.html,sha256=9kxXy6PHsSsou9sJOb0-xFoPAjqP9XBonj_wt_-9Cgw,5356
+scout/server/blueprints/cases/templates/cases/case_bionano.html,sha256=PLoRv7hDJcHwxhi-0hC9fQSZc7V_aUYHBhhQqcn_2G8,5946
+scout/server/blueprints/cases/templates/cases/case_report.html,sha256=1tosH5xEl6CCZ1P6qlR5OKvWbAC5z3ewKL_JGdgPMBM,63635
+scout/server/blueprints/cases/templates/cases/case_sma.html,sha256=SAcElb4kH05mkPdEdaEbed-vbgQQGfxioCoNZsHljDc,4962
 scout/server/blueprints/cases/templates/cases/case_tabular_view.html,sha256=ko-LDUKmIoTazMZ2nFWvPEZsgObU07RwqIkDYFjokoY,4317
 scout/server/blueprints/cases/templates/cases/chanjo2_form.html,sha256=5Wmk7DM8LI3MynqzxeTzAr_EoEBwVVo31djcI5ZlTdo,2164
 scout/server/blueprints/cases/templates/cases/collapsible_actionbar.html,sha256=5CEHrjCXLS4VVqZSGOob0SNKxjyhg2f0oy7r2f64TK0,29252
 scout/server/blueprints/cases/templates/cases/diseases.html,sha256=ETTQI0Nrl_v86NoX9mFZcvWD-qM1IJoqPmHPWn__Grw,1677
 scout/server/blueprints/cases/templates/cases/gene_panel.html,sha256=fR2fCb5A_dBUTTyI4GfwARtOC6k9LeFunx8flbb6qko,12309
 scout/server/blueprints/cases/templates/cases/index.html,sha256=oUmjFyUvwP4yo21CxcWy-6eepMFI65hpznMEpSEqKfM,1207
-scout/server/blueprints/cases/templates/cases/individuals_table.html,sha256=Y_OeIsEnLe_0_AzqgZdO4KMyoQ94auRLnVboLgBUPW8,11861
+scout/server/blueprints/cases/templates/cases/individuals_table.html,sha256=DXE7gE0f81B5CxCV1e5bqWv27_HS-9-8nc0pcFkMoOg,11497
 scout/server/blueprints/cases/templates/cases/institutes_sidebar.html,sha256=u0oPGHJ0ipZ1LkjHkbwlWfkUWc1h6XH1nh3tkbX17z0,4546
 scout/server/blueprints/cases/templates/cases/matchmaker.html,sha256=1vwGBhM4HgvRMlO1foKBAwV-Wfvfs1MRvzteOETCZeM,13142
 scout/server/blueprints/cases/templates/cases/phenotype.html,sha256=38BIwPzTgv5_9BLaTi8beafU2fOrVIfnlV-s88WAx3k,15982
-scout/server/blueprints/cases/templates/cases/utils.html,sha256=8kBXaLRqqNxRW2zVmkhIlV9N9kAJNTkwi0ASJOdMG3Q,34332
+scout/server/blueprints/cases/templates/cases/utils.html,sha256=kYctb7PKlKKjYHHJ0LpdqYsBpJf2tq_yzrwsRQ8td_w,34803
 scout/server/blueprints/clinvar/__init__.py,sha256=BV3aH2AbiA2WWrUEMbGd0H9MefFd2eTsRE9ShywbzpI,30
 scout/server/blueprints/clinvar/controllers.py,sha256=TEOdUTVYI-I_lzts0F3M_TFPMkeeweWIUxWug5HUhDw,24059
 scout/server/blueprints/clinvar/form.py,sha256=d0EBJouYsk-kIpGtAr_SfNCyLoBNchfLt25uFR9HxO0,5155
@@ -605,7 +605,7 @@ scout/server/blueprints/variant/templates/variant/utils.html,sha256=EPwtCxHKhtMD
 scout/server/blueprints/variant/templates/variant/variant.html,sha256=bgO3kb4u45IrgCPUJrHT4paNDOQzcKx5dw0ZYbBmCsc,18914
 scout/server/blueprints/variant/templates/variant/variant_details.html,sha256=J-pF8LRXFnCxIbNfL7klTLj172rlpWF8PznO4ie9Igc,19921
 scout/server/blueprints/variants/__init__.py,sha256=W1KCz9kEbVlNO0o3NvLitYLQoP_3JSJ5KSjhpcjlUBQ,55
-scout/server/blueprints/variants/controllers.py,sha256=7MWNdEHW-LH2yr317VRYiezNprXbltF0x5JxqCJQ4gQ,73067
+scout/server/blueprints/variants/controllers.py,sha256=Kg88oWq86nSJfJG8YqO4J2QxpbsLiGR_VwPW0BFMGRo,73074
 scout/server/blueprints/variants/forms.py,sha256=5BRl2mhiqjuOhsjWXDJjfX95im-NIMxKS-oSbeHiYuM,8944
 scout/server/blueprints/variants/utils.py,sha256=ifFBoyigx0A5KPE4iz9NSpyuUeF1bElrb4ohQLD2GlU,919
 scout/server/blueprints/variants/views.py,sha256=h2z5x7_eA0niXlhOAkYI4eduz3je5XGw_EUnbMenuNA,28136
@@ -616,7 +616,7 @@ scout/server/blueprints/variants/templates/variants/components.html,sha256=oNeLa
 scout/server/blueprints/variants/templates/variants/fusion-variants.html,sha256=XGaLgWobzeFHwyQLXr_Yq9THssf8tGU91VbFKdGOFBg,4801
 scout/server/blueprints/variants/templates/variants/indicators.html,sha256=BX6Wg8OpsALCGGozR1eXT57D0Ixrf-OFXVg6G20Wjr0,4400
 scout/server/blueprints/variants/templates/variants/mei-variants.html,sha256=0-wYjaiUByDduWMgmRS4AMg3IppPNtjZL1vvAdFuIPI,5994
-scout/server/blueprints/variants/templates/variants/str-variants.html,sha256=6A8S3h5tvoBIbaisIbCpZ6GuZuiJhldbn5nOqgwyw_g,10182
+scout/server/blueprints/variants/templates/variants/str-variants.html,sha256=sMM6GiuOU8anACtxrSF6YETsuwWUbEQZyyWhl06ev20,10186
 scout/server/blueprints/variants/templates/variants/sv-variants.html,sha256=SgAdgIPdr7pd2TDB2PJlXOmSAjX4WUslfm4eu0cjIBI,6310
 scout/server/blueprints/variants/templates/variants/utils.html,sha256=2WriO5n0IGzVw4kvt1D_hz47TAkdxhHsgAfFnfO_sww,49231
 scout/server/blueprints/variants/templates/variants/variants.html,sha256=nfSZXVGmsjjUuRC-54G9UsNBMhlNjnvBafN34uL73tY,9333
@@ -660,9 +660,9 @@ scout/utils/hgvs.py,sha256=P5i3fIK8WZZlUnjZ8XpMDUG5KDXRCDSOs55DfK5acsc,898
 scout/utils/link.py,sha256=RuCUwnOtGDf9ACaC64_1FqWyWDaBv7dqNEGjmCq59kk,9001
 scout/utils/md5.py,sha256=KkgdxOf7xbF9AF40ZjQKCgWaxFWJ9tp9RKjd8SU6IoA,649
 scout/utils/scout_requests.py,sha256=owL_XvsrQJG4e0EUuUiY6y_hqKKep2Qljg1nMukzp8Y,12855
-scout_browser-4.82.1.dist-info/LICENSE,sha256=TM1Y9Cqbwk55JVfxD-_bpGLtZQAeN9RovQlqHK6eOTY,1485
-scout_browser-4.82.1.dist-info/METADATA,sha256=h7k7EwlAyH5yWKi7iWR9g7qQ7IxIBYsgF9z_eAXkFxU,14280
-scout_browser-4.82.1.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
-scout_browser-4.82.1.dist-info/entry_points.txt,sha256=E6vGg1OwvvKYIsXdHxmlIj7RmcTF0K77Q_PU8laImGg,46
-scout_browser-4.82.1.dist-info/top_level.txt,sha256=qM75h71bztMaLYsxn1up4c_n2rjc_ZnyaW6Q0K5uOXc,6
-scout_browser-4.82.1.dist-info/RECORD,,
+scout_browser-4.82.2.dist-info/LICENSE,sha256=TM1Y9Cqbwk55JVfxD-_bpGLtZQAeN9RovQlqHK6eOTY,1485
+scout_browser-4.82.2.dist-info/METADATA,sha256=QYoeVAZXLiAZ03LhP9VPsklCcz0fasyK60PvsFE8HGs,14280
+scout_browser-4.82.2.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
+scout_browser-4.82.2.dist-info/entry_points.txt,sha256=E6vGg1OwvvKYIsXdHxmlIj7RmcTF0K77Q_PU8laImGg,46
+scout_browser-4.82.2.dist-info/top_level.txt,sha256=qM75h71bztMaLYsxn1up4c_n2rjc_ZnyaW6Q0K5uOXc,6
+scout_browser-4.82.2.dist-info/RECORD,,