scout-browser 4.89__py3-none-any.whl → 4.89.2__py3-none-any.whl

scout/__version__.py

@@ -1 +1 @@
-__version__ = "4.89"
+__version__ = "4.89.2"

scout/adapter/mongo/hgnc.py

@@ -335,7 +335,7 @@ class GeneHandler(object):
         Returns:
             alias_genes(dict): {<hgnc_alias>: {'true': <hgnc_id>, 'ids': {<hgnc_id_1>, <hgnc_id_2>, ...}}}
         """
-        LOG.debug("Fetching all genes by alias")
+
         # Collect one entry for each alias symbol that exists
         alias_genes = {}
 

scout/parse/panel.py

@@ -2,7 +2,7 @@
 
 import logging
 from datetime import datetime
-from typing import Dict, List, Optional
+from typing import Dict, Optional
 
 from scout.constants import (
     INCOMPLETE_PENETRANCE_MAP,
@@ -383,7 +383,7 @@ def parse_panel_app_panel(
     return gene_panel
 
 
-def get_omim_panel_genes(genemap2_lines, mim2gene_lines, alias_genes):
+def get_omim_panel_genes(genemap2_lines: list, mim2gene_lines: list, alias_genes: dict):
     """Return all genes that should be included in the OMIM-AUTO panel
     Return the hgnc symbols
 
@@ -424,6 +424,19 @@ def get_omim_panel_genes(genemap2_lines, mim2gene_lines, alias_genes):
                 break
 
         if hgnc_id_info:
-            yield {"hgnc_id": hgnc_id_info["true"], "hgnc_symbol": hgnc_symbol}
+            if hgnc_id_info["true"]:
+                hgnc_id = hgnc_id_info["true"]
+            elif len(hgnc_id_info.get("ids", ())) == 1:
+                hgnc_id = list(hgnc_id_info["ids"])[0]
+                LOG.warning(
+                    "Gene symbol %s does not exist: using an apparently unique alias for hgnc_id %s",
+                    hgnc_symbol,
+                    hgnc_id,
+                )
+            else:
+                LOG.warning(
+                    "Gene symbol %s does not exist, and as an alias it is not unique", hgnc_symbol
+                )
+            yield {"hgnc_id": hgnc_id, "hgnc_symbol": hgnc_symbol}
         else:
             LOG.warning("Gene symbol %s does not exist", hgnc_symbol)

scout/server/blueprints/cases/templates/cases/case_report.html

@@ -1099,7 +1099,9 @@
               <td>
                 <ul>
                 {% for disease_term in gene.disease_terms %}
-                   <li class="d-flex align-items-baseline"><span class="badge bg-secondary m-1">{{ disease_term._id}}</span>&nbsp;<span>{{ disease_term.description }}&nbsp;{{ disease_term.inheritance }}</span></li>
+                   <li class="d-flex align-items-baseline"><span class="badge bg-secondary m-1">{{ disease_term._id}}</span>&nbsp;<span>{{ disease_term.description }}&nbsp;{% if disease_term.source != 'ORPHA' and disease_term.inheritance %}
+                      {% for model in disease_term.inheritance %} {{ inheritance_badge(model,inherit_palette) }}{% endfor %}
+                   {% endif %}</span></li>
                 {% endfor %}
                 </ul>
               </td>
@@ -1140,7 +1142,7 @@
     {{ variant_phenotypes(variant) }}
   </div>
   <div class="card-body">
-    <table id="panel-table" class="table table-sm table-bordered" style="background-color: transparent; margin-left:-.3rem;>
+    <table id="panel-table" class="table table-sm table-bordered" style="background-color: transparent; margin-left:-.3rem;">
       <thead>
         <tr class="table-secondary">
           <th>Variant type</th>
@@ -1262,7 +1264,7 @@
             {{ variant.str_inheritance_mode if variant.str_inheritance_mode else "-" }}
           </td>
           <td>
-            {% if variant.str_source.display %}
+            {% if variant.str_source and variant.str_source.display %}
               <a style="text-decoration:none;" href="{{variant.str_source_link}}" target="_blank" rel="noopener noreferrer">{{ variant.str_source.display }} </a>
             {% else %}
               "-"

scout/server/templates/report_base.html

@@ -6,11 +6,69 @@
 	{% block css %}
   <link href="https://cdn.jsdelivr.net/npm/bootstrap@5.1.3/dist/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-1BmE4kWBq78iYhFldvKuhfTAU6auU8tT94WrHftjDbrCEXSU1oBoqyl2QvZ6jIW3" crossorigin="anonymous">
   <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/all.min.css" integrity="sha512-1ycn6IcaQQ40/MKBW2W4Rhis/DbILU74C1vSrLJxCq57o941Ym01SwNsOMqvEBFlcgUa6xLiPY/NS5R+E6ztJQ==" crossorigin="anonymous" referrerpolicy="no-referrer" />
-  <link rel="stylesheet" href="{{ url_for('static', filename='bs_styles.css') }}">
     <style>
 		tr.light-grey td{
 			background-color: LightGray;
 		}
+
+    /* affected, archived and similar accents */
+    .bg-danger-light {
+        background-color: var(--bs-info);
+    }
+
+    /* define colors to be used as class items */
+    .bg-red {
+     background-color: var(--bs-red);
+    }
+
+    .bg-orange {
+      background-color: var(--bs-orange);
+    }
+
+    .bg-blue {
+     background-color: var(--bs-blue);
+    }
+
+    .bg-teal {
+     background-color: var(--bs-teal);
+    }
+
+    .bg-green {
+     background-color: var(--bs-green);
+    }
+
+    .bg-gray {
+     background-color: var(--bs-gray);
+    }
+
+    .bg-pink {
+     background-color: var(--bs-pink);
+    }
+
+    .bg-purple {
+     background-color: var(--bs-purple);
+    }
+
+    .bg-cyan {
+     background-color: var(--bs-cyan);
+    }
+
+    .bg-gray-400 {
+       background-color: var(--bs-gray-400);
+    }
+
+    .bg-gray-dark {
+     background-color: var(--bs-gray-dark);
+    }
+
+    .bg-yellow {
+     background-color: var(--bs-yellow);
+    }
+
+    .bg-light {
+       background-color: var(--bs-light);
+    }
+    /* End of css colors */
   </style>
 	{% endblock %}
 

{scout_browser-4.89.dist-info → scout_browser-4.89.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: scout-browser
-Version: 4.89
+Version: 4.89.2
 Summary: Clinical DNA variant visualizer and browser.
 Home-page: https://github.com/Clinical-Genomics/scout
 Author: Måns Magnusson

{scout_browser-4.89.dist-info → scout_browser-4.89.2.dist-info}/RECORD

@@ -1,5 +1,5 @@
 scout/__init__.py,sha256=Z4liXvmEcLkC67ElsWvYHfemPKdWgWI5O6MB6XlDM8M,232
-scout/__version__.py,sha256=uHM9R1HpJEivvV6bRxxdV4CnINQ5HpyCHvuWWIFpq9w,21
+scout/__version__.py,sha256=T7ThRIRkePjiRTDa6aeTTkyfBdSPI1nLqcsHeWWi8Ig,23
 scout/adapter/__init__.py,sha256=-iX_hx2NI1EMAqX0pMd5_90Nnd9uvIMxv9EbefYBzsc,86
 scout/adapter/client.py,sha256=IuajRsEwTG41ZP14X09Q1Cj94zIgmIvUtlXfcAFn0EA,1513
 scout/adapter/mongo/__init__.py,sha256=NdHYCUXWUAuX5cUS3-6HCws2hW9uoGep8i0SC-oJd3k,31
@@ -13,7 +13,7 @@ scout/adapter/mongo/cytoband.py,sha256=2NoIAoQ7RPqcipiSymD2O9qH8lXscP3T5ejquOrD7
 scout/adapter/mongo/disease_terms.py,sha256=4qcQRLuP5xn_RkB2RlNtwCrONmDuWwdlngZrj87BUEo,5637
 scout/adapter/mongo/event.py,sha256=NnURFhS5odOXk7So_gGMHmALPAJM0PWzESI4FC06azE,19842
 scout/adapter/mongo/filter.py,sha256=vzBJS_6vq2z76SH8PszdRR-MNuZ7_RA4VJvnkNYUs7s,8937
-scout/adapter/mongo/hgnc.py,sha256=9jbrkaTtlnnuE5gsSM8ylb8Kero4lC2zCWr-90QlyAY,16420
+scout/adapter/mongo/hgnc.py,sha256=FUzzj9at62jW-ypII6mWrfeDTdQzW4BWgXg3bWRTqGo,16372
 scout/adapter/mongo/hpo.py,sha256=ps2Pix3sGeea7DenboZVP5j7Vh9WAgX3-sgpbAj0Eck,6871
 scout/adapter/mongo/index.py,sha256=TZPVv6xBWsEtZpBUWp5uhjuPjQMfVss4lZZju49g1Lw,3577
 scout/adapter/mongo/institute.py,sha256=GQmMKb_VzsvWwadp6gXHlSSpcG5ovF1ozdTzvpTFLpA,7025
@@ -410,7 +410,7 @@ scout/parse/matchmaker.py,sha256=5e9NCFQ2rKXNCJTW-ThXoEylEPl3H41cCfQzPATQ2QM,952
 scout/parse/mitodel.py,sha256=3uvEXI9v9wIw97NUL7gqLLxHay0mpQpDgKaIxUbIyrE,803
 scout/parse/omim.py,sha256=nrCaFZgjUKZo9Jfku2-jcNjdsIYHsvjdWcydz4nCpZA,12465
 scout/parse/orpha.py,sha256=5u9xqGpAn8vgoJ0uVqbYiqQBiNfBwXOiTzX16kAnmFU,4392
-scout/parse/panel.py,sha256=4HYjokWh2sF-effLQxPf4ZzRHsf9grqF1Z9f-HAaRmk,13153
+scout/parse/panel.py,sha256=xNIzUhyCOBIWtH2avbVvJgZioanMztImG6dV1wXnyO4,13722
 scout/parse/peddy.py,sha256=uM49GaZMtr8waCsZDvCHDS5JDQ43JUlhdWh9C7f7ZvU,5418
 scout/parse/smn.py,sha256=iOK1N8iYm9dFigsKtWq0Y0ZCa1CH29s9zeR_tH0bPuc,1153
 scout/parse/omics_variant/__init__.py,sha256=vq8Ew4_Xr2vPy_3Fg0eTpPWsQpWnUXYBhjRndBUvtTw,422
@@ -460,7 +460,7 @@ scout/server/blueprints/cases/static/edit_pedigree.js,sha256=ntC5fie7SsOYJau8qkk
 scout/server/blueprints/cases/static/madeline.js,sha256=KHxKMBVlYVJODNu5QkY9hhsGkDJNoaCoCZZ0DRu0YN0,1175
 scout/server/blueprints/cases/templates/cases/case.html,sha256=9Fcn-OFA1yIHchD0PjDs7-Y8I7Qqr8o6cavN0eOi5rI,37183
 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=CzOIec3hbCXCwIQpB0L0vGQPtYvQjJbJXcir61jUM2Q,63091
+scout/server/blueprints/cases/templates/cases/case_report.html,sha256=y7aSvMGQoM8jOt93sBrXBvTkhtE7hIVU2jaoSA6FpM8,63309
 scout/server/blueprints/cases/templates/cases/case_sma.html,sha256=5kpvNPhOO15wTP_WjYX22wQ_B5-pw4jIQweNXYLbsAU,6281
 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
@@ -649,7 +649,7 @@ scout/server/static/humans.txt,sha256=UdqAR07_5LAWWfgH2Ty4RR8BhoHS1WXpx9euKtXqqh
 scout/server/static/robots.txt,sha256=fFX0beQN4x3mzR3evnZjrOUYOTNkezYAwqMowTUpmxM,106
 scout/server/templates/bootstrap_global.html,sha256=yPauZKUzPvDCj6LUrKnCtkYgn7fPt07-Letxqd-hLw8,2634
 scout/server/templates/layout.html,sha256=-uhRxFA89L0gocv8sPLcODUHmWLNuV6xsjB34Zjq-8o,4635
-scout/server/templates/report_base.html,sha256=uRSpk-KaE7ZCE0UOGftWH0bGDQVUTU1bpcVKnDKitq0,1335
+scout/server/templates/report_base.html,sha256=bNYzoJFgtYMnfxQYeguwQK9c15ZASdmXd72DaiCfZto,2281
 scout/server/templates/utils.html,sha256=Wd-glkGqmfJeusnqi1fIjCBSgUflWh0V3MOAnr5V_MU,13000
 scout/server/translations/sv/LC_MESSAGES/messages.mo,sha256=eI53pCtlYj1MXduDicMZRxBhgOV_TlmMUpH7IhncgDY,4452
 scout/server/translations/sv/LC_MESSAGES/messages.po,sha256=Wp7Mx4LoiFNtzsV1tpAoWjMxYnq8SpfpU9a4XWJ7L6g,4531
@@ -672,9 +672,9 @@ scout/utils/md5.py,sha256=KkgdxOf7xbF9AF40ZjQKCgWaxFWJ9tp9RKjd8SU6IoA,649
 scout/utils/scout_requests.py,sha256=JjHOJW1XmenG05mNQ33kvOKq_IicveIfQMcPZeRcQdo,12856
 scout/utils/sort.py,sha256=1AcbeZ6vdt_UXM3BLDBa3aQmN4qxrqtskxwD19oBhvw,756
 scout/utils/track_resources.py,sha256=eUjSEe-Ff8BIb4BHPC_COkJocQO2PaWueiPz1GAuiwY,2614
-scout_browser-4.89.dist-info/LICENSE,sha256=TM1Y9Cqbwk55JVfxD-_bpGLtZQAeN9RovQlqHK6eOTY,1485
-scout_browser-4.89.dist-info/METADATA,sha256=N51ZBLfSeqt_rWMckEQocMR34WNvAEXjE8FFyDq321M,14260
-scout_browser-4.89.dist-info/WHEEL,sha256=eOLhNAGa2EW3wWl_TU484h7q1UNgy0JXjjoqKoxAAQc,92
-scout_browser-4.89.dist-info/entry_points.txt,sha256=q_mxFwbMFTwXRDDIRVcqKram2ubMVmvs3CSNvZri1nY,45
-scout_browser-4.89.dist-info/top_level.txt,sha256=qM75h71bztMaLYsxn1up4c_n2rjc_ZnyaW6Q0K5uOXc,6
-scout_browser-4.89.dist-info/RECORD,,
+scout_browser-4.89.2.dist-info/LICENSE,sha256=TM1Y9Cqbwk55JVfxD-_bpGLtZQAeN9RovQlqHK6eOTY,1485
+scout_browser-4.89.2.dist-info/METADATA,sha256=stc_17UT_s4jOKJezGHaktPrwY-h3IJqt1VnGQfm6uI,14262
+scout_browser-4.89.2.dist-info/WHEEL,sha256=eOLhNAGa2EW3wWl_TU484h7q1UNgy0JXjjoqKoxAAQc,92
+scout_browser-4.89.2.dist-info/entry_points.txt,sha256=q_mxFwbMFTwXRDDIRVcqKram2ubMVmvs3CSNvZri1nY,45
+scout_browser-4.89.2.dist-info/top_level.txt,sha256=qM75h71bztMaLYsxn1up4c_n2rjc_ZnyaW6Q0K5uOXc,6
+scout_browser-4.89.2.dist-info/RECORD,,