scout-browser 4.83__py3-none-any.whl → 4.85__py3-none-any.whl

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

@@ -9,7 +9,7 @@
         <thead class="table-light thead">
           <tr style="cursor: pointer; white-space: nowrap">
             <th>Panel <i class="fas fa-sort" data-bs-toggle="tooltip" title="Sort by gene panel name"></i></th>
-            <th >Default <i class="fas fa-sort" data-bs-toggle="tooltip" title="Sort by default panel"></i></th>
+            <th>Default <i class="fas fa-sort" data-bs-toggle="tooltip" title="Sort by if panel is default"></i></th>
             <th>Version <i class="fas fa-sort" data-bs-toggle="tooltip" title="Sort by panel version"></i></th>
             <th>Genes <i class="fas fa-sort" data-bs-toggle="tooltip" title="Sort by number of genes"></i></th>
           </tr>
@@ -20,10 +20,10 @@
               <td>
                 <a {% if panel.is_default %} class="text-white" {% endif %} href="{{ url_for('panels.panel', panel_id=panel.panel_id, case_id=case._id, institute_id=institute._id) }}">
                   {{ panel.display_name|truncate(30, True) }}
-                  {% if panel.removed %}
-                    <span class="badge bg-danger">Removed</span>
-                  {% endif %}
                 </a>
+                {% if panel.removed %}
+                  <span class="badge bg-danger">Removed</span>
+                {% endif %}
               </td>
               <td >
                 {% if panel.is_default %}
@@ -35,53 +35,39 @@
             </tr>
           {% else %}
             <tr>
-              <td colspan="5">No panels linked to case</td>
+              <td colspan="4">No panels linked to case</td>
             </tr>
           {% endfor %}
         </tbody>
       </table>
     </div>
-    <div class="card-body">
-      <form action="{{ url_for('cases.default_panels', institute_id=institute._id, case_name=case.display_name) }}" method="POST">
-        <div class="row">
-          <label>Change default gene panels</label>
-        </div>
-        <div class="row">
-          <div class="col-8">
-            <select name="panel_ids" class="selectpicker" multiple="multiple" data-style="btn-secondary">
-              {% for panel in case.panels %}
-                <option value="{{ panel.panel_id }}" {% if panel.is_default %} selected {% endif %}>{{ panel.display_name }}</option>
-              {% endfor %}
-            </select>
-          </div>
-          <div class="col-4">
-            <button class="btn btn-secondary form-control">Save</button>
-          </div>
-        </div>
-      </form>
-    </div>
+    {{ change_default_panels(case, institute) }}
+
   </div>
 {% endmacro %}
 
 {% macro change_default_panels(case, institute) %}
-  <div class="card panel-default">
-    <div class="panel-heading">Change default gene panels</div>
-    <div class="card-body">
-      <form action="{{ url_for('cases.default_panels', institute_id=institute._id, case_name=case.display_name) }}" method="POST">
-        <div class="row">
-          <div class="col-xs-4">
-            <select name="panel_ids" class="form-control" multiple>
-              {% for panel in case.panels %}
-                <option value="{{ panel.panel_id }}" {% if panel.is_default %} selected {% endif %}>{{ panel.display_name }}</option>
-              {% endfor %}
-            </select>
-          </div>
-          <div class="col-xs-4">
-            <button class="btn btn-secondary form-control">Save</button>
-          </div>
+  <div class="card-body">
+    <form action="{{ url_for('cases.default_panels', institute_id=institute._id, case_name=case.display_name) }}" method="POST">
+      <div class="row">
+        <label>Change default gene panels</label>
+      </div>
+
+      <div class="row">
+        <div class="col-8">
+          <select name="panel_ids" class="selectpicker" multiple="multiple" data-style="btn-secondary">
+            {% for panel in case.panels|sort(attribute='display_name')  %}
+              <option value="{{ panel.panel_id }}" {% if panel.is_default %} selected {% endif %}>
+                {{ panel.display_name }} {% if panel.removed %} (Removed) {% endif %}
+              </option>
+            {% endfor %}
+          </select>
         </div>
-      </form>
-    </div>
+        <div class="col-4">
+          <button class="btn btn-secondary form-control">Save</button>
+        </div>
+      </div>
+    </form>
   </div>
 {% endmacro %}
 

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

@@ -676,7 +676,7 @@
               name="{{ button_name if button_name }}"
               value="{{ button_value if button_value }}"
               type="submit">
-        <i class="fa fa-remove text-danger""></i>
+        <i class="fa fa-times text-danger"></i>
       </button>
     </div>
   </form>

scout/server/blueprints/panels/forms.py

@@ -1,4 +1,5 @@
 """Code for panel gene form"""
+
 from flask_wtf import FlaskForm
 from wtforms import BooleanField, SelectMultipleField, StringField
 

scout/server/blueprints/variant/controllers.py

@@ -486,26 +486,21 @@ def observations(store: MongoAdapter, loqusdb: LoqusDB, variant_obj: dict) -> Di
     loqus_query = loqusdb.get_loqus_query(variant_obj, category)
 
     for loqus_id in inst_loqus_ids:  # Loop over all loqusdb instances of an institute
-        obs_data[loqus_id] = {}
-        loqus_settings = loqusdb.loqusdb_settings.get(loqus_id)
+        # collect observation on that loqusdb instance
+        obs_data[loqus_id] = loqusdb.get_variant(loqus_query, loqusdb_id=loqus_id)
 
-        if loqus_settings is None:  # An instance might have been renamed or removed
+        if obs_data[loqus_id] is None:
             flash(
-                f"Could not connect to the preselected loqusdb '{loqus_id}' instance",
+                f"Could not find a Loqus instance with id:{loqus_id}",
                 "warning",
             )
-            obs_data[loqus_id]["total"] = "N/A"
+            obs_data[loqus_id]["observations"] = "N/A"
             continue
-        obs_data[loqus_id] = loqusdb.get_variant(
-            loqus_query, loqusdb_id=loqus_id
-        )  # collect observation on that loqus instance
-
-        if not obs_data[loqus_id]:  # data is an empty dictionary
-            # Collect count of variants in variant's case
-            obs_data[loqus_id] = loqusdb.get_variant(loqus_query, loqusdb_id=loqus_id)
-            if obs_data[loqus_id].get("total"):
-                obs_data[loqus_id]["observations"] = 0
+
+        if obs_data[loqus_id] == {}:  # Variant was not found
+            obs_data[loqus_id]["observations"] = 0
             continue
+
         # Check if the current case is represented in the loqusdb instance
         obs_data[loqus_id]["case_match"] = variant_obj["case_id"] in obs_data[loqus_id].get(
             "families", []

scout/server/blueprints/variants/controllers.py

@@ -3,12 +3,10 @@ import logging
 import re
 from typing import Any, Dict, List, Optional
 
-import bson
 from flask import Response, flash, session, url_for
 from flask_login import current_user
 from markupsafe import Markup
 from pymongo.cursor import CursorType
-from pymongo.errors import DocumentTooLarge
 from werkzeug.datastructures import Headers, ImmutableMultiDict, MultiDict
 from wtforms import DecimalField
 
@@ -513,7 +511,7 @@ def update_variant_genes(store, variant_obj, genome_build):
 
     if variant_genes is not None:
         for gene_obj in variant_genes:
-            # If there is no hgnc id there is nothin we can do
+            # If there is no hgnc id there is nothing we can do
             if not gene_obj["hgnc_id"]:
                 continue
             # Else we collect the gene object and check the id
@@ -530,27 +528,6 @@ def update_variant_genes(store, variant_obj, genome_build):
     return has_changed
 
 
-def update_variant_store(store, variant_obj):
-    """
-    Update variants in db store if anything changed.
-    Args:
-        store(scout.adapter.MongoAdapter)
-        variant_obj(scout.models.Variant)
-
-        update(boolean): upsert only if this is set true
-
-        get_compounds(bool): if compounds should be added to added to the returned variant object
-
-    """
-    try:
-        variant_obj = store.update_variant(variant_obj)
-    except DocumentTooLarge:
-        flash(
-            f"An error occurred while updating info for variant: {variant_obj['_id']} (pymongo_errors.DocumentTooLarge: {len(bson.BSON.encode(variant_obj))})",
-            "warning",
-        )
-
-
 def _compound_follow_filter_freq(compound, compound_var_obj, query_form):
     """When compound follow filter is selected, apply relevant settings from the query filter onto dismissing compounds.
 
@@ -895,11 +872,18 @@ def parse_variant(
     compounds_have_changed = False
     if get_compounds:
         compounds_have_changed = update_compounds(store, variant_obj, case_dismissed_vars)
+        if update and compounds_have_changed:
+            store.variant_update_field(
+                variant_id=variant_obj["_id"],
+                field_name="compounds",
+                field_value=variant_obj["compounds"],
+            )
 
     genes_have_changed = update_variant_genes(store, variant_obj, genome_build)
-
-    if update and (compounds_have_changed or genes_have_changed):
-        update_variant_store(store, variant_obj)
+    if update and genes_have_changed:
+        store.variant_update_field(
+            variant_id=variant_obj["_id"], field_name="genes", field_value=variant_obj["genes"]
+        )
 
     variant_obj["comments"] = store.events(
         institute_obj,

scout/server/extensions/bionano_extension.py

@@ -6,6 +6,7 @@
     For further development, the server has a Swagger-like demo interface at https://bionano-access.scilifelab.se/Bnx/
     which is useful for details, and for sniffing actual message content structure, required cookie variable names etc.
 """
+
 import json
 import logging
 from typing import Dict, Iterable, List, Optional, Tuple

scout/server/extensions/chanjo_extension.py

@@ -9,21 +9,22 @@ from flask_babel import Babel
 from markupsafe import Markup
 
 LOG = logging.getLogger(__name__)
-try:
-    from chanjo_report.server.app import configure_template_filters
-    from chanjo_report.server.blueprints import report_bp
-    from chanjo_report.server.extensions import api as chanjo_api
-except ImportError as error:
-    chanjo_api = None
-    report_bp = None
-    configure_template_filters = None
-    LOG.warning("chanjo-report is not properly installed! %s.", error)
 
 
 class ChanjoReport:
     """Interfaces with chanjo-report. Creates the /reports endpoints in scout domain. Use Babel to set report language."""
 
     def init_app(self, app):
+        try:
+            from chanjo_report.server.app import configure_template_filters
+            from chanjo_report.server.blueprints import report_bp
+            from chanjo_report.server.extensions import api as chanjo_api
+        except ImportError as error:
+            chanjo_api = None
+            report_bp = None
+            configure_template_filters = None
+            LOG.error(error)
+
         if not chanjo_api:
             raise ImportError(
                 "An SQL db path was given, but chanjo-report could not be registered."

scout/server/extensions/gens_extension.py

@@ -2,6 +2,7 @@
 
 * Requires gens version 1.1.1 or greater
 """
+
 import logging
 
 LOG = logging.getLogger(__name__)

scout/server/extensions/ldap_extension.py

@@ -43,9 +43,11 @@ class LdapManager(LDAPConn):
         self.tls = Tls(
             local_private_key_file=app.config["LDAP_CLIENT_PRIVATE_KEY"],
             local_certificate_file=app.config["LDAP_CLIENT_CERT"],
-            validate=app.config["LDAP_REQUIRE_CERT"]
-            if app.config.get("LDAP_CLIENT_CERT")
-            else ssl.CERT_NONE,
+            validate=(
+                app.config["LDAP_REQUIRE_CERT"]
+                if app.config.get("LDAP_CLIENT_CERT")
+                else ssl.CERT_NONE
+            ),
             version=app.config["LDAP_TLS_VERSION"],
             ca_certs_file=app.config["LDAP_CA_CERTS_FILE"],
             valid_names=app.config["LDAP_VALID_NAMES"],

scout/server/extensions/loqus_extension.py

@@ -3,11 +3,15 @@
 * Requires loqusdb version 2.5 or greater.
 * If multiple instances are configured, version will be default's.
 """
+
 import json
 import logging
 import subprocess
 import traceback
 from subprocess import CalledProcessError
+from typing import Dict, Optional
+
+from flask import flash
 
 from scout.exceptions.config import ConfigError
 from scout.utils.scout_requests import get_request_json as api_get
@@ -180,16 +184,9 @@ class LoqusDB:
         }
         return loqus_query
 
-    def get_variant(self, variant_info, loqusdb_id="default"):
-        """Return information for a variant (SNV or SV) from loqusdb
-
-        Args:
-            variant_info(dict)
-            loqusdb_id(string)
+    def get_variant(self, variant_info: dict, loqusdb_id: str = "default") -> Optional[Dict]:
+        """Return information for a variant (SNV or SV) from loqusdb"""
 
-        Returns:
-            loqus_variant(dict)
-        """
         loqus_instance = self.loqusdb_settings.get(loqusdb_id)
         if loqus_instance is None:
             LOG.error(f"Could not find a Loqus instance with id:{loqusdb_id}")
@@ -202,7 +199,7 @@ class LoqusDB:
         return self.get_api_loqus_variant(loqus_instance.get(API_URL), variant_info)
 
     @staticmethod
-    def get_api_loqus_variant(api_url, variant_info):
+    def get_api_loqus_variant(api_url, variant_info) -> dict:
         """get variant data using a Loqus instance available via REST API
 
         SNV/INDELS can be queried in loqus by defining a simple id. For SVs we need to call them
@@ -230,10 +227,15 @@ class LoqusDB:
             search_url = f"{search_url}/?chrom={chrom}&end_chrom={end_chrom}&pos={pos}&end={end}&sv_type={sv_type}"
 
         search_resp = api_get(search_url)
-        if search_resp.get("status_code") != 200:
-            LOG.info(search_resp.get("detail"))
-            return {}
-        return search_resp.get("content")
+
+        if search_resp.get("status_code") == 200:
+            return search_resp.get("content")
+        if search_resp.get("message"):  # An error occurred during the request
+            flash(
+                f"Connection to Loqusdb instance returned error: '{search_resp['message']}'",
+                "warning",
+            )
+        return {}
 
     def get_exec_loqus_variant(self, loqus_instance, variant_info):
         """Get variant data using a local executable instance of Loqus

scout/server/extensions/matchmaker_extension.py

@@ -1,6 +1,7 @@
 """Code for MatchMaker Exchange integration
    Tested with PatientMatcher: https://github.com/Clinical-Genomics/patientMatcher
 """
+
 import datetime
 import json
 import logging

scout/server/extensions/mongo_extension.py

@@ -1,4 +1,5 @@
 """Code for flask mongodb extension in scout"""
+
 import os
 
 from scout.adapter.client import get_connection

scout/server/extensions/rerunner_extension.py

@@ -1,4 +1,5 @@
 """Code for Rerunner integration."""
+
 import logging
 
 LOG = logging.getLogger(__name__)

scout/server/links.py

@@ -159,7 +159,7 @@ def genemania(hgnc_symbol):
 
 
 def genenames(hgnc_id):
-    link = "https://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=HGNC:{}"
+    link = "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:{}"
     if not hgnc_id:
         return None
     return link.format(hgnc_id)
@@ -679,9 +679,9 @@ def snp_links(variant_obj):
         if "rs" in snp:
             snp_links[snp] = f"https://www.ncbi.nlm.nih.gov/snp/{snp}"  # dbSNP
         elif snp.isnumeric():
-            snp_links[
-                snp
-            ] = f"https://www.ncbi.nlm.nih.gov/clinvar/variation/{snp}"  # ClinVar variation
+            snp_links[snp] = (
+                f"https://www.ncbi.nlm.nih.gov/clinvar/variation/{snp}"  # ClinVar variation
+            )
 
     return snp_links
 

scout/server/static/bs_styles.css

@@ -333,7 +333,7 @@ body {
 
 /* Closed submenu icon */
 #sidebar-container .list-group .list-group-item[aria-expanded="false"] .submenu-icon::after {
-  content: " \f0d7";
+  content: " \f0da";
   font-family: "Font Awesome 5 Free", ui-monospace;
   font-weight: 900;
   display: inline;
@@ -342,7 +342,7 @@ body {
 }
 /* Opened submenu icon */
 #sidebar-container .list-group .list-group-item[aria-expanded="true"] .submenu-icon::after {
-  content: " \f0da";
+  content: " \f0d7";
   font-family: "Font Awesome 5 Free", ui-monospace;
   font-weight: 900;
   display: inline;
@@ -353,15 +353,15 @@ body {
 
 /* Closed submenu icon - general case */
 .text-body[aria-expanded="false"] .collapse-icon::after {
-  content: " \f0d7";
+  content: " \f0da";
   font-family: "Font Awesome 5 Free", ui-monospace;
   font-weight: 900;
   display: inline;
   text-align: left;
 }
-/* Opened submenu icon - general case */
+/* Open submenu icon - general case */
 .text-body[aria-expanded="true"] .collapse-icon::after {
-  content: " \f0da";
+  content: " \f0d7";
   font-family: "Font Awesome 5 Free", ui-monospace;
   font-weight: 900;
   display: inline;

scout/server/templates/utils.html

@@ -145,7 +145,7 @@
                   <span class='badge bg-secondary'>edited</span>
                 {% endif %}
                 {% if comment.user_id == current_user.email %}
-                  <button class="btn btn-link btn-sm" type="submit" name="remove"><i class="fa fa-remove"></i></button>
+                  <button class="btn btn-link btn-sm" type="submit" name="remove"><i class="fa fa-times"></i></button>
                   <button class="btn btn-link btn-sm" type="button" data-bs-toggle="modal" data-bs-target="#editComment_{{index}}"><i class="fa fa-edit"></i></button>
                 {% endif %}
               </small>

scout/utils/ensembl_rest_clients.py

@@ -1,4 +1,5 @@
 """Code for talking to ensembl rest API"""
+
 import logging
 from urllib.parse import urlencode
 

scout/utils/scout_requests.py

@@ -1,4 +1,5 @@
 """Code for performing requests"""
+
 import logging
 import urllib.request
 import zlib

scout/utils/sort.py

@@ -0,0 +1,21 @@
+from scout.constants import FILE_TYPE_MAP
+
+
+def get_load_priority(category: str = None, variant_type: str = None, file_type: str = None) -> int:
+    """
+    Returns most urgent, highest load priority (numerically the lowest prio number) for the given variables
+    from a FILE_TYPE_MAP dict of dicts. Helper useful in a sort function.
+    """
+    ordered_file_type_map = sorted(FILE_TYPE_MAP.items(), key=lambda ftm: ftm[1]["load_priority"])
+
+    for ftm in ordered_file_type_map:
+        if file_type and file_type != ftm[0]:
+            continue
+
+        if category and category != ftm[1]["category"]:
+            continue
+
+        if variant_type and variant_type != ftm[1]["variant_type"]:
+            continue
+
+        return ftm[1]["load_priority"]

{scout_browser-4.83.dist-info → scout_browser-4.85.dist-info}/METADATA

@@ -1,12 +1,10 @@
 Metadata-Version: 2.1
 Name: scout-browser
-Version: 4.83
+Version: 4.85
 Summary: Clinical DNA variant visualizer and browser.
 Home-page: https://github.com/Clinical-Genomics/scout
 Author: Måns Magnusson
 Author-email: mans.magnusson@scilifelab.se
-License: UNKNOWN
-Platform: UNKNOWN
 Classifier: Environment :: Web Environment
 Classifier: Intended Audience :: Developers
 Classifier: License :: OSI Approved :: BSD License
@@ -16,7 +14,8 @@ Classifier: Topic :: Internet :: WWW/HTTP :: Dynamic Content
 Classifier: Topic :: Software Development :: Libraries
 Classifier: Programming Language :: Python :: 3.6
 Description-Content-Type: text/markdown
-Requires-Dist: werkzeug <3
+License-File: LICENSE
+Requires-Dist: werkzeug
 Requires-Dist: Flask >=2.0
 Requires-Dist: Flask-Bootstrap
 Requires-Dist: Flask-CORS
@@ -338,5 +337,3 @@ be found in [CONTRIBUTING](CONTRIBUTING.md).
 [black-url]: https://github.com/psf/black
 [woke-image]: https://github.com/Clinical-Genomics/scout/actions/workflows/woke.yml/badge.svg
 [woke-url]: https://github.com/Clinical-Genomics/scout/actions/workflows/woke.yml
-
-