bugfixes & update changelog

src/common/db_IO.py

@@ -619,8 +619,6 @@ def sort_consequences(self, a, b):
 
     def get_variants_page_merged(self, page, page_size, sort_by, include_hidden, user_id, ranges = None, genes = None, consensus = None, user = None, hgvs = None, variant_ids_oi = None):
         # get one page of variants determined by offset & pagesize
-        page_size = int(page_size)
-        offset = (page - 1) * page_size
 
         prefix = "SELECT id, chr, pos, ref, alt FROM variant"
         postfix = ""
@@ -727,6 +725,8 @@ def get_variants_page_merged(self, page, page_size, sort_by, include_hidden, use
         elif sort_by == 'recent':
             command += " ORDER BY id DESC"
         if page_size != 'unlimited':
+            page_size = int(page_size)
+            offset = (page - 1) * page_size
             command = command + " LIMIT %s, %s"
             actual_information += (offset, page_size)
         #print(command % actual_information)

src/common/functions.py

@@ -12,6 +12,7 @@
 from dotenv import load_dotenv
 import json
 import uuid
+from functools import cmp_to_key
 
 
 def basedir():
@@ -624,4 +625,25 @@ def str2datetime(datetime_str, fmt):
     if datetime_str is None:
         return None
     else:
-        return datetime.datetime.strptime(datetime_str, fmt)
+        return datetime.datetime.strptime(datetime_str, fmt)
+
+
+
+def order_classes( classes):
+    keyfunc = cmp_to_key(mycmp = sort_classes)
+    classes = [str(x) for x in classes]
+    classes.sort(key = keyfunc) # sort by preferred transcript
+    return classes
+
+def sort_classes(a, b):
+    # sort by ensembl/refseq
+    class_sequence = ['1', '2', '3-', '3', '3+', '4', '5', 'M']
+
+    a_importance = class_sequence.index(a)
+    b_importance = class_sequence.index(b)
+
+    if a_importance > b_importance:
+        return 1
+    elif a_importance < b_importance:
+        return -1
+    return 0

src/common/models.py

@@ -3,6 +3,7 @@
 from typing import Any
 import common.functions as functions
 from functools import cmp_to_key
+import datetime
 
 @dataclass
 class Annotation:
@@ -875,9 +876,7 @@ def sort_consequences(self, a:Consequence, b:Consequence):
                         return 1
                     else:
                         return 0
-
 
-import datetime
 
 @dataclass
 class import_request:

src/frontend_celery/webapp/templates/index.html

@@ -126,6 +126,8 @@ <h4>Changelog</h4>
             <li>Fixed a bug where the ClinVar annotation was erroneous which happened when there were missing submissions</li>
             <li>Fixed a bug where the consequence annotation was erroneous which happened when the variant was large and spanned multiple exons / introns</li>
             <li>Fixed a bug where the user was unable to download variants which are not annotated</li>
+            <li>Fixed a bug where the user could not search for class 3+</li>
+            <li>The date is now inserted correctly when classifying variants. Preexisting classifications did not change (this is fixed starting from 24.10.23).</li>
         </ul>
         Known issues:
         <ul>

src/frontend_celery/webapp/utils/search_utils.py

@@ -70,18 +70,20 @@ def extract_consensus_classifications(request_obj, allowed_classes):
     consensus_classifications = request_obj.args.getlist('consensus')
     consensus_classifications = ';'.join(consensus_classifications)
     regex_inner = '|'.join(allowed_classes)
+    regex_inner = regex_inner.replace('+', '\+')
     consensus_classifications = preprocess_query(consensus_classifications, r'(' + regex_inner + r')?')
     if consensus_classifications is None:
-        flash("You have an error in your consensus class query(s). It must consist of a number between 1-5. Results are not filtered by consensus classification.", "alert-danger")
+        flash("You have an error in your consensus class query(s). It must consist of a number between 1-5, 3+, 3- or M. Results are not filtered by consensus classification.", "alert-danger")
     return consensus_classifications
 
 def extract_user_classifications(request_obj, allowed_classes):
     user_classifications = request_obj.args.getlist('user')
     user_classifications = ';'.join(user_classifications)
     regex_inner = '|'.join(allowed_classes)
+    regex_inner = regex_inner.replace('+', '\+')
     user_classifications = preprocess_query(user_classifications, r'(' + regex_inner + r')?')
     if user_classifications is None:
-        flash("You have an error in your consensus class query(s). It must consist of a number between 1-5. Results are not filtered by consensus classification.", "alert-danger")
+        flash("You have an error in your consensus class query(s). It must consist of a number between 1-5, 3+, 3- or M. Results are not filtered by consensus classification.", "alert-danger")
     return user_classifications
 
 def extract_hgvs(request_obj):

src/frontend_celery/webapp/variant/variant_routes.py

@@ -29,8 +29,8 @@ def search():
     conn = get_connection()
     user_id = session['user']['user_id']
 
-    allowed_user_classes = conn.get_enumtypes('user_classification', 'classification')
-    allowed_consensus_classes = conn.get_enumtypes('consensus_classification', 'classification')
+    allowed_user_classes = functions.order_classes(conn.get_enumtypes('user_classification', 'classification'))
+    allowed_consensus_classes = functions.order_classes(conn.get_enumtypes('consensus_classification', 'classification'))
 
     genes = extract_genes(request)
     ranges = extract_ranges(request)
@@ -64,7 +64,7 @@ def search():
             else:
                 num_inserted = 0
                 if select_all_variants:
-                    variants_for_list, _ = conn.get_variants_page_merged(1, "unlimited", user_id=user_id, ranges=ranges, genes = genes, consensus=consensus_classifications, user=user_classifications, hgvs=hgvs, variant_ids_oi=variant_ids_oi)
+                    variants_for_list, _ = conn.get_variants_page_merged(1, "unlimited", sort_by=selected_sort_by, include_hidden=include_hidden, user_id=user_id, ranges=ranges, genes = genes, consensus=consensus_classifications, user=user_classifications, hgvs=hgvs, variant_ids_oi=variant_ids_oi)
                     variant_ids = [variant.id for variant in variants_for_list]
                     for variant_id in variant_ids:
                         if str(variant_id) not in selected_variants: