fixed some issues and implemented a workaround for wrong hg38 positions

src/common/db_IO.py

@@ -1059,8 +1059,10 @@ def get_variants_page_merged(self, page, page_size, sort_by, include_hidden, use
 
             if len(ids_unknown_source) > 0:
                 placeholders = self.get_placeholders(len(ids_unknown_source))
-                new_constraints.append("id IN (SELECT variant_id FROM variant_ids WHERE external_id IN " + placeholders + " UNION SELECT id FROM variant WHERE id IN " + placeholders + ")")
-                actual_information += tuple(ids_unknown_source) * 2
+                annotation_type_ids_oi = list(self.get_recent_annotation_type_ids().values())
+                annotation_type_id_placeholders = self.get_placeholders(len(annotation_type_ids_oi))
+                new_constraints.append("id IN (SELECT variant_id FROM variant_ids WHERE external_id IN " + placeholders + " AND annotation_type_id IN " + annotation_type_id_placeholders + " UNION SELECT id FROM variant WHERE id IN " + placeholders + ")")
+                actual_information += tuple(ids_unknown_source) + tuple(annotation_type_ids_oi) + tuple(ids_unknown_source)
             new_constraints = ' OR '.join(new_constraints)
             postfix = self.add_constraints_to_command(postfix, new_constraints)
 
@@ -1085,7 +1087,7 @@ def get_variants_page_merged(self, page, page_size, sort_by, include_hidden, use
             offset = (page - 1) * page_size
             command = command + " LIMIT %s, %s"
             actual_information += (offset, page_size)
-        print(command % actual_information)
+        #print(command % actual_information)
         self.cursor.execute(command, actual_information)
         variants_raw = self.cursor.fetchall()
 

src/frontend_celery/webapp/tasks.py

@@ -392,6 +392,24 @@ def insert_variants_vcf_file(vcf_file, genome_build, user_id, import_queue_id, c
     return status, message
 
 
+# this is basically a workaround for a liftover error when the reference base was missing: ex: vid:9476493	chrom:22	pos_hg19:29090030	ref_hg19:GG	alt_hg19:A
+# some of these variants have an erroneous hg38 variant in heredicare. However, when lifting them from hg19 they are recovered correctly
+def skip_hg38(variant) -> bool:
+    chrom = variant.get('CHROM')
+    pos_38 = variant.get('POS_HG38')
+    ref_38 = variant.get('REF_HG38')
+    alt_38 = variant.get('ALT_HG38')
+
+    pos_19 = variant.get('POS_HG19')
+    ref_19 = variant.get('REF_HG19')
+    alt_19 = variant.get('ALT_HG19')
+
+    if all([chrom, pos_38, ref_38, alt_38]):
+        if all([chrom, pos_19, ref_19, alt_19]):
+            if (ref_19[0] != alt_19[0]) and (len(ref_19) > 1 or len(alt_19) > 1) and (len(ref_19) != len(alt_19)):
+                return True
+
+    return False
 
 
 
@@ -411,7 +429,7 @@ def map_hg38(variant, user_id, conn:Connection, insert_variant = True, perform_a
     genome_build = "GRCh38"
 
     was_successful = False
-    if all([x is not None for x in [chrom, pos, ref, alt]]):
+    if all([x is not None for x in [chrom, pos, ref, alt]]) and not skip_hg38(variant):
         was_successful, new_message, variant_id = validate_and_insert_variant(chrom, pos, ref, alt, genome_build, conn, user_id, allowed_sequence_letters = allowed_sequence_letters, insert_variant = insert_variant, perform_annotation=perform_annotation)
         if new_message not in message:
             message = functions.collect_info(message, "hg38_msg=", new_message, sep = " ~~ ")

src/frontend_celery/webapp/templates/index.html

@@ -106,6 +106,7 @@ <h4>Changelog</h4>
             <li>Fixed some minor issues with HerediCaRe up- and downloads</li>
             <li>Downgraded CrossMap to v0.7.0 because v0.7.3 yields wrong results for specific variants</li>
             <li>Fixed a bug where the tooltip of status pills would persist if the pill was updated</li>
+            <li>Fixed a bug where the user was able to search for deprecated variant ids using the browse variant table</li>
         </ul>
     </div>