improved range search & fixed a bug in classification search when sea…

…rching for heredicare variants

src/common/db_IO.py

@@ -444,15 +444,12 @@ def add_constraints_to_command(self, command, constraints, operator = 'AND'): #
         return command
 
     def preprocess_range(self, range_constraint):
-        parts = range_constraint.split(':')
-        if len(parts) != 2:
+        parts = range_constraint.split('-')
+        if len(parts) != 3:
             return None, None, None
         chr = parts[0]
-        positions = parts[1].split('-')
-        if len(positions) != 2:
-            return None, None, None
-        start = int(positions[0])
-        end = int(positions[1])
+        start = int(parts[1])
+        end = int(parts[2])
         return chr, start, end
 
     def convert_to_gene_id(self, string):
@@ -663,7 +660,8 @@ def get_variants_page_merged(self, page, page_size, sort_by, include_hidden, use
                 new_constraints_inner = new_constraints_inner + "SELECT variant_id FROM consensus_classification WHERE classification IN " + placeholders + " AND is_recent = 1"
                 actual_information += tuple(consensus_without_dash)
             new_constraints = "variant.id IN (" + new_constraints_inner + ")"
-            postfix = self.add_constraints_to_command(postfix, new_constraints)
+            #postfix = self.add_constraints_to_command(postfix, new_constraints)
+            constraints_complete = new_constraints
 
             if include_heredicare_consensus and len(consensus_without_dash) > 0:
                 heredicare_consensus = []
@@ -674,7 +672,9 @@ def get_variants_page_merged(self, page, page_size, sort_by, include_hidden, use
                 new_constraints = "variant.id IN (SELECT variant_id FROM variant_heredicare_annotation WHERE consensus_class IN " + placeholders1 +  " AND variant_id NOT IN (SELECT variant_id FROM consensus_classification WHERE classification NOT IN " + placeholders2 + " AND is_recent = 1))"
                 actual_information += tuple(heredicare_consensus)
                 actual_information += tuple(consensus_without_dash)
-                postfix = self.add_constraints_to_command(postfix, new_constraints, 'OR')
+                constraints_complete = functions.enbrace(constraints_complete + " OR " + new_constraints)
+
+            postfix = self.add_constraints_to_command(postfix, constraints_complete)
 
         if user is not None and len(user) > 0:
             new_constraints_inner = ''

src/frontend_celery/webapp/templates/index.html

@@ -98,6 +98,8 @@ <h4>Changelog</h4>
         <ul>
             <li>Added option to include heredicare consensus classififcations in consensus classification search</li>
             <li>Added BayesDEL annotation</li>
+            <li>Improved ClinVar review status & summary display</li>
+            <li>Improved range search. Each range search entry must now be of the format: chrom&lt;sep&gt;start&lt;sep&gt;end. With &lt;sep&gt;  being either :, -, space or tabulator. The chromosome number can start with 'chr', but you can also choose to omit it.</li>
         </ul>
         Bugfixes:
         <ul>

src/frontend_celery/webapp/templates/macros.html

@@ -485,6 +485,13 @@
                                >{{ request.args.get('hgvs', '') }}</textarea>
                     </div>
 
+                    <div class="form-group sst">
+                        <label for="external_ids" class="form-label">External IDs</label>
+                        <textarea type="text" name="external_ids" id="external_ids"
+                               placeholder="..." class="form-control"
+                               >{{ request.args.get('external_ids', '') }}</textarea>
+                    </div>
+
                     <div class="form-group sst">
                         {% set selected_consensus = request.args.getlist('consensus') %}
                         <label for="consensus-select" class="form-label">Consensus classification</label>

src/frontend_celery/webapp/templates/variant/variant_base.html

@@ -208,12 +208,23 @@ <h4 class="card-subcaption">HerediCare center classifications</h4>
                         <h4 class="card-subcaption">ClinVar classifications</h4>
 
                         <div class="ssl sst ssb">
-                            <div>
-                                <abbr title="The review status from ClinVar"><a class="dashed_underline">review status:</a></abbr>&nbsp;{{ clinvar.review_status }}
+                            <div class="d-flex">
+                                <abbr class="ssr width_small" title="The review status from ClinVar"><a class="dashed_underline">review status:</a></abbr>
+                                <div>{{ clinvar.review_status }}</div>
                             </div>
 
-                            <div>
-                                <abbr title="A summary of the ClinVar interpretations. The numbers in brackets display the number of ClinVar submissions reporting the specific type of interpretation."><a class="dashed_underline">interpretation summary:</a></abbr>&nbsp;{{ clinvar.interpretation_summary }}
+                            <div class="d-flex">
+                                <abbr class="ssr width_small" title="A summary of the ClinVar interpretations. The numbers in brackets display the number of ClinVar submissions reporting the specific type of interpretation.">
+                                    <a class="dashed_underline">summary:</a>
+                                </abbr>
+                                <ul class="list-group list-group-horizontal-sm list-nopad-td list-nobackground" >
+                                    {% for item in clinvar.interpretation_summary.split('|') %}
+                                    <li class="list-group-item noboarder-td" >
+                                        {{ item.replace('(', ' (') }}
+                                    </li>
+                                    {% endfor %}
+                                </ul>
+
                             </div>
                         </div>
                         <!-- clinvar submission table -->

src/frontend_celery/webapp/utils/search_utils.py

@@ -23,40 +23,68 @@ def preprocess_query(query, pattern = '.*'):
 def get_search_query_separators():
     return '[;,\n]'
 
-def bed_ranges_to_heredivar_ranges(ranges):
-    ranges = re.split('[\n]', ranges)
-    result = []
-    for range_entry in ranges:
-        range_entry = range_entry.strip()
-        if '\t' in range_entry: # it is a bed style range
-            new_heredivar_range = convert_bed_line_to_heredivar_range(range_entry)
-            if new_heredivar_range is not None:
-                result.append(new_heredivar_range)
-        else: # it is already a heredivar style range
-            result.append(range_entry)
-    return ';'.join(result)
-
-
-def convert_bed_line_to_heredivar_range(bed_line):
-    parts = bed_line.split('\t')
+#def bed_ranges_to_heredivar_ranges(ranges):
+#    ranges = re.split('[\n]', ranges)
+#    result = []
+#    for range_entry in ranges:
+#        range_entry = range_entry.strip()
+#        if '\t' in range_entry: # it is a bed style range
+#            new_heredivar_range = convert_bed_line_to_heredivar_range(range_entry)
+#            if new_heredivar_range is not None:
+#                result.append(new_heredivar_range)
+#        else: # it is already a heredivar style range
+#            result.append(range_entry)
+#    return ';'.join(result)
+#
+#
+#def convert_bed_line_to_heredivar_range(bed_line):
+#    parts = bed_line.split('\t')
+#    chrom = parts[0]
+#    chr_num = functions.validate_chr(chrom)
+#    if chr_num is None:
+#        return None
+#    chrom = 'chr' + str(chr_num)
+#    start = parts[1] # bed ranges are zero based at the start position
+#    end = int(parts[2]) - 1 # bed ranges are one based at the end position -> need to substract one because mysql has start and end zero based when using BETWEEN operator
+#    return chrom + ':' + str(start) + '-' + str(end)
+
+def preprocess_ranges(ranges):
+    if ranges is None:
+        return None
+    seps = get_search_query_separators()
+    ranges_split = re.split(seps, ranges)
+    ranges_split = [proprocess_range_worker(r) for r in ranges_split]
+    ranges_split_filtered = [r for r in ranges_split if r is not None] # filter out erroneous
+    if len(ranges_split) != len(ranges_split_filtered):
+        flash("At least one of your range query(s) has an error. Please check the syntax. The erroneous range query(s) were removed. You still have " + str(len(ranges_split_filtered)) + " ranges after removing the erroneous ones.", 'alert-danger')
+    ranges_split = ';'.join(ranges_split_filtered)
+    return ranges_split
+
+def proprocess_range_worker(r):
+    r = r.strip()
+    r = r.replace(':', '-').replace('\t', '-').replace(' ', '-')
+    parts = r.split('-')
     chrom = parts[0]
     chr_num = functions.validate_chr(chrom)
     if chr_num is None:
         return None
-    chrom = 'chr' + str(chr_num)
-    start = parts[1] # bed ranges are zero based at the start position
-    end = int(parts[2]) - 1 # bed ranges are one based at the end position -> need to substract one because mysql has start and end zero based when using BETWEEN operator
-    return chrom + ':' + str(start) + '-' + str(end)
+    parts[0] = 'chr' + str(chr_num)
+    r = '-'.join(parts)
+    return r
+
 
 def extract_ranges(request_obj):
     ranges = request_obj.args.get('ranges', '')
-    if '\t' in ranges:
-        ranges = bed_ranges_to_heredivar_ranges(ranges)
-    ranges = preprocess_query(ranges, pattern= r"chr.+:\d+-\d+")
-    if ranges is None:
-        flash("You have an error in your range query(s). Please check the syntax! Results are not filtered by ranges.", "alert-danger")
+    if ranges != '':
+        ranges = preprocess_ranges(ranges)
+        ranges = preprocess_query(ranges, pattern= r"(chr)?.+-\d+-\d+")
+        if ranges is None:
+            flash("You have an error in your range query(s). Please check the syntax! Results are not filtered by ranges.", "alert-danger")
+    else:
+        return []
     return ranges
 
+
 def extract_genes(request_obj):
     genes = request_obj.args.get('genes', '')
     genes = preprocess_query(genes)