added check consistency script and fixed search bug

src/common/db_IO.py

@@ -778,7 +778,7 @@ def get_variants_page_merged(self, page, page_size, sort_by, include_hidden, use
                     new_constraints.append("(LENGTH(ref) = 1 AND LENGTH(alt) = 1 AND variant_type = 'small')")
                 elif 'struct' in variant_type:
                     new_constraints.append("(variant_type = 'sv')")
-            new_constraints = ' OR '.join(new_constraints)
+            new_constraints = functions.enbrace(' OR '.join(new_constraints))
             postfix = self.add_constraints_to_command(postfix, new_constraints)
         if cdna_ranges is not None and len(cdna_ranges) > 0:
             new_constraints = []

src/frontend_celery/webapp/__init__.py

@@ -1,12 +1,14 @@
+
+import sys
+import os
 from flask import Flask
 from authlib.integrations.flask_client import OAuth
 from flask_session import Session # alternatives: flask-caching, flask-kvsesssion
 from urllib.parse import urlparse, urljoin
 # for celery
 from celery import Celery
+sys.path.append(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
 from config import Config
-import sys
-import os
 sys.path.append(os.path.dirname(os.path.dirname(os.path.dirname(os.path.abspath(__file__)))))
 from common import paths, functions
 #from annotation_service.heredicare_interface import Heredicare_Flask
@@ -18,7 +20,6 @@
 from flask_mail import Mail
 
 
-
 oauth = OAuth()
 sess = Session()
 celery = Celery(__name__, backend="redis", 

src/frontend_celery/webapp/tasks.py

@@ -249,7 +249,7 @@ def fetch_heredicare(vid, user_id, conn:Connection, insert_variant = True, perfo
     if status != 'success': # error in variant retrieval from heredicare
         return status, message
 
-    if str(variant.get("VISIBLE", "0")) == "0" or len(variant) == 0: # skip invisible vid or vid that is unknown by heredicare
+    if (str(variant.get("VISIBLE", "0")) == "0" or len(variant) == 0) and insert_variant: # skip invisible vid or vid that is unknown by heredicare
         annotation_type_id = conn.get_most_recent_annotation_type_id("heredicare_vid")
         variant_id = conn.get_variant_id_from_external_id(vid, annotation_type_id) # check if heredivar knows the vid
         if variant_id is not None: # heredivar knows the vid, but heredicare doesnt OR vid is now invisible

src/frontend_celery/webapp/templates/index.html

@@ -93,8 +93,16 @@ <h4>Overview</h4>
 <div class="bst bsb">
     <h4>Changelog</h4>
 
-    <div class="underline">v 1.13.2 (22.07.2024)</div>
+    <div class="underline">v 1.13.3 (23.07.2024)</div>
     <div class="btn-pvs">!! Scores from likelihood ratio tests are currently not available from HerediCaRe.</div>
+    <div>
+        Bugfixes:
+        <ul>
+            <li>Searching for specific variants would not apply filters correctly</li>
+        </ul>
+    </div>
+
+    <div class="underline">v 1.13.2 (22.07.2024)</div>
     <div>
         General changes:
         <ul>
@@ -111,7 +119,6 @@ <h4>Changelog</h4>
     </div>
 
     <div class="underline">v 1.13.1 (18.07.2024)</div>
-    <div class="btn-pvs">!! Scores from likelihood ratio tests are currently not available from HerediCaRe.</div>
     <div>
         General changes:
         <ul>

src/frontend_celery/webapp/templates/macros.html

@@ -531,7 +531,7 @@
                         <div id="variant_type-select" class="d-flex">
                             {% for variant_type in static_information['allowed_variant_types'] %}
                                 <div class="form-check d-flex bsr align-items-center">
-                                    <input class="form-check-input ssr" type="checkbox" value="{{variant_type}}" id="variant_type_{{variant_type}}" name="variant_type" {% if variant_type in selected_variant_types or selected_variant_types | length == 0 %}checked{% endif %}>
+                                    <input class="form-check-input ssr" type="checkbox" value="{{variant_type}}" id="variant_type_{{variant_type}}" name="variant_type" {% if variant_type in selected_variant_types %}checked{% endif %}>
                                     <label class="form-check-label" for="variant_type_{{variant_type}}">{{variant_type.replace('_', ' ')}}</label>
                                 </div>
                             {% endfor %}

src/frontend_celery/webapp/utils/check_consistency.py

@@ -0,0 +1,68 @@
+# this script checks that all HerediCaRe VIDs are consistent with the HerediVar variants
+
+
+import sys
+from os import path
+sys.path.append(path.dirname(path.dirname(path.dirname(path.dirname(path.abspath(__file__))))))
+from common.db_IO import Connection
+import common.functions as functions
+from common.heredicare_interface import Heredicare
+import frontend_celery.webapp.tasks as tasks
+
+def print_progress_bar(iteration, total, prefix = '', suffix = '', decimals = 1, length = 100, fill = '█', printEnd = "\r"):
+    percent = ("{0:." + str(decimals) + "f}").format(100 * (iteration / float(total)))
+    filledLength = int(length * iteration // total)
+    bar = fill * filledLength + '-' * (length - filledLength)
+    print(f'\r{prefix} |{bar}| {percent}% {suffix}', end = printEnd)
+    # Print New Line on Complete
+    if iteration == total: 
+        print()
+
+
+conn = Connection()
+heredicare = Heredicare()
+
+err_out_path = path.dirname(path.abspath(__file__)) + "/heredicare_errors.tsv"
+err_out_file = open(err_out_path, 'w')
+
+user_id = -1
+
+variant_ids = conn.get_all_valid_variant_ids()
+print_progress_bar(0, len(variant_ids), prefix = 'Progress:', suffix = 'Complete', length = 50)
+
+for i, variant_id in enumerate(variant_ids):
+    variant = conn.get_variant(variant_id, include_external_ids = True, include_annotations = False, include_consensus = False, include_user_classifications = False, include_automatic_classification = False, include_clinvar = False, include_consequences = False, include_assays = False, include_literature = False)
+    variant_id = str(variant.id)
+    vids = variant.get_external_ids('heredicare_vid', how = 'list')
+
+    for vid in vids:
+        status, message = tasks.fetch_heredicare(vid, user_id, conn, insert_variant = False, perform_annotation = False)
+        if status != 'success':
+            line = "\t".join([variant.get_string_repr(), "", variant_id, vid, "HerediCaRe API error: " + message])
+            err_out_file.write(line + "\n")
+            continue
+
+        heredicare_variant = functions.find_between(message, 'HG38 variant would be: ', '( ~~ |$)')
+        if heredicare_variant is None:
+            line = "\t".join([variant.get_string_repr(), '', variant_id, vid, "The heredicare_variant was not found in message: " + message])
+            err_out_file.write(line + "\n")
+            continue
+        heredicare_variant = heredicare_variant.strip().split('-')
+
+        if len(heredicare_variant) != 4:
+            line = "\t".join([variant.get_string_repr(), '-'.join(heredicare_variant), variant_id, vid, "Number of fields of heredicare variant is incorrect: " + str(len(heredicare_variant))])
+            err_out_file.write(line + "\n")
+            continue
+
+        if variant.chrom != heredicare_variant[0] or str(variant.pos) != heredicare_variant[1] or variant.ref != heredicare_variant[2] or variant.alt != heredicare_variant[3]:
+            line = "\t".join([variant.get_string_repr(), '-'.join(heredicare_variant), variant_id, vid, "Incorrect variant match!"])
+            err_out_file.write(line + "\n")
+            continue
+
+    print_progress_bar(i+1, len(variant_ids), prefix = 'Progress:', suffix = 'Complete', length = 50)
+
+
+
+
+err_out_file.close()
+conn.close()