added mutually inclusive criteria

resources/backups/database_dumper/users/user_privileges.sql

@@ -49,6 +49,7 @@ GRANT INSERT, UPDATE, DELETE ON HerediVar_ahdoebm1.user_classification_selected_
 GRANT SELECT ON HerediVar_ahdoebm1.gene_alias TO 'HerediVar_user';
 GRANT SELECT ON HerediVar_ahdoebm1.variant_heredicare_annotation TO 'HerediVar_user';
 GRANT SELECT ON HerediVar_ahdoebm1.variant_transcript_annotation TO 'HerediVar_user';
+GRANT SELECT ON HerediVar_ahdoebm1.mutually_inclusive_criteria TO 'HerediVar_user';
 
 /* grant priviliges to super user */
 GRANT SELECT, INSERT, UPDATE ON HerediVar_ahdoebm1.user TO 'HerediVar_superuser';
@@ -83,6 +84,7 @@ GRANT INSERT,UPDATE,DELETE ON HerediVar_ahdoebm1.classification_criterium_streng
 GRANT INSERT,UPDATE,DELETE ON HerediVar_ahdoebm1.mutually_exclusive_criteria TO 'HerediVar_superuser';
 
 GRANT SELECT ON HerediVar_ahdoebm1.variant_transcript_annotation TO 'HerediVar_superuser';
+GRANT SELECT ON HerediVar_ahdoebm1.mutually_inclusive_criteria TO 'HerediVar_superuser';
 
 /* grant priviliges to read only user */
 GRANT SELECT, SHOW VIEW ON HerediVar_ahdoebm1.* TO 'HerediVar_read_only';

resources/classification_schemes/ClinGen_BRCA1_v1.0.0.json

@@ -55,6 +55,9 @@
             ],
             "mutually_exclusive_criteria": [
                 "PP3"
+            ],
+            "mutually_inclusive_criteria": [
+                "PM5"
             ]
         },
 

src/common/db_IO.py

@@ -960,7 +960,7 @@ 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()
 
@@ -2507,7 +2507,7 @@ def get_annotation_queue_entry(self, annotation_queue_id):
     def get_classification_schemas(self):
         # it should look like this:
         # {schema_id -> display_name(description), scheme_type, reference, criteria}
-        #                                         -> {name,description,default_strength,possible_strengths,selectable,disable_group,mutually_exclusive_buttons}
+        #                                         -> {name,description,default_strength,possible_strengths,selectable,disable_group,mutually_exclusive_buttons,mutually_inclusive_buttons}
         command = "SELECT * FROM classification_scheme WHERE is_active = 1"
         self.cursor.execute(command)
         classification_schemas = self.cursor.fetchall()
@@ -2519,10 +2519,24 @@ def get_classification_schemas(self):
         for mutually_exclusive_criterium in mutually_exclusive_criteria:
             source = mutually_exclusive_criterium[0]
             target = mutually_exclusive_criterium[2]
-            if source not in mutually_exclusive_criteria:
-                mutually_exclusive_criteria_dict[source] = [target]
-            else:
-                mutually_exclusive_criteria_dict[source].append(target)
+            functions.extend_dict(mutually_exclusive_criteria_dict, source, target)
+            #if source not in mutually_exclusive_criteria:
+            #    mutually_exclusive_criteria_dict[source] = [target]
+            #else:
+            #    mutually_exclusive_criteria_dict[source].append(target)
+
+        command = "SELECT source,target,name FROM mutually_inclusive_criteria INNER JOIN (SELECT id as inner_id,name FROM classification_criterium)x ON x.inner_id = mutually_inclusive_criteria.target"
+        self.cursor.execute(command)
+        mutually_inclusive_criteria = self.cursor.fetchall()
+        mutually_inclusive_criteria_dict = {}
+        for mutually_inclusive_criterium in mutually_inclusive_criteria:
+            source = mutually_inclusive_criterium[0]
+            target = mutually_inclusive_criterium[2]
+            functions.extend_dict(mutually_inclusive_criteria_dict, source, target)
+            #if source not in mutually_inclusive_criteria_dict:
+            #    mutually_inclusive_criteria_dict[source] = [target]
+            #else:
+            #    mutually_inclusive_criteria_dict[source].append(target)
 
         result = {}
         for classification_schema in classification_schemas:
@@ -2567,7 +2581,8 @@ def get_classification_schemas(self):
                     strength_display_titles[classification_criterium_strength_name] = strength_display_name
                 new_criterium_dict["possible_strengths"] = all_criteria_strengths
                 new_criterium_dict["strength_display_names"] = strength_display_titles
-                new_criterium_dict['mutually_exclusive_criteria'] = mutually_exclusive_criteria_dict.get(classification_criterium_id, []) 
+                new_criterium_dict['mutually_exclusive_criteria'] = mutually_exclusive_criteria_dict.get(classification_criterium_id, [])
+                new_criterium_dict["mutually_inclusive_criteria"] = mutually_inclusive_criteria_dict.get(classification_criterium_id, [])
 
                 classification_criteria_dict[classification_criterium_name] = new_criterium_dict
 

src/frontend_celery/webapp/static/js/classify.js

@@ -366,8 +366,6 @@ function scheme_select_action(do_revert=true) {
         $('#classification_schema_wrapper').collapse('show');
         create_criteria_buttons()
         //colors = load_colors()
-        set_default_strengths()
-        set_activatable_property()
 
         if (do_revert) {
             preselect_criteria_from_database(scheme)
@@ -867,6 +865,15 @@ function create_criteria_buttons() {
         document.querySelector("#uncertain_criteria_container").closest(".card").hidden = true
     }
 
+    set_default_strengths()
+    set_activatable_property()
+
+    // enable/disable buttons -- mainly for mutually inclusive criteria
+    for (const i in criteria_ids) {
+        var criterium_id = criteria_ids[i]
+        update_mutual_criteria(criterium_id)
+    }
+
 }
 
 
@@ -1286,7 +1293,7 @@ function enable_disable_buttons(criterium_ids, is_disable) {
         const current_criterium_id = criterium_ids[i];
         const current_criterium_button = document.getElementById(current_criterium_id)
         // this is just a sanity check to make sure that the disabled buttons are not checked!
-        if (current_criterium_button.checked) {
+        if (current_criterium_button.checked && document.getElementById(current_criterium_id + "_state").value != "unchecked") {
             set_criterium(current_criterium_id, "unchecked")
         }
         if (current_criterium_button.getAttribute('activateable') === 'true') {
@@ -1402,15 +1409,24 @@ function update_criterium_button_label(criterium_id) {
     }
 }
 
+function update_mutual_criteria(criterium_id) {
+    is_selected = document.getElementById(criterium_id + '_state').value == 'selected'
+    // mutually exclusive criteria
+    const current_disable_group = classification_schemas[scheme]['criteria'][criterium_id]['mutually_exclusive_criteria']
+    enable_disable_buttons(current_disable_group, is_selected)
+
+    // mutually inclusive criteria
+    const current_enable_group = classification_schemas[scheme]['criteria'][criterium_id]['mutually_inclusive_criteria']
+    enable_disable_buttons(current_enable_group, !is_selected)
+}
+
 // select and unselect the criterium itself + its associated strength input check which holds information about its user-assigned strenght
 function toggle_criterium(criterium_id) {
     var obj = document.getElementById(criterium_id)
     obj.checked = !obj.checked
     update_criterium_button_background(criterium_id)
     document.getElementById(criterium_id + '_strength').checked = obj.checked
-    const current_disable_group = classification_schemas[scheme]['criteria'][criterium_id]['mutually_exclusive_criteria']
-    const is_selected =  obj.checked && (document.getElementById(criterium_id + '_state').value == 'selected')
-    enable_disable_buttons(current_disable_group, is_selected)
+    update_mutual_criteria(criterium_id)
 }
 
 
@@ -1441,11 +1457,7 @@ function set_criterium(criterium_id, state, is_intermediate = false) {
 
     update_criterium_button_label(criterium_id)
     update_criterium_button_background(criterium_id)
-    const current_disable_group = classification_schemas[scheme]['criteria'][criterium_id]['mutually_exclusive_criteria']
-    const is_selected = is_checked && (document.getElementById(criterium_id + '_state').value == 'selected')
-    if (state != 'unchecked') { // prevent recursion
-        enable_disable_buttons(current_disable_group, is_selected)
-    }
+    update_mutual_criteria(criterium_id)
 }
 
 

src/frontend_celery/webapp/variant/variant_routes.py

@@ -270,9 +270,6 @@ def display(variant_id=None, chr=None, pos=None, ref=None, alt=None):
 
     clinvar_submission = check_update_clinvar_status(variant_id, conn)
 
-
-    print(variant.get_genes("best"))
-
     return render_template('variant/variant.html',
                             current_annotation_status=current_annotation_status,
                             clinvar_submission = clinvar_submission,