improved assay submission form & bugfixes

src/annotation_service/main.py

@@ -54,7 +54,7 @@ def get_default_job_config():
         'do_taskforce_domains': True,
         'do_coldspots': True,
         'do_litvar': True,
-        'do_auto_class': True
+        'do_auto_class': False
 
         # outdated
         #'do_arup': True,

src/common/db_IO.py

@@ -2280,7 +2280,7 @@ def get_variant(self, variant_id,
                         criterium_evidence = criterium_raw[4]
                         criterium_strength = criterium_raw[7]
                         strength_display_name = criterium_raw[8]
-                        is_selected = True
+                        is_selected = criterium_raw[9]
                         criterium = models.HerediVarCriterium(id = criterium_id, name = criterium_name, type=criterium_type, evidence = criterium_evidence, strength = criterium_strength, strength_display_name = strength_display_name, is_selected = is_selected)
                         criteria.append(criterium)
                     scheme = models.Scheme(id = scheme_id, display_name = scheme_display_name, type = scheme_type, criteria = criteria, reference = reference, selected_class = scheme_class, is_active = is_active, is_default = is_default)
@@ -2624,14 +2624,14 @@ def get_assay_metadata(self, assay_id):
         return res
 
     def get_assay_metadata_type(self, assay_metadata_type_id):
-        #!!!! SELECT MUST BE EQUAL TO the one in get_assay_metadata_types
+        #!!!! SELECT columns MUST BE EQUAL TO the one in get_assay_metadata_types
         command = "SELECT id, title, display_title, assay_type_id, value_type, is_deleted, is_required FROM assay_metadata_type WHERE id= %s AND is_deleted = 0"
         self.cursor.execute(command, (assay_metadata_type_id, ))
         res = self.cursor.fetchone()
         return res
 
     def get_assay_metadata_types(self, assay_type_id, format = "dict"):
-        #!!!! SELECT MUST BE EQUAL TO the one in get_assay_metadata_type
+        #!!!! SELECT columns MUST BE EQUAL TO the one in get_assay_metadata_type
         command = "SELECT id, title, display_title, assay_type_id, value_type, is_deleted, is_required FROM assay_metadata_type WHERE assay_type_id = %s AND is_deleted = 0"
         self.cursor.execute(command, (assay_type_id, ))
         assay_metadata_types_raw = self.cursor.fetchall()
@@ -2656,8 +2656,8 @@ def insert_assay_metadata(self, assay_id, assay_metadata_type_id, value):
             self.conn.commit()
 
     def convert_assay_metadata_type(self, assay_metadata_type_raw):
-        is_deleted = assay_metadata_type_raw[5] == "1"
-        is_required = assay_metadata_type_raw[6] == "1"
+        is_deleted = assay_metadata_type_raw[5] == 1
+        is_required = assay_metadata_type_raw[6] == 1
         assay_metadata_type = models.Assay_Metadata_Type(id = int(assay_metadata_type_raw[0]), title = assay_metadata_type_raw[1], display_title = assay_metadata_type_raw[2], assay_type_id = int(assay_metadata_type_raw[3]),
                                                          value_type = assay_metadata_type_raw[4], is_deleted = is_deleted, is_required = is_required)
         return assay_metadata_type

src/common/models.py

@@ -688,7 +688,7 @@ def to_vcf(self, prefix = True):
             new_element = "~2B".join([assay_metadata.metadata_type.display_title, assay_metadata.value])
             metadata_parts.append(new_element)
         metadata = "~24".join(metadata_parts)
-        info = '~7C'.join([self.type_title, str(self.date), self.link, metadata]) # sep: |
+        info = '~7C'.join([self.type_title, str(self.date), str(self.link), metadata]) # sep: |
         if prefix:
             info = 'assays~1Y' + info
         return info

src/frontend_celery/webapp/__init__.py

@@ -21,7 +21,7 @@
 
 oauth = OAuth()
 sess = Session()
-celery = Celery(__name__, broker=Config.CELERY_BROKER_URL)
+celery = Celery(__name__, backend="redis", broker=Config.CELERY_BROKER_URL)
 mail = Mail()
 #heredicare = Heredicare_Flask()
 

src/frontend_celery/webapp/io/variant_io_routes.py

@@ -256,50 +256,90 @@ def get_assertion_criteria(scheme_type, assertion_criteria_source):
 @variant_io_blueprint.route('/submit_assay/<int:variant_id>', methods=['GET', 'POST'])
 @require_permission(['edit_resources'])
 def submit_assay(variant_id):
+    conn = get_connection()
+
+    assay_type2id = conn.get_assay_type_id_dict()
+    possible_assays = {}
+    for assay_type in assay_type2id:
+        assay_type_id = assay_type2id[assay_type]
+        metadata_types = conn.get_assay_metadata_types(assay_type_id, format = "dict")
+        possible_assays[assay_type] = {"id": assay_type_id, "metadata_types": metadata_types}
 
     do_redirect = False
     if request.method == 'POST':
         assay_type = request.form.get('assay_type')
-        assay_report = request.files.get('report')
-        assay_score = request.form.get('score')
 
-        #print(assay_type)
-        #print(assay_report)
-        #print(assay_score)
+        selected_assay = possible_assays.get(assay_type)
 
-
-        if not assay_type or not assay_report or not assay_score or not assay_report.filename:
-            flash('All fields are required!', 'alert-danger')
+        if selected_assay is None:
+            flash("Assay type is not supported!", "alert-danger")
         else:
-
-            assay_report.filename = secure_filename(assay_report.filename)
-
-            # the buffer is required as larger files (>500kb) are saved to /tmp upon upload
-            # this file must be read back in
-            buffer = io.BytesIO()
-            for line in assay_report:
-                buffer.write(line)
-            buffer.seek(0)
-
-            b_64_assay_report = functions.buffer_to_base64(buffer)
-
-            if len(b_64_assay_report) > 16777215: # limited by the database mediumblob
-                current_app.logger.error(session['user']['preferred_username'] + " attempted uploading an assay which excedes the maximum filesize. The filesize was: " + str(len(b_64_assay_report)))
-                abort(500, "The uploaded file is too large. Please upload a smaller file.")
-
-            conn = get_connection()
-            conn.insert_assay(variant_id, assay_type, b_64_assay_report, assay_report.filename, assay_score, functions.get_today())
-
-            flash("Successfully uploaded a new assay for variant " + str(variant_id), "alert-success")
-
-            current_app.logger.info(session['user']['preferred_username'] + " successfully uploaded a new assay for variant " + str(variant_id))
-
-            do_redirect = True
-
-
-            #functions.base64_to_file(b_64_assay_report, '/mnt/users/ahdoebm1/HerediVar/src/frontend/webapp/io/test.pdf')
+            # extract selected data from request and make sure that only valid data is submitted
+            metadata_types = selected_assay["metadata_types"]
+            status = "success"
+            extracted_data = {}
+            for metadata_type_name in metadata_types:
+                metadata_type = metadata_types[metadata_type_name]
+
+                current_data = request.form.get(str(metadata_type.id))
+                if metadata_type.is_required and metadata_type.value_type != 'bool' and (current_data is None or current_data.strip() == ''):
+                    flash("The metadata " + str(metadata_type.display_title) + " is required", "alert-danger")
+                    status = "error"
+                    break
+                if metadata_type.value_type == "text" and current_data.strip() != '':
+                    extracted_data[metadata_type.id] = str(current_data)
+                elif metadata_type.value_type == "bool":
+                    current_data = str(current_data)
+                    if current_data not in ["None", "on"]:
+                        flash("The value " + str(current_data) + " is not allowed for a boolean input field", "alert-danger")
+                        status = "error"
+                        break
+                    extracted_data[metadata_type.id] = current_data == "on"
+                elif metadata_type.value_type == "float" and current_data.strip() != '':
+                    try:
+                        extracted_data[metadata_type.id] = float(current_data)
+                    except:
+                        flash("The metadata " + str(metadata_type.display_title) + " is not numeric.", "alert-danger")
+                        status = "error"
+                        break
+                elif "ENUM" in metadata_type.value_type:
+                    possible_values = metadata_type.value_type.split(':')[1].split(',')
+                    if current_data not in possible_values:
+                        flash("The value " + str(current_data) + " is not allowed for field " + str(metadata_type.display_title), "alert-danger")
+                        status = "error"
+                        break
+                    extracted_data[metadata_type.id] = current_data
+
+            if status == "success":
+                # extract report
+                assay_report = request.files.get("report")
+                if not assay_report or not assay_report.filename:
+                    flash("No assay report provided or filename is missing", "alert-danger")
+                    status = "error"
+
+            if status == "success":
+                assay_report.filename = secure_filename(assay_report.filename)
+                # the buffer is required as larger files (>500kb) are saved to /tmp upon upload
+                # this file must be read back in
+                buffer = io.BytesIO()
+                for line in assay_report:
+                    buffer.write(line)
+                buffer.seek(0)
+
+                b_64_assay_report = functions.buffer_to_base64(buffer)
+
+                if len(b_64_assay_report) > 16777215: # limited by the database mediumblob
+                    current_app.logger.error(session['user']['preferred_username'] + " attempted uploading an assay which excedes the maximum filesize. The filesize was: " + str(len(b_64_assay_report)))
+                    abort(500, "The uploaded file is too large. Please upload a smaller file.")
+
+                assay_id = conn.insert_assay(variant_id, assay_type_id, b_64_assay_report, assay_report.filename, link = None, date = functions.get_today(), user_id = session["user"]["user_id"])
+                for metadata_type_id in extracted_data:
+                    conn.insert_assay_metadata(assay_id, metadata_type_id, extracted_data[metadata_type_id])
+
+                flash("Successfully inserted new assay for variant " + str(variant_id), "alert-success")
+                do_redirect = True
 
 
     if do_redirect :
         return redirect(url_for('variant_io.submit_assay', variant_id = variant_id))
-    return render_template('variant_io/submit_assay.html')
+    return render_template('variant_io/submit_assay.html', possible_assays = possible_assays)

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

@@ -295,9 +295,6 @@ $(document).ready(function() {
     $('#scheme').change(function () {
         scheme_select_action();
     });
-    //$('#select_criterium_check').change(function () {
-    //    select_criterium(this);
-    //});
     $('#blank_row_button').click(function () {
         create_literature_select(document.getElementById('selectedLiteratureList'));
     });
@@ -1078,8 +1075,8 @@ function create_user_acmg_details_table() {
     header_row.appendChild(create_sortable_header('User', 'width_small'))
     header_row.appendChild(create_sortable_header('Affiliation', 'width_small'))
     header_row.appendChild(create_sortable_header('Strength', 'width_small'))
-    var evidence_header = create_sortable_header('Evidence')
-    header_row.appendChild(evidence_header)
+    header_row.appendChild(create_sortable_header('Evidence'))
+    header_row.appendChild(create_sortable_header('Selected', 'width_very_small'))
     header_row.appendChild(create_sortable_header('Date', 'width_small'))
     header_row.appendChild(create_non_sortable_header('Copy', 'width_minimal'))
     header.appendChild(header_row)
@@ -1131,12 +1128,13 @@ function create_subcaption(text) {
 }
 
 // this returns one row of the user scheme table shown when making a consensus classification
-function create_row_user_acmg_details(user, affiliation, strength, evidence, date) {
+function create_row_user_acmg_details(user, criterium_id, affiliation, strength, evidence, date, is_selected) {
     var new_row = document.createElement('tr')
     new_row.appendChild(create_table_data(user))
     new_row.appendChild(create_table_data(affiliation))
     new_row.appendChild(create_table_data(criterium_strength_to_description(strength)))
     new_row.appendChild(create_table_data(evidence))
+    new_row.appendChild(create_table_data(is_selected))
     new_row.appendChild(create_table_data(date))
     //new_row.appendChild(create_table_data('copy...')) // TODO
     var copy_evidence_td = document.createElement('td')
@@ -1152,6 +1150,8 @@ function create_row_user_acmg_details(user, affiliation, strength, evidence, dat
     `
     copy_evidence_text.value = evidence
     copy_evidence_text.setAttribute('strength', strength)
+    copy_evidence_text.setAttribute('is_selected', is_selected)
+    copy_evidence_text.setAttribute('criterium_id', criterium_id)
     copy_evidence_text.onclick = function() {copy_evidence(this)}
     copy_evidence_text.classList.add('clickable')
     copy_evidence_td.appendChild(copy_evidence_text)
@@ -1169,6 +1169,18 @@ function copy_evidence(obj) {
     if (radio_to_select != null) {
         radio_to_select.click()
     }
+
+    const is_selected = obj.getAttribute('is_selected')
+    const criterium_id = obj.getAttribute('criterium_id')
+
+    var state = "unchecked"
+    if (is_selected == "true") {
+        state = "selected"
+    } else if (is_selected == "false") {
+        state = "unselected"
+    }
+    select_criterium_check.value = state
+    set_criterium(criterium_id, state, is_intermediate = true)
 }
 
 function add_user_acmg_classification_details(criterium_id) {
@@ -1192,8 +1204,9 @@ function add_user_acmg_classification_details(criterium_id) {
                     var current_criterium_id = criterium['name']
                     var current_strength = criterium['type']
                     var current_evidence = criterium['evidence']
+                    var is_selected = criterium['is_selected']
                     if (current_criterium_id === criterium_id) {
-                        var new_row = create_row_user_acmg_details(user, affiliation, current_strength, current_evidence, current_date)
+                        var new_row = create_row_user_acmg_details(user, criterium_id, affiliation, current_strength, current_evidence, current_date, is_selected)
                         document.getElementById('user_acmg_details').appendChild(new_row)
                     }
                 }

src/frontend_celery/webapp/static/js/submit_assay.js

@@ -7,6 +7,7 @@ $(document).ready(function(){
     $('#assay_type').click(function() {
         select_assay_type_action(this.value);
     });
+
 });
 
 
@@ -19,18 +20,12 @@ function on_page_load() {
 
 
 
-
 function select_assay_type_action(assay_type) {
-    var score_label_obj = document.getElementById('score_label')
+    $('form').each(function(i, obj) {
+        obj.hidden=true;
+    })
 
     if (assay_type !== '') {
-        document.getElementById('report_form_group').hidden=false
-        document.getElementById('score_form_group').hidden=false
-    }
-
-    if (assay_type === 'functional') {
-        score_label_obj.innerText = "Functional assay score"
-    } else if (assay_type === 'splicing') {
-        score_label_obj.innerText = "Splicing assay score"
+        document.getElementById(assay_type + '_assay').hidden=false
     }
 }

src/frontend_celery/webapp/templates/index.html

@@ -104,6 +104,7 @@ <h4>Changelog</h4>
             <li>Added gnomAD non-cancer scores</li>
             <li>Added HerediCaRe center specific classifications</li>
             <li>Added CSpec BRCA1/2 assays to annotation algorithm</li>
+            <li>Copy evidence of user classifications to a consensus classification now also automatically selects the state correctly</li>
         </ul>
         Bugfixes:
         <ul>
@@ -116,10 +117,8 @@ <h4>Changelog</h4>
             <li>Fixed a bug when updating ClinVar submissions</li>
             <li>When selecting any BP criterium the enigma BRCA1/2 schemes would instantly switch to class 2. This is now fixed and only BP1_str triggers class 2</li>
             <li>Previously the class by scheme was not updated correctly when the user updated their classification</li>
-        </ul>
-        Known issues:
-        <ul>
-            <li>HerediCare priors, log likelihood, segregation & cooccurance are not available</li>
+            <li>Fixed a bug in the criteria column of the automatic classification results that would shrink to width zero when the screen is resized</li>
+            <li>Fixed a bug where unselected criteria where shown as selected for consensus classifications</li>
         </ul>
     </div>
     <a class="btn btn-outline-primary" href="{{url_for('main.changelog')}}">previous changelog</a>