diff --git a/resources/backups/database_dumper/dump_database.sh b/resources/backups/database_dumper/dump_database.sh
index aeac1c95..c0f78fb5 100755
--- a/resources/backups/database_dumper/dump_database.sh
+++ b/resources/backups/database_dumper/dump_database.sh
@@ -90,9 +90,9 @@ then
echo $DATE > $SCRIPTPATH/most_recent_dump.txt
fi
-if [ "${WEBAPP_ENV}" == "prod" ]
+if [ "${WEBAPP_ENV}" == "prod" ] || [ "${WEBAPP_ENV}" == "demo" ]
then
- dump_path=$SCRIPTPATH/prod
+ dump_path=$SCRIPTPATH/$WEBAPP_ENV
mkdir -p $dump_path
dump_name=production-dump-$DATE.sql
diff --git a/src/annotation_service/annotation_jobs/automatic_classification_job.py b/src/annotation_service/annotation_jobs/automatic_classification_job.py
index 723c0533..639aac9e 100644
--- a/src/annotation_service/annotation_jobs/automatic_classification_job.py
+++ b/src/annotation_service/annotation_jobs/automatic_classification_job.py
@@ -316,7 +316,7 @@ def get_autoclass_json(self, variant_id, conn: Connection) -> str:
minigene = assay.get_metadata_value("minigene", "False") == "True"
patient_rna = assay.get_metadata_value("patient_rna", "False") == "True"
allelic = assay.get_metadata_value("allele_specific", "False")
- quantification = functions.percent_to_decimal(assay.metadata.get("minimal_percentage", None))
+ quantification = functions.percent_to_decimal(assay.get_metadata_value("minimal_percentage", None))
all_splicing_assays.append({"minigene": minigene,
"patient_rna": patient_rna,
"allelic": allelic,
diff --git a/src/frontend_celery/webapp/static/css/colors.css b/src/frontend_celery/webapp/static/css/colors.css
index 9543b96e..32827816 100644
--- a/src/frontend_celery/webapp/static/css/colors.css
+++ b/src/frontend_celery/webapp/static/css/colors.css
@@ -171,7 +171,13 @@ input[type=checkbox]:checked + label.btn-ba {
background-color: #000d58;
}
-
+/*
+input {
+ appearance: unset;
+ -webkit-appearance: unset;
+ -moz-appearance: unset;
+}
+*/
.btn-check:disabled + label.acmg-button {
color: rgb(170, 170, 170);
diff --git a/src/frontend_celery/webapp/static/js/classify.js b/src/frontend_celery/webapp/static/js/classify.js
index ca75f7fb..6c993c7f 100644
--- a/src/frontend_celery/webapp/static/js/classify.js
+++ b/src/frontend_celery/webapp/static/js/classify.js
@@ -328,6 +328,7 @@ $(document).ready(function() {
});
add_default_for_important_information()
+ hide_important_information_heading()
});
@@ -342,8 +343,10 @@ function add_default_for_important_information() {
$(this).append(default_empty)
}
})
+
}
+
// update global scheme field variable
function update_scheme_field_variable() {
scheme = $('#scheme').val()
@@ -427,10 +430,12 @@ function set_user_selection_counts(scheme) {
var selected_criteria = scheme_with_info['criteria'] ?? [] // propagate the above
for (var i in selected_criteria) {
var criterium = selected_criteria[i]
- var criterium_id = criterium['name']
- var count_label = document.getElementById('users_selected_' + criterium_id)
- count_label.innerText = parseInt(count_label.innerText) + 1
- count_label.hidden = false;
+ if (criterium["state"] == "selected") {
+ var criterium_id = criterium['name']
+ var count_label = document.getElementById('users_selected_' + criterium_id)
+ count_label.innerText = parseInt(count_label.innerText) + 1
+ count_label.hidden = false;
+ }
}
}
}
@@ -459,8 +464,28 @@ function preselect_criteria_from_database(scheme) {
if (typeof current_scheme_with_info !== "undefined") { // only preselect if there is data for it
selected_criteria = current_scheme_with_info['scheme']['criteria']
preselect_criteria_from_list(selected_criteria)
+ remove_criterium_button_backgrounds()
}
+}
+function remove_criterium_button_backgrounds() {
+ $(".acmg-button").each(function() {
+ var criterium_label = this
+ var all_btn_classes = []
+ for (var i = 0; i < criterium_label.classList.length; i++) {
+ var current_class = criterium_label.classList[i]
+ if (current_class.indexOf("btn-") >= 0) {
+ all_btn_classes.push(current_class)
+ //criterium_label.classList.remove(current_class)
+ //criterium_label.classList.toggle(current_class)
+ }
+ }
+ all_btn_classes.pop()
+
+ all_btn_classes.forEach(css_class => {
+ criterium_label.classList.remove(css_class)
+ });
+ })
}
function preselect_criteria_from_list(selected_criteria, is_intermediate = false) {
@@ -478,6 +503,8 @@ function preselect_criteria_from_list(selected_criteria, is_intermediate = false
set_criterium(criterium_id, state, is_intermediate)
}
}
+
+
}
@@ -629,6 +656,12 @@ function hide_all_information() {
})
}
+function hide_important_information_heading() {
+ if ($("#important_information_container").find("visually_hidden").length > 0) {
+ document.getElementById('important_information_heading').classList.remove('visually_hidden')
+ }
+}
+
function revert_strength_selects() {
var all_buttons = document.querySelectorAll('.btn-check')
for (var i = 0; i < all_buttons.length; i++) {
@@ -1204,6 +1237,7 @@ function copy_evidence(obj) {
select_criterium_check.value = state
set_criterium(criterium_id, state, is_intermediate = true)
+ update_classification_preview()
}
function add_user_acmg_classification_details(criterium_id) {
@@ -1568,14 +1602,17 @@ function set_criterium(criterium_id, state, is_intermediate = false) {
state_check.value = state
- console.log("set_criterium: " + criterium_id + " to state: " + state)
+ console.log("set_criterium: " + criterium_id + " to state: " + state + " with strength: " + strength_check.value)
update_criterium_button_label(criterium_id)
+ //remove_criterium_button_background(criterium_id)
update_criterium_button_background(criterium_id)
if (!(['unchecked', 'unselected'].includes(previous_state) && ['unchecked', 'unselected'].includes(state))) {
update_mutual_criteria(criterium_id)
}
+
+
}
diff --git a/src/frontend_celery/webapp/static/js/variant_addition.js b/src/frontend_celery/webapp/static/js/variant_addition.js
index 01f67201..a86cab5c 100644
--- a/src/frontend_celery/webapp/static/js/variant_addition.js
+++ b/src/frontend_celery/webapp/static/js/variant_addition.js
@@ -279,8 +279,8 @@ function show_heredicare_upload_status(color_class, summary, inner_text) {
const pill_holder_id = "heredicare_status_pill_holder"
const pill_id = "heredicare_status_pill"
var prepend_html = null
-
- if (summary["needs_upload"] && ["error", "api_error", "success", "requested", "multiple stati"].includes(summary["status"])) {
+
+ if (summary["needs_upload"] && ["error", "api_error", "success", "requested", "multiple stati", "unknown"].includes(summary["status"])) {
prepend_html = create_exclamation_mark()
add_tooltip(prepend_html, "The consensus classification needs to be uploaded to HerediCaRe!")
}
diff --git a/src/frontend_celery/webapp/templates/index.html b/src/frontend_celery/webapp/templates/index.html
index 3ce78963..343d6330 100644
--- a/src/frontend_celery/webapp/templates/index.html
+++ b/src/frontend_celery/webapp/templates/index.html
@@ -95,9 +95,19 @@
Changelog
v 1.14.5 ()
+ General changes:
+
+
Removed "Important Information" heading on classify page if there is no important information to show
+
CSpecBRCA splicing assay quantification is now the sum of percent abberant transcript. It was the minimal value previously.
+
CSpecBRCA splicing assay quantification is now explicitly set to 0 if the assay is minigene or patient RNA and the result is "no abberation" which is not ignored
+
Consensus classify count labels now only count criteria which were selected and ignore unselected criteria
+
Bugfixes:
Fixed a bug where assay annotations would not be considered for automatic classification
+
Fixed a bug which was causing criteria buttons to show the default color after page reload even though the strength was non-default. This problem only existed in Firefox.
+
When copying evidence on the consensus classify page, the classifcation preview would not update
+
Needs HerediCaRe upload for consensus classifications was not showing when there was no HerediCaRe submission