improved popovers & added heredicare n_fam & n_pat to variant details…

… page

src/common/db_IO.py

@@ -1643,7 +1643,11 @@ def get_user_classifications_extended(self, variant_id, user_id='all', scheme_id
 
 
 
-
+    def get_heredicare_annotations(self, variant_id):
+        command = "SELECT id, vid, n_fam, n_pat, consensus_class, comment, date FROM variant_heredicare_annotation WHERE variant_id = %s"
+        self.cursor.execute(command, (variant_id, ))
+        res = self.cursor.fetchall()
+        return res
 
 
 
@@ -1671,6 +1675,7 @@ def get_variant(self, variant_id,
         is_hidden = True if variant_raw[5] == 1 else False
 
         annotations = None
+        all_heredicare_annotations = None
         if include_annotations:
             annotations = models.AllAnnotations()
             annotations_raw = self.get_recent_annotations(variant_id)
@@ -1690,6 +1695,24 @@ def get_variant(self, variant_id,
                 #annotations.insert_annotation(new_annotation)
 
             annotations.flag_linked_annotations()
+
+            heredicare_annotations_raw = self.get_heredicare_annotations(variant_id)
+
+            all_heredicare_annotations = []
+            for annot in heredicare_annotations_raw:
+                #id, vid, n_fam, n_pat, consensus_class, comment, date
+                heredicare_annotation_id = annot[0]
+                vid = annot[1]
+                n_fam = annot[2]
+                n_pat = annot[3]
+                consensus_class = annot[4]
+                comment = annot[5]
+                date = annot[6]
+
+                classification = models.HeredicareClassification(id = heredicare_annotation_id, selected_class = consensus_class, comment = comment, date = date, center = "VUSTF")
+                new_heredicare_annotation = models.HeredicareAnnotation(id = heredicare_annotation_id, vid = vid, n_fam = n_fam, n_pat = n_pat, vustf_classification = classification)
+                all_heredicare_annotations.append(new_heredicare_annotation)
+
 
         # add all consensus classifications
         consensus_classifications = None
@@ -1878,10 +1901,12 @@ def get_variant(self, variant_id,
                                 consensus_classifications = consensus_classifications, 
                                 user_classifications = user_classifications,
                                 heredicare_classifications = heredicare_classifications,
+                                heredicare_annotations = all_heredicare_annotations,
                                 clinvar = clinvar,
                                 consequences = consequences,
                                 assays = assays,
-                                literature = literature)
+                                literature = literature
+                            )
         return variant
 
 
@@ -2210,4 +2235,3 @@ def clear_heredicare_annotation(self, variant_id):
         self.cursor.execute(command, (variant_id, ))
         self.conn.commit()
 
-

src/common/models.py

@@ -76,9 +76,6 @@ class AllAnnotations:
     tp53db_domain_function: Annotation = None
     tp53db_transactivation_class: Annotation = None
 
-    heredicare_cases_count: Annotation = None
-    heredicare_family_count: Annotation = None
-
     task_force_protein_domain: Annotation = None
     task_force_protein_domain_source: Annotation = None
 
@@ -184,8 +181,6 @@ def get_group(self, group_identifier):
                                        self.tp53db_DNE_LOF_class, 
                                        self.tp53db_domain_function, 
                                        self.tp53db_transactivation_class])
-        if group_identifier == 'HerediCare':
-            return self.prepare_group([self.heredicare_cases_count, self.heredicare_family_count])
 
     def prepare_group(self, group):
         prepared_group = [x for x in group if x is not None]
@@ -399,26 +394,6 @@ def get_header(self, simple = False):
         return header
 
 
-@dataclass
-class HeredicareClassification:
-    id: int
-    selected_class: int
-    comment: str
-    date: str
-    center: str
-
-    def to_vcf(self, prefix = True):
-        info = '~7C'.join([str(self.selected_class), self.center, self.comment, self.date])
-        info = info
-        if prefix:
-            info = 'heredicare~1Y' + info
-        return info
-
-    def get_header(self):
-        header = {'heredicare_center_classifications': '##INFO=<ID=heredicare_center_classifications,Number=.,Type=String,Description="An & separated list of the variant classifications from centers imported from HerediCare. Format:class|center|comment|date">\n'}
-        return header
-
-
 @dataclass
 class ClinvarCondition:
     condition_id: str
@@ -552,6 +527,36 @@ def to_vcf(self, prefix = True):
         return info
 
 
+
+@dataclass
+class HeredicareClassification:
+    id: int
+    selected_class: int
+    comment: str
+    date: str
+    center: str
+
+    def to_vcf(self, prefix = True):
+        info = '~7C'.join([str(self.selected_class), self.center, self.comment, self.date])
+        info = info
+        if prefix:
+            info = 'heredicare~1Y' + info
+        return info
+
+    def get_header(self):
+        header = {'heredicare_center_classifications': '##INFO=<ID=heredicare_center_classifications,Number=.,Type=String,Description="An & separated list of the variant classifications from centers imported from HerediCare. Format:class|center|comment|date">\n'}
+        return header
+
+@dataclass
+class HeredicareAnnotation:
+    id: int
+    vid: str
+    n_fam: int
+    n_pat: int
+    vustf_classification: HeredicareClassification
+
+
+
 @dataclass
 class Variant:
     id: int
@@ -564,14 +569,24 @@ class Variant:
 
     consensus_classifications: Any = None # list of classifications
     user_classifications: Any = None # list of classifications
-    heredicare_classifications: Any = None # list of heredicare classifications
+    heredicare_classifications: Any = None # list of heredicare center classifications
+    heredicare_annotations: Any = None # list of heredicare annotatins
     clinvar: Any = None # a clinvar object
     consequences: Any = None # list of consequences
     assays: Any = None # list of assays
     literature: Any = None # list of papers
 
     annotations: AllAnnotations = AllAnnotations()
 
+    def get_total_heredicare_counts(self):
+        total_n_fam = 0
+        total_n_pat = 0
+        if self.heredicare_annotations is not None:
+            for annot in self.heredicare_annotations:
+                total_n_fam += annot.n_fam
+                total_n_pat += annot.n_pat
+        return total_n_fam, total_n_pat
+
     def get_unique_genes(self):
         result = []
         gene_ids = []

src/frontend_celery/webapp/static/css/utils.css

@@ -61,6 +61,15 @@
     padding-left:1rem;
 }
 
+.nomargin {
+    margin: 0em;
+}
+.nomargin_bottom {
+    margin-bottom: 0em;
+}
+.nomargin_top {
+    margin-top: 0em;
+}
 
 /************** sizing **************/
 .full_page {
@@ -217,3 +226,8 @@
 .visually_hidden {
     display: none;
 }
+
+.popover_fix{
+    width: fit-content !important;
+    max-width: 25em !important;
+}

src/frontend_celery/webapp/static/js/startup.js

@@ -105,8 +105,18 @@ $(document).ready(function()
     $('#consequence_refseq_tab').click(function() {
         filter_consequence_table('refseq', variant_consequence_table_default_sorting_columns)
     })
+
+    $(document).click(function (e) {
+        close_popovers(e)
+    });
 });
 
+function close_popovers(e) {
+    if (($('.popover').has(e.target).length == 0) || $(e.target).is('.close')) {
+        $('[data-bs-toggle="popover"]').popover('hide');
+    }
+}
+
 
 // functionality for the consequence table switch between ensembl & refseq
 function filter_consequence_table(source, variant_consequence_table_default_sorting_columns) {

src/frontend_celery/webapp/templates/index.html

@@ -111,12 +111,14 @@ <h4>Changelog</h4>
             <li>Changed SpliceAI annotations to masked ones</li>
             <li>Added variant import from HerediCare</li>
             <li>Added HerediCare number of families and heredicare number of cases annotations</li>
+            <li>Improved criteria popover</li>
         </ul>
         Bugfixes:
         <ul>
             <li>Variants are now not selected by default on the search variants page</li>
             <li>Abbreviations for criteria are now written with upper case letters</li>
             <li>Disabled criteria were not shown correctly</li>
+            <li>Popovers now stay open when clicked and close when the user does not click inside the popover</li>
         </ul>
         Known issues:
         <ul>

src/frontend_celery/webapp/templates/macros.html

@@ -135,10 +135,37 @@
 
 {% macro draw_criteria_display(criteria, source='user') %}
     {% for criterium in criteria %}
+    <!--
     <span class="d-inline-block ssr tooltip-lg" tabindex="0" data-bs-toggle="tooltip" data-bs-html="true" {% if source=="user" %} user_criterium_applied_id="{{ criterium.id }}" {% else %} consensus_criterium_applied_id="{{ criterium.id }}" {% endif %}
         title="Strength: {{ criterium.strength }} <br> Evidence: {{ criterium.evidence }}">
         <div class="btn-{{ criterium.type }} light-hover acmg-button acmg-button-small">{{ criterium.display_name() }}</div>
     </span>
+    -->
+
+    <span class="d-inline-block ssr criterium-display" data-bs-toggle="popover" 
+       data-bs-placement="top" data-bs-custom-class="popover_fix" data-bs-html="true" 
+       {% if source=="user" %} user_criterium_applied_id="{{ criterium.id }}" {% else %} consensus_criterium_applied_id="{{ criterium.id }}" {% endif %} 
+       data-bs-content="
+            <div class='width_large'></div>
+            <div class='row gx-2 border-bottom bg-light'>
+                <div class='col-3 text-center'>Type</div>
+                <div class='col-8 text-center border-start'>Info</div>
+            </div>
+            <div class='row gx-2'>
+                <div class='col-3'>Strength</div>
+                <div class='col-8 text-center border-start'>{{ criterium.strength }}</div>
+            </div>
+            <div class='row gx-2'>
+                <div class='col-3'>Evidence</div>
+                <div class='col-8 text-center border-start'>{{ criterium.evidence }}</div>
+            </div>
+            "
+    >
+        <div class="btn-{{ criterium.type }} light-hover acmg-button acmg-button-small">{{ criterium.display_name() }}</div>
+    </span>
+
+
+
     {% endfor %}
 {% endmacro %}
 
@@ -173,7 +200,7 @@
                         <li class="list-group-item noboarder-td" >
                             <div class="d-flex">
                                 <div class="ssr">{{ spliceai.split('|')[0] }}:</div> <div class="ssr">{{ spliceai.split('|')[1:5] | map('float') | max }}</div>
-                                <a class="link" tabindex="0" role="button" data-bs-toggle="popover" data-bs-html="true" data-bs-trigger="focus" 
+                                <a class="link" tabindex="0" role="button" data-bs-toggle="popover" data-bs-html="true"
                                     data-bs-content="{{ spliceai_details.description }} <br/> {{ spliceai }}">
                                         details
                                 </a>
@@ -183,6 +210,7 @@
                     </ul>
                 </div>
             {% endif %}
+
             <!-- cancerhotspots cancertypes -->
             {% if annot.title == 'cancerhotspots_cancertypes' %} <!-- cancerhotspots cancertypes -->
             {% set cancerhotspots_cancertypes = annot.value.split('|') %}
@@ -205,7 +233,8 @@
                     </tbody>
                 </table>
             </div>
-        {% endif %}
+            {% endif %}
+
             <!-- Hexplorer -->
             {% if annot.title == 'hexplorer' %} <!-- details for hexplorer score -->
                 {% set delta, wt, mut = annotations.get_hexplorer() %}
@@ -223,22 +252,80 @@
                 {% set delta, wt, mut = annotations.get_max_hbond_rev() %}
                 {{ draw_hexplorer_score(delta, wt, mut) }}
             {% endif %}
-            <!-- HerediCare -->
-            {% if annot.title == 'heredicare' %} <!-- add red exclamation mark for heredicare counts -->
+
+            <!-- HerediCare  add red exclamation mark for heredicare counts
+            {% if annot.title == 'heredicare' %}
             <div annotation_id="{{ annot.id }}">
                 {% if has_multiple_vids  %}
                     {{ draw_exclamation_mark('Multiple VIDs in HerediCare for this variant. Thus, these counts might be inaccurate!') }}
                 {% endif %}
                 <abbr class="ssr" title="{{ annot.description }}"><a class="dashed_underline">{{ annot.display_title }}:</a></abbr>{{ annot.value }}
             </div>
             {% endif %}
+            -->
         {% endfor %}
     </td>
 </tr>
 {% endif %}
 {% endmacro %}
 
 
+{% macro draw_heredicare_annotations(variant) %}
+<tr>
+    <td class="li-label nowrap">HerediCare</td>
+    <td>
+        {% set heredicare_annotations = variant.heredicare_annotations %}
+
+        {% set total_n_fam, total_n_pat = variant.get_total_heredicare_counts() %}
+        <div>
+            {% if heredicare_annotations | length > 1 %}
+                {{ draw_exclamation_mark('Multiple VIDs in HerediCare for this variant. Thus, these counts might be inaccurate!') }}
+            {% endif %}
+            <abbr class="ssr" title="The number of families in HerediCare reported to have this variant"><a class="dashed_underline">n_fam:</a></abbr>{{ total_n_fam }}
+            <a class="link" tabindex="0" role="button" data-bs-toggle="popover" data-bs-html="true" data-bs-placement="top" data-bs-custom-class="popover_fix" data-bs-html="true" 
+            data-bs-content="
+                <div class='row gx-2 border-bottom bg-light width_very_medium'>
+                    <div class='col-7'>HerediCare VID</div>
+                    <div class='col-4 text-center border-start'>n_fam</div>
+                </div>
+                {% for annot in heredicare_annotations %}
+                <div class='row gx-2 width_very_medium'>
+                    <div class='col-7'>{{annot.vid}}</div>
+                    <div class='col-4 text-center border-start'>{{annot.n_fam}}</div>
+                </div>
+                {% endfor %}
+            ">
+                details
+            </a>
+        </div>
+        <div>
+            {% if heredicare_annotations | length > 1 %}
+                {{ draw_exclamation_mark('Multiple VIDs in HerediCare for this variant. Thus, these counts might be inaccurate!') }}
+            {% endif %}
+            <abbr class="ssr" title="The number of cases in HerediCare reported to have this variant"><a class="dashed_underline">n_pat:</a></abbr>{{ total_n_pat }}
+            <a class="link" tabindex="0" role="button" data-bs-toggle="popover" data-bs-html="true" data-bs-placement="top" data-bs-custom-class="popover_fix" data-bs-html="true" 
+            data-bs-content="
+                <div class='row gx-2 border-bottom bg-light width_very_medium'>
+                    <div class='col-7'>HerediCare VID</div>
+                    <div class='col-4 text-center border-start'>n_pat</div>
+                </div>
+                {% for annot in heredicare_annotations %}
+                <div class='row gx-2 width_very_medium'>
+                    <div class='col-7'>{{annot.vid}}</div>
+                    <div class='col-4 text-center border-start'>{{annot.n_pat}}</div>
+                </div>
+                {% endfor %}
+            ">
+                details
+            </a>
+        </div>
+
+
+    </td>
+</tr>
+{% endmacro %}
+
+
 {% macro draw_transcript_annotation(annot) %}
 {% if annot is not none %}
 <div class="d-flex">
@@ -248,7 +335,7 @@
         <li class="list-group-item noboarder-td" >
             <div class="d-flex">
                 <div class="ssr">{{ annot.value[transcript] }}</div>
-                <a class="link" tabindex="0" role="button" data-bs-toggle="popover" data-bs-html="true" data-bs-trigger="focus" 
+                <a class="link" tabindex="0" role="button" data-bs-toggle="popover" data-bs-html="true"
                     data-bs-content="Transcript: {{ transcript }}">
                         details
                 </a>
@@ -691,7 +778,7 @@
     {{ draw_exclamation_mark('There is no wildtype or mutant score. Thus, one of the sequences is missing the motiv! Be careful with the interpretation of the delta score!') }}
    {% endif %}
    <abbr class="ssr" title="{{ delta.description }}"><a class="dashed_underline">{{ delta.display_title }}:</a></abbr>{{ delta.value }}
-   <a class="link" tabindex="0" data-bs-html="true" role="button" data-bs-toggle="popover" data-bs-trigger="focus" data-bs-content="reference score: {% if wt is not none %}{{ wt.value }}{% else %}-{% endif %} <br/> mutant score: {% if mut is not none %}{{ mut.value }}{% else %}-{% endif %}">details</a>
+   <a class="link" tabindex="0" data-bs-html="true" role="button" data-bs-toggle="popover" data-bs-content="reference score: {% if wt is not none %}{{ wt.value }}{% else %}-{% endif %} <br/> mutant score: {% if mut is not none %}{{ mut.value }}{% else %}-{% endif %}">details</a>
 </div>
 
 {% endmacro %}