#3429 Replace Classification Visual ID with CR_(labid) (#879)

* #3429 Replace Classification Visual ID with CR_(labid) * #3429 Replace Classification Visual ID with CR_(labid)
SACGF · Aug 29, 2023 · fbb0116 · fbb0116
1 parent 8757bb1
commit fbb0116
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Showing 11 changed files with 60 additions and 15 deletions.
diff --git a/classification/models/classification.py b/classification/models/classification.py
@@ -689,9 +689,15 @@ def _evidence(self):
     def id_str(self):
         return str(self.id)
 
+    @property
+    def cr_lab_id(self):
+        if settings.VARIANT_CLASSIFICATION_ID_OVERRIDE_PREFIX:
+            return f"CR_{self.id}"
+        return self.lab_record_id
+
     @property
     def friendly_label(self):
-        return self.lab.name + ' / ' + self.lab_record_id
+        return self.lab.name + ' / ' + self.cr_lab_id
 
     @staticmethod
     def to_date(date_str: str) -> Optional[datetime]:
@@ -1816,6 +1822,7 @@ def as_json(self, params: ClassificationJsonParams) -> dict:
             'lab_record_id': self.lab_record_id,
             'institution_name': self.lab.organization.name,
             'lab_id': self.lab.group_name,
+            'cr_lab_id': self.cr_lab_id,
             'org_name': self.lab.organization.shortest_name,
             'lab_name': self.lab.name,
             'title': title,
@@ -2276,6 +2283,12 @@ def _evidence(self):
     def id_str(self) -> str:
         return self.classification.id_str + '.' + str(self.created.timestamp())
 
+    @property
+    def cr_lab_id(self) -> str:
+        if settings.VARIANT_CLASSIFICATION_ID_OVERRIDE_PREFIX:
+            return f"CR_{self.classification.id_str}"
+        return self.classification.lab_record_id
+
     @property
     def curated_date(self) -> datetime:
         return CuratedDate(self).date

diff --git a/classification/signals/classification_search.py b/classification/signals/classification_search.py
@@ -2,6 +2,7 @@
 from functools import reduce
 from typing import Optional, List
 
+from django.conf import settings
 from django.contrib.auth.models import User
 from django.db.models import Q
 from django.dispatch import receiver
@@ -18,16 +19,19 @@
     search_type=Classification,
     example=SearchExample(
         note="The lab record ID",
-        examples=["vc1545"]
+        examples=["CR_1545" if settings.VARIANT_CLASSIFICATION_ID_OVERRIDE_PREFIX else "vc1545"]
     )
 )
 def classification_search(search_input: SearchInputInstance):
 
     search_string = search_input.search_string
     """ Search for LabId which can be either:
-        "vc1080" or "Molecular Genetics, Frome Road / vc1080" (as it appears in classification) """
-
-    filters = [Q(classification__lab_record_id__iexact=search_string)]  # exact match
+        "vc1080" or "Molecular Genetics/ Frome Road / vc1080" (as it appears in classification) or CR_1080 or Molecular Genetics/ Frome Road / CR_1080 """
+    if search_string.startswith("CR_"):
+        search_string = search_string[3:]
+        filters = [Q(classification__id=search_string)]
+    else:
+        filters = [Q(classification__lab_record_id__iexact=search_string)]  # exact match
     slash_index = search_string.find("/")
     if slash_index > 0:
         parts = [p.strip() for p in search_string.split("/")]
@@ -50,7 +54,11 @@ def classification_search(search_input: SearchInputInstance):
                 lab_qs = lab_qs.filter(organization=org)
 
             if lab_qs:
-                filters.append(Q(classification__lab_record_id=lab_record_id) & Q(classification__lab__in=lab_qs))
+                if lab_record_id.startswith("CR_"):
+                    lab_record_id = lab_record_id[3:]
+                    filters.append(Q(classification__id=lab_record_id) & Q(classification__lab__in=lab_qs))
+                else:
+                    filters.append(Q(classification__lab_record_id=lab_record_id) & Q(classification__lab__in=lab_qs))
 
     q_cm = reduce(operator.or_, filters)
     cm_qs = ClassificationModification.filter_for_user(search_input.user).filter(is_last_published=True)

diff --git a/classification/templates/classification/classification.html b/classification/templates/classification/classification.html
@@ -22,6 +22,7 @@
             vcform.init(
                 {
                     userAdmin: {{ user.is_superuser | jsonify }},
+                    lab_record_id: "{{ record.lab_record_id }}",
                     genomeBuild: "{{ genome_build.pk }}",
                     // citations: new Citations($('#citations')),
                     citations: $('#citations'),
@@ -124,7 +125,7 @@ <h5 class="mt-4">Literature Citations</h5>
         </div>
         <div id="vc-extras">
             <div id="vcform-summary" class="card m-2">
-                <div class="card-header">{{ record.org_name }} / {{ record.lab_name }} / {{ record.lab_record_id }}</div>
+                <div class="card-header">{{ record.org_name }} / {{ record.lab_name }} / {{ record.cr_lab_id }}</div>
                 <div class="card-body"></div>
             </div>
             <div id="vcform-flags" class="card m-2">

diff --git a/classification/templates/classification/tags/classification_group_row.html b/classification/templates/classification/tags/classification_group_row.html
@@ -112,7 +112,7 @@
             <div>
                 {% for record in group.modifications %}
                     <div class="mt-2 d-flex" style="align-items:center;position:relative;top:5px">
-                        <a class="hover-link" style="font-weight:bold" href="{% url 'view_classification' record.classification_id %}">{{ record.classification.lab_record_id }}</a>
+                        <a class="hover-link" style="font-weight:bold" href="{% url 'view_classification' record.classification_id %}">{{ record.classification.cr_lab_id}}</a>
                         {{ record.classification.allele_info.issue_icon|default_if_none:'' }}
                         <div class="flags d-inline-block" style="margin-left:12px" data-flags="{{ record.classification.flag_collection_id }}">...</div>
                     </div>

diff --git a/classification/templates/classification/tags/classification_quick.html b/classification/templates/classification/tags/classification_quick.html
@@ -2,7 +2,7 @@
 {% load static %}
 {% if vcm and vcm.classification.id %}
     {% if mode == "compact" %}
-        <a class="hover-link" href="{% url 'view_classification' vcm.classification.id %}">{{ vcm.classification.lab }} / {{ vcm.classification.lab_record_id }}</a>
+        <a class="hover-link" href="{% url 'view_classification' vcm.classification.id %}">{{ vcm.classification.lab }} / {{ vcm.cr_lab_id }}</a>
     {% else %}
         <span class="share-level-{{ vcm.share_level_enum.name }} sig-level-{{ vcm.evidence.clinical_significance.value}}">
             {% if show_clinical_grouping %}{% if vcm.classification.clinical_grouping_name != 'default' %}<span class="font-weight-bold text-uppercase text-secondary mr-1">{{ vcm.classification.clinical_grouping_name }} </span>{% endif %}{% endif %}
@@ -11,9 +11,9 @@
                 &nbsp;
             <img src="{% static vcm.share_level_enum.icon %}" width="12px" height="12px" style="margin-right:4px;" />
             {% if vcm.vc.withdrawn %}
-                <span style="text-decoration: line-through">{{vcm.classification.lab.name}} / {{vcm.classification.lab_record_id }}</span>
+                <span style="text-decoration: line-through">{{vcm.classification.lab.name}} / {{vcm.cr_lab_id }}</span>
             {% else %}
-            {{vcm.classification.lab.name}} / {{vcm.classification.lab_record_id }}
+            {{vcm.classification.lab.name}} / {{vcm.cr_lab_id }}
             {% endif %}
             </a>
     {% endif %}

diff --git a/classification/views/classification_datatables.py b/classification/views/classification_datatables.py
@@ -79,13 +79,17 @@ def classification_id(self, row: Dict[str, Any]) -> JsonDataType:
                     value = str(value)
                     if id_filter.lower() in value.lower():
                         matches[key] = value
+        if settings.VARIANT_CLASSIFICATION_ID_OVERRIDE_PREFIX:
+            cr_lab_id = f"CR_{row.get('classification__id')}"
+        else:
+            cr_lab_id = row.get('classification__lab_record_id')
 
         return {
             "id": row.get('classification__id'),
             # should we start using short names?
             "org_name": row.get('classification__lab__organization__short_name') or row.get('classification__lab__organization__name'),
             "lab_name": row.get('classification__lab__name'),
-            "lab_record_id": row.get('classification__lab_record_id'),
+            "lab_record_id": cr_lab_id,
             "share_level": row.get('classification__share_level'),
             "matches": matches,
             "search": id_filter

diff --git a/classification/views/exports/classification_export_formatter_csv.py b/classification/views/exports/classification_export_formatter_csv.py
@@ -2,7 +2,7 @@
 from enum import Enum
 from functools import cached_property
 from typing import List, Optional, Dict, Set, Any
-
+from django.conf import settings
 from django.http import HttpRequest
 
 from classification.models import Classification, ClassificationModification, EvidenceKeyMap
@@ -85,6 +85,8 @@ def genome_build(self) -> GenomeBuild:
 
     @export_column(categories={"transient": True})
     def id(self):
+        if settings.VARIANT_CLASSIFICATION_ID_OVERRIDE_PREFIX:
+            return self.vc.cr_lab_id
         return self.vc.id
 
     @export_column()

diff --git a/variantgrid/settings/components/default_settings.py b/variantgrid/settings/components/default_settings.py
@@ -340,6 +340,9 @@
 
 PREFER_ALLELE_LINKS = False
 
+# if True, CR_lab_id will be used in all instances
+VARIANT_CLASSIFICATION_ID_OVERRIDE_PREFIX = False
+
 CLINGEN_ALLELE_REGISTRY_DOMAIN = "http://reg.genome.network"
 CLINGEN_ALLELE_REGISTRY_MAX_RECORDS = 2000
 CLINGEN_ALLELE_REGISTRY_LOGIN = get_secret("CLINGEN_ALLELE_REGISTRY.login")

diff --git a/variantgrid/settings/env/shariant.py b/variantgrid/settings/env/shariant.py
@@ -260,3 +260,6 @@
 VIEW_GENE_HOTSPOT_GRAPH = False
 
 GENE_RELATION_PANEL_APP_LIVE_UPDATE = True
+
+# if False lab record ID will be used for records instead of CR_lab_id
+VARIANT_CLASSIFICATION_ID_OVERRIDE_PREFIX = True
diff --git a/variantgrid/static_files/default_static/js/vc_diff.js b/variantgrid/static_files/default_static/js/vc_diff.js
@@ -149,7 +149,7 @@ const Diff = (function() {
                 }
 
                 let ltd = $('<td>').appendTo(tr);
-                let label = $('<label>', {for: `ch-${uniqueId}`, text: `${v.lab_name} / ${v.lab_record_id}`}).appendTo(ltd);
+                let label = $('<label>', {for: `ch-${uniqueId}`, text: `${v.org_name} / ${v.lab_name} / ${v.cr_lab_id}`}).appendTo(ltd);
             });
             modalContent.on('');
             modalContent.modal({
@@ -279,7 +279,7 @@ const Diff = (function() {
 
                 let titleDom = $('<a>', {class:'hover-link text-center d-flex flex-column flex-align-center', href: url});
 
-                let titlePart = $('<div>', {text: v.lab_name + ' / ' + v.lab_record_id}).appendTo(titleDom);
+                let titlePart = $('<div>', {text:  v.org_name + ' / ' + v.lab_name + ' / ' + v.cr_lab_id}).appendTo(titleDom);
                 if (v.first_seen) {
                     let first_seen_date = moment(v.first_seen * 1000).format('DD/MMM/YYYY HH:mm');
                     let last_seen_date = moment(v.version * 1000).format('DD/MMM/YYYY HH:mm');
@@ -334,6 +334,13 @@ const Diff = (function() {
                         // conditionRow
                     ]}).appendTo(headerRow);
             });
+
+            let rowLabRecordId = $('<tr>', {class: 'group no-compare'}).appendTo(table);
+            $('<th>', {text: "Lab Id", style: 'font-weight:normal'}).appendTo(rowLabRecordId);
+            includedVersions.forEach(v => {
+                $('<td>', {text: v.lab_record_id}).appendTo(rowLabRecordId);
+            });
+
             let all_db_refs = {};
 
             // loop through groups of keys

diff --git a/variantgrid/static_files/default_static/js/vc_form.js b/variantgrid/static_files/default_static/js/vc_form.js
@@ -803,6 +803,9 @@ const VCForm = (function() {
 
             jSyncStatus.empty();
 
+            if (this.lab_record_id) {
+                appendLabelHeading('Lab ID', $('<span>', {text: this.lab_record_id}));
+            }
             appendLabelHeadingForKey(SpecialEKeys.GENOME_BUILD, true, 'Build');
 
             if (this.record.allele && this.record.allele.resolved) {
@@ -1130,6 +1133,7 @@ const VCForm = (function() {
             jLinks = $(params.links);
             jShareButtons = $(params.shareButtons);
             this.userAdmin = params.userAdmin;
+            this.lab_record_id = params.lab_record_id;
             this.citations = params.citations;
             this.attachmentsEnabled = params.attachmentsEnabled || false;