From 62a10f0e081f46886c94e4f0eb76842d3f4330ea Mon Sep 17 00:00:00 2001
From: Manuel Holtgrewe <manuel.holtgrewe@bihealth.de>
Date: Fri, 6 May 2022 13:54:25 +0200
Subject: [PATCH] Adding "variant carrier" popup modal (#470).

Related-Issue: #470
Closes: #470
Projected-Results-Impact: none
---
 HISTORY.rst                                   |  2 +
 varfish/static/js/variant_carrier.js          | 17 +++++++
 .../templates/variants/filter_result/row.html | 27 ++++++++++
 .../variant_carriers_result.html              | 51 +++++++++++++++++++
 variants/templates/variants/scripts.html      |  2 +
 variants/templatetags/variants_tags.py        |  9 ++++
 variants/tests/test_views.py                  | 47 +++++++++++++++++
 variants/urls.py                              |  5 ++
 variants/views.py                             | 47 +++++++++++++++++
 9 files changed, 207 insertions(+)
 create mode 100644 varfish/static/js/variant_carrier.js
 create mode 100644 variants/templates/variants/filter_result/variant_carriers_result.html

diff --git a/HISTORY.rst b/HISTORY.rst
index c72a1d326..c5394abda 100644
--- a/HISTORY.rst
+++ b/HISTORY.rst
@@ -19,6 +19,7 @@ End-User Summary
 - Fixing paths in "Variant Ingest" documentation (#472).
 - Small extension of "Resolution proposal" template (#472).
 - Adjusting wrong release name to "anthenea" (#479).
+- Adding "show all variant carriers" feature (#470).
 
 Full Change List
 ================
@@ -33,6 +34,7 @@ Full Change List
 - Fixing paths in "Variant Ingest" documentation (#472).
 - Small extension of "Resolution proposal" template (#472).
 - Adjusting wrong release name to "anthenea" (#479).
+- Adding "show all variant carriers" feature (#470).
 
 ------
 v1.2.0
diff --git a/varfish/static/js/variant_carrier.js b/varfish/static/js/variant_carrier.js
new file mode 100644
index 000000000..de79f3f32
--- /dev/null
+++ b/varfish/static/js/variant_carrier.js
@@ -0,0 +1,17 @@
+function showVariantCarrierModal(obj, release, chromosome, start, reference, alternative) {
+    const box = $(`#variantcarriermodal-${release}-${chromosome}-${start}-${reference}-${alternative}`).find('.variant-carrier-results');
+    box.html(`<div class="text-center"><i class="iconify spin" data-icon="fa-solid:spinner"></i></div>`);
+    $.ajax({
+        type: 'GET',
+        url: `${variant_carriers_url}?release=${release}&chromosome=${chromosome}&position=${start}` +
+            `&reference=${reference}&alternative=${alternative}`,
+        success: (response) => {
+            // icon.removeClass('spin').attr('data-icon', 'fa-solid:cloud-upload');
+            box.html(response);
+        },
+        error: (jqXHR, textStatus, errorThrown) => {
+            alert("Error during AJAX call:", textStatus, + errorThrown);
+        },
+        timeout: 0
+    });
+}
diff --git a/variants/templates/variants/filter_result/row.html b/variants/templates/variants/filter_result/row.html
index 078b6d8e9..af35be879 100644
--- a/variants/templates/variants/filter_result/row.html
+++ b/variants/templates/variants/filter_result/row.html
@@ -455,6 +455,15 @@
   {% endif %}
   <td>
     <div class="btn-group sodar-list-btn-group pr-2">
+      <button
+        class="btn btn-primary sodar-list-btn"
+        type="button"
+        data-toggle="modal"
+        data-target="#variantcarriermodal-{{ entry.release }}-{{ entry.chromosome }}-{{ entry.start }}-{{ entry.reference }}-{{ entry.alternative }}"
+        onclick="showVariantCarrierModal(this, '{{ entry.release }}', '{{ entry.chromosome }}', '{{ entry.start }}', '{{ entry.reference }}', '{{ entry.alternative }}');"
+      >
+        <span class="iconify" data-icon="mdi:binoculars"></span>
+      </button>
       {% if entry.release == "GRCh37" %}
         <a
           href="https://www.genecascade.org/MTc2021/ChrPos102.cgi?chromosome={{ entry.chromosome }}&position={{ entry.start }}&ref={{ entry.reference }}&alt={{ entry.alternative }}"
@@ -634,6 +643,24 @@
       </div>
     </div>
     <!-- Modal -->
+    <div class="modal fade" id="variantcarriermodal-{{ entry.release }}-{{ entry.chromosome }}-{{ entry.start }}-{{ entry.reference }}-{{ entry.alternative }}">
+      <div class="modal-dialog modal-lg" role="document">
+        <div class="modal-content">
+          <div class="modal-header">
+            <h4 class="modal-title" id="variantcarriermodallabel-{{ entry.release }}-{{ entry.chromosome }}-{{ entry.start }}-{{ entry.reference }}-{{ entry.alternative }}">In-House Variant Carriers</h4>
+            <button type="button" class="close" data-dismiss="modal" aria-label="Close">
+              <span aria-hidden="true">&times;</span>
+            </button>
+          </div>
+          <div class="modal-body">
+            <div class="variant-carrier-results container-fluid">
+            </div>
+          </div>
+          <div class="modal-footer">
+            <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
+          </div>
+        </div>
+    </div>
     <div class="modal fade" id="variantvalidatormodal-{{ entry.release }}-{{ entry.chromosome }}-{{ entry.start }}-{{ entry.reference }}-{{ entry.alternative }}" tabindex="-1" role="dialog" aria-labelledby="variantvalidatormodallabel-{{ entry.release }}-{{ entry.chromosome }}-{{ entry.start }}-{{ entry.reference }}-{{ entry.alternative }}" aria-hidden="true">
       <div class="modal-dialog modal-lg" role="document">
         <div class="modal-content">
diff --git a/variants/templates/variants/filter_result/variant_carriers_result.html b/variants/templates/variants/filter_result/variant_carriers_result.html
new file mode 100644
index 000000000..20f7d0a11
--- /dev/null
+++ b/variants/templates/variants/filter_result/variant_carriers_result.html
@@ -0,0 +1,51 @@
+{% load dict %}
+{% load variants_tags %}
+
+<div>
+  <p>
+    {% if small_var %}
+      A total of {{ count_total }} carriers were found for variant <code>{{ small_var.human_readable }}</code>.
+      {% if count_total == count_noaccess %}
+        You do not have access to any of them, though.
+      {% elif count_noaccess == 0 %}
+        They are displayed below (you have access to all of them).
+      {% else %}
+        You do not have access to {{ count_noaccess }} but the remaining {{ count_access }} are displayed below.
+      {% endif %}
+    {% else %}
+      ERROR: variant not found!
+    {% endif %}
+  </p>
+
+  <table class="table-sm table-striped">
+    <thead>
+      <tr>
+        <th style="width: 20%;">case</th>
+        <th style="width: 60%;">project</th>
+        <th style="width: 20%;">genotype</th>
+      </tr>
+    </thead>
+    <tbody>
+      {% for case, var in case_vars %}
+        {% for name, genotype in var.genotype.items %}
+          <tr>
+            <td>
+              <a href="{% url 'variants:case-detail' case.project.sodar_uuid case.sodar_uuid %}">
+                {{ case.name }}
+              </a>
+            </td>
+            <td>
+              <a href="{% url 'projectroles:detail' case.project.sodar_uuid %}">
+                {{ case.project.title }}
+              </a>
+            </td>
+            <td>
+              <span class="small">{{ name|strip_sample_suffix }}</span>
+              <strong>{{ genotype|keyvalue:"gt" }}</strong>
+            </td>
+          </tr>
+        {% endfor %}
+      {% endfor %}
+    </tbody>
+  </table>
+</div>
diff --git a/variants/templates/variants/scripts.html b/variants/templates/variants/scripts.html
index 35c49e3e6..6819e80f4 100644
--- a/variants/templates/variants/scripts.html
+++ b/variants/templates/variants/scripts.html
@@ -15,6 +15,7 @@
       settings_restored = true;
   }
   var variant_validator_url = "{% url 'variants:variant-validator-api' %}"
+  var variant_carriers_url = "{% url 'variants:variant-carriers' %}"
 </script>
 <script type="text/javascript" src="{% static "js/helpers.js" %}"></script>
 <script type="text/javascript" src="{% static "js/state_machine.js" %}"></script>
@@ -22,6 +23,7 @@
 <script type="text/javascript" src="{% static "js/flags_comments.js" %}"></script>
 <script type="text/javascript" src="{% static "js/variant_comments.js" %}"></script>
 <script type="text/javascript" src="{% static "js/variant_validator.js" %}"></script>
+<script type="text/javascript" src="{% static "js/variant_carrier.js" %}"></script>
 <script type="text/javascript">
   $(document).ready(function() {
     let data = {};
diff --git a/variants/templatetags/variants_tags.py b/variants/templatetags/variants_tags.py
index 724128eaa..0428b60d7 100644
--- a/variants/templatetags/variants_tags.py
+++ b/variants/templatetags/variants_tags.py
@@ -592,3 +592,12 @@ def entry_chr(entry):
         return "chr" + entry.chromosome
     else:
         return entry.chromosome
+
+
+@register.filter
+def strip_sample_suffix(value):
+    """Strip the SNAPPY suffix ``-N1-DNA1-*``."""
+    value = value or ""
+    if "-N1-DNA1" in value:
+        return value.split("-N1-DNA1")[0]
+    return value
diff --git a/variants/tests/test_views.py b/variants/tests/test_views.py
index e92c074b6..17bc0343a 100644
--- a/variants/tests/test_views.py
+++ b/variants/tests/test_views.py
@@ -4981,3 +4981,50 @@ def test_get_json(self, r_mock):
                 }
             }
             self.assertEqual(json.loads(response.content.decode("utf-8")), expected)
+
+
+class TestVariantCarriersView(ViewTestBase):
+    """Test view that displays other variant carriers."""
+
+    def setUp(self):
+        super().setUp()
+        self.case, self.variant_set, _ = CaseWithVariantSetFactory.get(project=self.project)
+        self.small_vars = SmallVariantFactory.create_batch(3, variant_set=self.variant_set)
+        self.variant = self.small_vars[0]
+        self.variant_args = {
+            "release": self.variant.release,
+            "chromosome": self.variant.chromosome,
+            "position": self.variant.start,
+            "reference": self.variant.reference,
+            "alternative": self.variant.alternative,
+        }
+
+    def test_with_role(self):
+        with self.login(self.user_contributor):
+            response = self.client.get(
+                reverse("variants:variant-carriers")
+                + "?"
+                + "&".join("%s=%s" % item for item in self.variant_args.items())
+            )
+            self.assert_http_200_ok(response)
+            self.assertIn(self.case.name, response.content.decode("utf-8"))
+
+    def test_as_superuser(self):
+        with self.login(self.superuser):
+            response = self.client.get(
+                reverse("variants:variant-carriers")
+                + "?"
+                + "&".join("%s=%s" % item for item in self.variant_args.items())
+            )
+            self.assert_http_200_ok(response)
+            self.assertIn(self.case.name, response.content.decode("utf-8"))
+
+    def test_without_role(self):
+        with self.login(self.user_no_roles):
+            response = self.client.get(
+                reverse("variants:variant-carriers")
+                + "?"
+                + "&".join("%s=%s" % item for item in self.variant_args.items())
+            )
+            self.assert_http_200_ok(response)
+            self.assertNotIn(self.case.name, response.content.decode("utf-8"))
diff --git a/variants/urls.py b/variants/urls.py
index f7599bbb4..f88c5bd68 100644
--- a/variants/urls.py
+++ b/variants/urls.py
@@ -370,6 +370,11 @@
         view=views.VariantValidatorApiView.as_view(),
         name="variant-validator-api",
     ),
+    url(
+        regex=r"^variant-carriers/$",
+        view=views.VariantCarriersView.as_view(),
+        name="variant-carriers",
+    ),
     #: Detail views for site-wide maintenance jobs.
     url(
         regex=r"^clear-expired-job/(?P<job>[0-9a-f-]+)/$",
diff --git a/variants/views.py b/variants/views.py
index 037e4de81..2043c24b7 100644
--- a/variants/views.py
+++ b/variants/views.py
@@ -4441,6 +4441,53 @@ def post(self, *args, **kwargs):
         )
 
 
+class VariantCarriersView(PluginContextMixin, TemplateView):
+    """Render HTML with other carriers of the variant."""
+
+    template_name = "variants/filter_result/variant_carriers_result.html"
+
+    def get_context_data(self, *args, **kwargs):
+        result = super().get_context_data(*args, **kwargs)
+
+        small_vars = SmallVariant.objects.filter(
+            release=self.request.GET.get("release"),
+            chromosome=self.request.GET.get("chromosome"),
+            start=self.request.GET.get("position"),
+            reference=self.request.GET.get("reference"),
+            alternative=self.request.GET.get("alternative"),
+        )
+
+        result["count_total"] = small_vars.count()
+        result["count_noaccess"] = 0
+        result["case_vars"] = []
+        case_ids = [var.case_id for var in small_vars]
+        cases = {
+            case.id: case
+            for case in Case.objects.prefetch_related("project")
+            .filter(id__in=case_ids)
+            .order_by("project__title", "name")
+        }
+        for small_var in small_vars:
+            case = cases[small_var.case_id]
+            has_access = (
+                self.request.user and self.request.user.is_superuser
+            ) or case.project.has_role(self.request.user)
+            if has_access:
+                result["case_vars"].append((case, small_var))
+            for name, gt in small_var.genotype.items():
+                if "1" in gt.get("GT", "0/0"):
+                    result["count_total"] += 1
+                    if not has_access:
+                        result["count_noaccess"] += 1
+        result["count_access"] = result["count_total"] - result["count_noaccess"]
+        if result["case_vars"]:
+            result["small_var"] = result["case_vars"][0][1]
+        else:
+            result["small_var"] = None
+
+        return result
+
+
 class KioskHomeView(PluginContextMixin, FormView):
     """Home view when the app is running in kiosk mode.