From 94513310831875a72d21b3e17af9541a328cabd6 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Tue, 1 Oct 2024 13:28:49 -0500
Subject: Extract privileges and use them for access control

---
 uploader/phenotypes/views.py                      |  8 ++-
 uploader/templates/phenotypes/view-dataset.html   |  5 +-
 uploader/templates/phenotypes/view-phenotype.html | 63 ++++++++++++++++++++---
 3 files changed, 64 insertions(+), 12 deletions(-)

(limited to 'uploader')

diff --git a/uploader/phenotypes/views.py b/uploader/phenotypes/views.py
index 7fc3b08..63e0b84 100644
--- a/uploader/phenotypes/views.py
+++ b/uploader/phenotypes/views.py
@@ -200,7 +200,11 @@ def view_phenotype(# pylint: disable=[unused-argument]
                 "xref_id": xref_id
             }
         ).then(
-            lambda resource: render_template(
+            lambda resource: tuple(
+                privilege["privilege_id"] for role in resource["roles"]
+                for privilege in role["privileges"])
+        ).then(
+            lambda privileges: render_template(
                 "phenotypes/view-phenotype.html",
                 species=species,
                 population=population,
@@ -210,7 +214,7 @@ def view_phenotype(# pylint: disable=[unused-argument]
                                           population["Id"],
                                           dataset["Id"],
                                           xref_id),
-                resource=resource,
+                privileges=privileges,
                 activelink="view-phenotype")
         ).either(
             make_either_error_handler(
diff --git a/uploader/templates/phenotypes/view-dataset.html b/uploader/templates/phenotypes/view-dataset.html
index 959b02a..e2ccb60 100644
--- a/uploader/templates/phenotypes/view-dataset.html
+++ b/uploader/templates/phenotypes/view-dataset.html
@@ -51,10 +51,9 @@
   <h2>Phenotype Data</h2>
 
   <p>This dataset has a total of {{phenotype_count}} phenotypes.</p>
-  <p class="text-danger">
+  <p class="text-warning">
     <span class="glyphicon glyphicon-exclamation-sign"></span>
-    Limit access here, according to the authorisation privileges the user has on
-    this dataset!</p>
+    Display pagination controls here &hellip;</p>
 
   <table class="table">
     <thead>
diff --git a/uploader/templates/phenotypes/view-phenotype.html b/uploader/templates/phenotypes/view-phenotype.html
index 5aef6c1..03935f5 100644
--- a/uploader/templates/phenotypes/view-phenotype.html
+++ b/uploader/templates/phenotypes/view-phenotype.html
@@ -24,18 +24,67 @@
 {{flash_all_messages()}}
 
 <div class="row">
-  {{resource}}
-</div>
+  <div class="panel panel-default">
+    <div class="panel-heading"><strong>Basic Phenotype Details</strong></div>
 
-<div class="row">
-  <h2>Dataset</h2>
-  {{dataset}}
+    <table class="table">
+      <tbody>
+        <tr>
+          <td><strong>Phenotype</strong></td>
+          <td>{{phenotype.Post_publication_description or phenotype.Pre_publication_abbreviation or phenotype.Original_description}}
+        </tr>
+        <tr>
+          <td><strong>Cross-Reference ID</strong></td>
+          <td>{{phenotype.xref_id}}</td>
+        </tr>
+        <tr>
+          <td><strong>Collation</strong></td>
+          <td>{{dataset.FullName}}</td>
+        </tr>
+      </tbody>
+    </table>
+  </div>
 </div>
 
 <div class="row">
-  <h2>Phenotype</h2>
-  {{phenotype}}
+  <div class="panel panel-default">
+    <div class="panel-heading"><strong>Phenotype Data</strong></div>
+    {%if "group:resource:view-resource" in privileges%}
+    <table class="table">
+      <thead>
+        <tr>
+          <th>#</th>
+          <th>Sample</th>
+          <th>Value</th>
+          <th>Symbol</th>
+          <th>SE</th>
+          <th>N</th>
+        </tr>
+      </thead>
+
+      <tbody>
+        {%for item in phenotype.data%}
+        <tr>
+          <td>{{loop.index}}</td>
+          <td>{{item.StrainName}}</td>
+          <td>{{item.value}}</td>
+          <td>{{item.Symbol or "-"}}</td>
+          <td>{{item.error or "-"}}</td>
+          <td>{{item.count or "-"}}</td>
+        </tr>
+        {%endfor%}
+      </tbody>
+    </table>
+    {%else%}
+    <p class="text-danger">
+      <span class="glyphicon glyphicon-exclamation-sign"></span>
+      You do not currently have privileges to view this phenotype in greater
+      detail.
+    </p>
+    {%endif%}
+  </div>
 </div>
+
 {%endblock%}
 
 {%block sidebarcontents%}
-- 
cgit v1.2.3