From c828bfa4a54570da67ae44d05cccce349a20b049 Mon Sep 17 00:00:00 2001
From: Martin Beracochea <mbc@ebi.ac.uk>
Date: Wed, 19 Jan 2022 12:00:13 +0000
Subject: [PATCH] Legacy assembly redirection

See https://github.com/EBI-Metagenomics/emgapi/pull/236/commits for the explanation
---
 ci/emg_sql_fixtures/emg_LEGACY_ASSEMBLIES.sql |  1 +
 cypress/integration/assembly.js               | 10 ++++++++++
 src/assembly.html                             | 19 ++++++++++++++++---
 src/js/modules/assembly.js                    | 16 +++++++++++++++-
 4 files changed, 42 insertions(+), 4 deletions(-)
 create mode 100644 ci/emg_sql_fixtures/emg_LEGACY_ASSEMBLIES.sql

diff --git a/ci/emg_sql_fixtures/emg_LEGACY_ASSEMBLIES.sql b/ci/emg_sql_fixtures/emg_LEGACY_ASSEMBLIES.sql
new file mode 100644
index 00000000..e28de63b
--- /dev/null
+++ b/ci/emg_sql_fixtures/emg_LEGACY_ASSEMBLIES.sql
@@ -0,0 +1 @@
+INSERT INTO `LEGACY_ASSEMBLY` (`id`, `LEGACY_ACCESSION`, `NEW_ACCESSION`) VALUES (1,'ERZ1111','ERZ477708');
diff --git a/cypress/integration/assembly.js b/cypress/integration/assembly.js
index fd4a4ba1..7dd5819d 100644
--- a/cypress/integration/assembly.js
+++ b/cypress/integration/assembly.js
@@ -139,4 +139,14 @@ describe('Assembly page', function() {
                 .should('not.exist');
         });
     });
+    context('Legacy assemblies redirection', function() {
+        const legacyAccession = 'ERZ1111';
+        const redirectUrl = 'assemblies/' + legacyAccession;
+
+        it('Should refresh the url and add a callout', function() {
+            openPage(redirectUrl);
+            cy.contains('Assembly ' + accession).should('be.visible');
+            cy.get(".callout").contains("The assembly " + legacyAccession + " has been re-assigned the accession " + accession);
+        });
+    });
 });
diff --git a/src/assembly.html b/src/assembly.html
index 4807ca3b..db0e7176 100644
--- a/src/assembly.html
+++ b/src/assembly.html
@@ -23,11 +23,15 @@
     <div class="column small-12 medium-12 large-12">
         <nav aria-label="You are here:" role="navigation">
             <ul class="breadcrumbs columns">
-                <li><a href="{{htmlWebpackPlugin.options.templateData.subfolder}}/">Home</a></li>
+                <li>
+                    <a href="{{htmlWebpackPlugin.options.templateData.subfolder}}/">Home</a>
+                </li>
                 <% if (samples.length === 1) { %>
-                <li><a href="<%= samples[0].url %>">Sample <%= samples[0].id %></a></li>
+                    <li>
+                        <a href="<%= samples[0].url %>">Sample <%= samples[0].id %></a>
+                    </li>
                 <% } else { %>
-                <li>Multiple samples</li>
+                    <li>Multiple samples</li>
                 <% } %>
                 <li>
                     <span class="show-for-sr">Current: </span>Assembly <%= assembly_id %>
@@ -35,6 +39,15 @@
             </ul>
         </nav>
         <h2>Assembly <%= assembly_id %></h2>
+        <% if (legacy_redirection) { %>
+            <section>
+                <div class="callout warning">
+                    <p>
+                        The assembly <%= legacy_redirection_accession %> has been re-assigned the accession <a href="<%= analysis_url %>"><%= assembly_id %></a>.
+                    </p>
+                </div>
+            </section>                 
+        <% } %>
         <section id="overview"></section>
         <section id="analyses"></section>
     </div>
diff --git a/src/js/modules/assembly.js b/src/js/modules/assembly.js
index 477651cb..2a5726fb 100644
--- a/src/js/modules/assembly.js
+++ b/src/js/modules/assembly.js
@@ -27,6 +27,20 @@ let AssemblyView = Backbone.View.extend({
             data: {},
             success(data) {
                 const attr = data.attributes;
+                /**
+                 * Handle legacy assemblies redirection.
+                 * Legacy assemblies were given new accessions, the api returns a 302 for those.
+                 * This code handles that case, and shows the user a warning message as the url changes.
+                 */
+                that.model.set({legacy_redirection: false});
+                if (accession !== attr["assembly_id"]) {
+                    that.model.set({
+                        legacy_redirection: true,
+                        legacy_redirection_accession: accession
+                    });
+                    accession = attr["assembly_id"];
+                    window.history.replaceState("", `${objType}: ${accession}`, attr["analysis_url"]);
+                }
                 that.render(attr).then(() => {
                     deferred.resolve();
                 });
@@ -141,9 +155,9 @@ let AssemblyAnalysesView = util.GenericTableView.extend({
 let assembly = new api.Assembly({id: accession});
 let assemblyView = new AssemblyView({model: assembly});
 
-let assemblyAnalyses = new api.AssemblyAnalyses({id: accession});
 assemblyView.init()
     .then(() => {
+        let assemblyAnalyses = new api.AssemblyAnalyses({id: accession});
         return new AssemblyAnalysesView({collection: assemblyAnalyses});
     }).then(() => {
     util.attachExpandButtonCallback();