Species column in genes search result table.

biosustain · Dec 12, 2024 · 3ac0760 · 3ac0760
2 parents eb06206 + baad15e
commit 3ac0760
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Showing 4 changed files with 23 additions and 14 deletions.
diff --git a/.github/workflows/deploy-preprod-to-azurevm.yaml b/.github/workflows/deploy-preprod-to-azurevm.yaml
@@ -22,7 +22,7 @@ jobs:
           target: "/projects/pankb_web/django_project"
 
       - name: Create the .env file and (re-)start containers over SSH
-        uses: appleboy/ssh-action@v0.1.7
+        uses: appleboy/ssh-action@v1.2.0
         with:
           host: ${{ secrets.PANKB_PREPROD_HOST }}
           username: ${{ secrets.PANKB_PREPROD_SSH_USERNAME }}
@@ -59,6 +59,6 @@ jobs:
             echo "## URL address of the separately deployed AI Assistant Web Application" >> .env
             echo AI_ASSISTANT_APP_URL="${{vars.PANKB_PREPROD_AI_ASSISTANT_APP_URL}}" >> .env
             cat .env
-            docker compose down
-            docker compose up -d --build --force-recreate --remove-orphans
+            docker compose --profile dev down
+            docker compose --profile dev up -d --build --force-recreate --remove-orphans
             docker system prune --all --force
diff --git a/.github/workflows/deploy-prod-to-azurevm.yml b/.github/workflows/deploy-prod-to-azurevm.yml
@@ -22,7 +22,7 @@ jobs:
           target: "/projects/pankb_web/django_project"
 
       - name: Create the .env file and (re-)start containers over SSH
-        uses: appleboy/ssh-action@v0.1.7
+        uses: appleboy/ssh-action@v1.2.0
         with:
           host: ${{ secrets.PANKB_PROD_HOST }}
           username: ${{ secrets.PANKB_PROD_SSH_USERNAME }}
@@ -59,6 +59,6 @@ jobs:
             echo "## URL address of the separately deployed AI Assistant Web Application" >> .env
             echo AI_ASSISTANT_APP_URL="${{vars.PANKB_PROD_AI_ASSISTANT_APP_URL}}" >> .env
             cat .env
-            docker compose down
-            docker compose up -d --build --force-recreate --remove-orphans
+            docker compose --profile prod down
+            docker compose --profile prod up -d --build --force-recreate --remove-orphans
             docker system prune --all --force
diff --git a/search/views.py b/search/views.py
@@ -194,6 +194,7 @@ def gene_annotation_json(request):
 
     gene_keys = [
         "gene",
+        "species",
         "cog_category",
         "cog_name",
         "description",

diff --git a/templates/search/search_results_genes.html b/templates/search/search_results_genes.html
@@ -12,6 +12,7 @@
     <thead>
     <tr>
         <th>Gene</th>
+        <th>Species</th>
         <th>Class</th>
         <th>COG</th>
         <th>COG Name</th>
@@ -26,6 +27,7 @@
     <tfoot>
         <tr>
             <th>Gene</th>
+            <th>Species</th>
             <th>Class</th>
             <th>COG</th>
             <th>COG Name</th>
@@ -54,46 +56,52 @@
             ],
             order: [],
             columns: [
-            {
+                {
                     data: '0',
                     render: function (data, type, row) {
-                        return '<a href=" {% url 'gene_info' %}?species=' + row[8] + '&gene=' + encodeURIComponent(data) + '">' + data + '</a>';
+                        return '<a href="{% url 'gene_info' %}?species=' + encodeURIComponent(row[9]) + '&gene=' + encodeURIComponent(data) + '">' + data + '</a>';
                     },
                 },
                 {
-                    data: '7',
+                    data: '1',
+                    render: function (data, type, row) {
+                        return '<a href="{% url 'pangenome_analyses_overview' %}?species=' + encodeURIComponent(row[9]) + '">' + data + '</a>';
+                    },
                 },
                 {
-                    data: '1',
+                    data: '8',
                 },
                 {
                     data: '2',
+                },
+                {
+                    data: '3',
                     render: function (data, type, row) {
                         return wrap_table_text(data, '160px')
                     },
                 },
                 {
-                    data: '3',
+                    data: '4',
                     render: function (data, type, row) {
                         return wrap_table_text(data, '240px')
                     },
                 },
                 {
-                    data: '4',
+                    data: '5',
                     render: function (data, type, row) {
                         return wrap_table_text(data, '220px')
                     },
                     className: 'protein',
                 },
                 {
-                    data: '5',
+                    data: '6',
                     render: function (data, type, row) {
                         return wrap_table_text(data, '120px')
                     },
                     className: 'pfams',
                 },
                 {
-                    data: '6',
+                    data: '7',
                     width: '80px',
                 }
             ],