Merge branch 'develop' into staging

.pre-commit-config.yaml

@@ -18,6 +18,7 @@ repos:
   - id: end-of-file-fixer
     exclude: static/vendor/
   - id: pretty-format-json
+    exclude: ^fixtures/
     args: [--autofix]
 
 

charts/apps/dash/chart/templates/deployment.yaml

@@ -39,7 +39,7 @@ spec:
         image: {{ .Values.appconfig.image }}
         imagePullPolicy: IfNotPresent
         ports:
-          - containerPort: {{ .Values.service.targetport }}
+          - containerPort: {{ .Values.appconfig.port }}
         securityContext:
           {{- toYaml .Values.securityContext | nindent 10 }}
         resources:

charts/apps/dash/chart/templates/service.yaml

@@ -9,6 +9,6 @@ spec:
   ports:
   - protocol: TCP
     port: {{ .Values.service.port }}
-    targetPort: {{ .Values.service.targetport }}
+    targetPort: {{ .Values.appconfig.port }}
   selector:
     release: {{ $.Release.Name }}

charts/apps/shiny/chart/templates/deployment.yaml

@@ -43,6 +43,6 @@ spec:
         resources:
           {{- toYaml .Values.flavor | nindent 10 }}
         ports:
-          - containerPort: {{ .Values.service.targetport }}
+          - containerPort: {{ .Values.appconfig.port }}
       terminationGracePeriodSeconds: 30
       dnsPolicy: ClusterFirst

charts/apps/shiny/chart/templates/service.yaml

@@ -9,6 +9,6 @@ spec:
   ports:
   - protocol: TCP
     port: {{ .Values.service.port }}
-    targetPort: {{ .Values.service.targetport }}
+    targetPort: {{ .Values.appconfig.port }}
   selector:
     release: {{ $.Release.Name }}

charts/apps/shinyproxy/chart/templates/deployment.yaml

@@ -44,8 +44,7 @@ spec:
           - containerPort: {{ .Values.appconfig.proxyport }}
         volumeMounts:
           - name: application-conf-{{ .Release.Name }}
-            mountPath: /opt/shinyproxy/application.yml
-            subPath: application.yml
+            mountPath: /opt/shinyproxy/config
         imagePullPolicy: IfNotPresent
         securityContext:
           {{- toYaml .Values.securityContext | nindent 10 }}

charts/apps/shinyproxy/chart/values.yaml

@@ -5,7 +5,7 @@ project:
   slug: project-slug
 
 appconfig:
-  proxyimage: ghcr.io/scilifelabdatacentre/serve-shinyproxy:231030-1144
+  proxyimage: ghcr.io/scilifelabdatacentre/serve-shinyproxy:231124-2126
   proxyport: 8080
   port: 3838
   image:

cypress/e2e/ui-tests/test-deploy-app.cy.js

@@ -89,7 +89,7 @@ describe("Test deploying app", () => {
             cy.get('tr:contains("' + app_name_public + '")').find('span').should('contain', 'Running')
 
             cy.visit("/apps")
-            cy.get("title").should("have.text", "Apps | SciLifeLab Serve")
+            cy.get("title").should("have.text", "Apps | SciLifeLab Serve (beta)")
             cy.get('h3').should('contain', 'Public apps')
             cy.get('h5.card-title').should('contain', app_name_public)
 
@@ -104,7 +104,7 @@ describe("Test deploying app", () => {
             cy.get('button').contains('Delete').click()
             cy.get('tr:contains("' + app_name_public + '")').find('span').should('contain', 'Deleted')
             cy.visit("/apps")
-            cy.get("title").should("have.text", "Apps | SciLifeLab Serve")
+            cy.get("title").should("have.text", "Apps | SciLifeLab Serve (beta)")
             cy.get('h3').should('contain', 'Public apps')
             cy.get('h5.card-title').should('not.exist')
 

cypress/e2e/ui-tests/test-homepage.cy.js

@@ -38,6 +38,6 @@ describe("Test of the home page", () => {
   })
 
     it("should have proper title", () => {
-	cy.get("title").should("have.text", "Home | SciLifeLab Serve")
+	cy.get("title").should("have.text", "Home | SciLifeLab Serve (beta)")
     })
 })

cypress/e2e/ui-tests/test-login.cy.js

@@ -48,6 +48,6 @@ describe("Test login", () => {
 
     it("Should have proper title", () => {
 	cy.visit("accounts/login/")
-        cy.get("title").should("have.text", "Login | SciLifeLab Serve")
+        cy.get("title").should("have.text", "Login | SciLifeLab Serve (beta)")
     })
 })

cypress/e2e/ui-tests/test-project-as-contributor.cy.js

@@ -40,10 +40,10 @@ describe("Test project contributor user functionality", () => {
 
         // Names of objects to create
         const project_name = "e2e-create-default-proj-test"
-        const project_title_name = project_name + " | SciLifeLab Serve"
+        const project_title_name = project_name + " | SciLifeLab Serve (beta)"
 
         cy.visit("/projects/")
-        cy.get("title").should("have.text", "My projects | SciLifeLab Serve")
+        cy.get("title").should("have.text", "My projects | SciLifeLab Serve (beta)")
 
         // Click button for UI to create a new project
         cy.get("a").contains('New project').click()
@@ -106,10 +106,10 @@ describe("Test project contributor user functionality", () => {
 
         // Names of objects to create
         const project_name = "e2e-create-ml-proj-test"
-        const project_title_name = project_name + " | SciLifeLab Serve"
+        const project_title_name = project_name + " | SciLifeLab Serve (beta)"
 
         cy.visit("/projects/")
-        cy.get("title").should("have.text", "My projects | SciLifeLab Serve")
+        cy.get("title").should("have.text", "My projects | SciLifeLab Serve (beta)")
 
         // Click button for UI to create a new project
         cy.get("a").contains('New project').click()

cypress/e2e/ui-tests/test-project-as-superuser.cy.js

@@ -39,7 +39,7 @@ describe("Test superuser access", () => {
         // Names of objects to create
         const project_name = "e2e-create-proj-test"
         const volume_name = "e2e-project-vol"
-        const project_title_name = project_name + " | SciLifeLab Serve"
+        const project_title_name = project_name + " | SciLifeLab Serve (beta)"
         const createResources = Cypress.env('create_resources');
 
         if (createResources === 'true') {

cypress/e2e/ui-tests/test-public-apps-page.cy.js

@@ -8,7 +8,7 @@ describe("Test of the public apps page", () => {
     it("should contain header with text Apps", () => {
 
         cy.get('h3').should('contain', 'apps')
-        cy.get("title").should("have.text", "Apps | SciLifeLab Serve")
+        cy.get("title").should("have.text", "Apps | SciLifeLab Serve (beta)")
     })
 
 })

cypress/e2e/ui-tests/test-public-models-page.cy.js

@@ -8,7 +8,7 @@ describe("Test of the public models page", () => {
     it("should contain header with text Models", () => {
 
         cy.get('h3').should('contain', 'Models')
-        cy.get("title").should("have.text", "Models | SciLifeLab Serve")
+        cy.get("title").should("have.text", "Models | SciLifeLab Serve (beta)")
     })
 
     it("should contain text about no public models", () => {

cypress/e2e/ui-tests/test-signup.cy.js

@@ -23,7 +23,7 @@ describe("Test sign up", () => {
     it("should create new user account with valid form input", () => {
 
         cy.visit("/signup/");
-        cy.get("title").should("have.text", "Register | SciLifeLab Serve")
+        cy.get("title").should("have.text", "Register | SciLifeLab Serve (beta)")
 
         cy.get('input[name=email]').type(users.signup_user.email);
         cy.get('input[name=first_name]').type("first name");

fixtures/apps_fixtures.json

@@ -431,7 +431,7 @@
       "category": "serve",
       "chart": "apps/custom-app/chart",
       "created_on": "2023-08-25T21:34:37.815Z",
-      "description": "",
+      "description": "Apps built with Gradio, Streamlit, Flask, etc.",
       "logo": "default-logo.png",
       "name": "Custom App",
       "priority": "400",
@@ -594,12 +594,12 @@
   },
   {
     "fields": {
-      "category": "admin-apps",
+      "category": "serve",
       "chart": "apps/shiny/chart",
       "created_on": "2023-08-25T21:34:37.815Z",
-      "description": "Shiny app without ShinyProxy as a middle layer.",
+      "description": "Shiny app without ShinyProxy as a middle layer. [admins only]",
       "logo": "shinyapp-logo.png",
-      "name": "Shiny App",
+      "name": "Shiny App (single copy)",
       "priority": "400",
       "settings": {
         "appconfig": {

fixtures/projects_templates.json

@@ -64,15 +64,6 @@
       "slug": "default",
       "template": {
         "apps": {
-          "project-minio": {
-            "app:volumeK8s": [
-              "project-vol"
-            ],
-            "credentials.access_key": "accesskey",
-            "credentials.secret_key": "secretkey123",
-            "permission": "project",
-            "slug": "minio"
-          },
           "project-netpolicy": {
             "slug": "netpolicy"
           },
@@ -85,6 +76,15 @@
             "volume.accessModes": "ReadWriteMany",
             "volume.size": "1Gi",
             "volume.storageClass": "microk8s-hostpath"
+          },
+          "project-minio": {
+            "app:volumeK8s": [
+              "project-vol"
+            ],
+            "credentials.access_key": "accesskey",
+            "credentials.secret_key": "secretkey123",
+            "permission": "project",
+            "slug": "minio"
           }
         },
         "environments": {

models/tests.py

@@ -118,7 +118,7 @@ def test_models_view(self):
 
         # Check status code
         assert response.status_code == 200
-        assert "<title>Models | SciLifeLab Serve</title>" in response.content.decode()
+        assert "<title>Models | SciLifeLab Serve (beta)</title>" in response.content.decode()
 
     @pytest.mark.skip(reason="It's not working")
     def test_public_model_details_view(self):
@@ -128,7 +128,7 @@ def test_public_model_details_view(self):
         assert response.status_code == 200
         self.assertTemplateUsed(response, "models/models_details_public.html")
         assert "Model Details" in response.content.decode()
-        assert "<title>Model public Details | SciLifeLab Serve</title>" in response.content.decode()
+        assert "<title>Model public Details | SciLifeLab Serve (beta)</title>" in response.content.decode()
 
     @pytest.mark.skip(reason="Could not make this work")
     def test_private_model_details_view(self):
@@ -143,7 +143,7 @@ def test_private_model_details_view(self):
         assert response.status_code == 200
         self.assertTemplateUsed(response, "models/models_details_private.html")
         assert "Model Details" in response.content.decode()
-        assert "<title>Private model test Details | SciLifeLab Serve</title>" in response.content.decode()
+        assert "<title>Private model test Details | SciLifeLab Serve (beta)</title>" in response.content.decode()
 
     @pytest.mark.skip(reason="I am even not sure that it's being invoked")
     def test_model_create_view(self):
@@ -153,7 +153,7 @@ def test_model_create_view(self):
         assert response.status_code == 200
         self.assertTemplateUsed(response, "models/models_details_private.html")
         assert "Model Details" in response.content.decode()
-        assert "<title>Private model test Details | SciLifeLab Serve</title>" in response.content.decode()
+        assert "<title>Private model test Details | SciLifeLab Serve (beta)</title>" in response.content.decode()
 
     @pytest.mark.skip(reason="I think that the project is not created for this")
     def test_models_list_view(self):
@@ -162,7 +162,7 @@ def test_models_list_view(self):
         assert response.status_code == 200
         self.assertTemplateUsed(response, "models/models_list.html")
         assert "Models" in response.content.decode()
-        assert f"<title>{self.project.name} - Models | SciLifeLab Serve</title>" in response.content.decode()
+        assert f"<title>{self.project.name} - Models | SciLifeLab Serve (beta)</title>" in response.content.decode()
 
 
 class ModelViewForbidden(TestCase):
@@ -194,7 +194,7 @@ def test_forbidden_models_list(self):
         response = self.client.get(reverse("models:list", kwargs={"user": owner, "project": project.slug}))
         self.assertTemplateUsed(response, "403.html")
         self.assertEqual(response.status_code, 403)
-        assert "<title>Forbidden | SciLifeLab Serve</title>" in response.content.decode()
+        assert "<title>Forbidden | SciLifeLab Serve (beta)</title>" in response.content.decode()
 
     def test_forbidden_models_create(self):
         """

portal/tests.py

@@ -22,7 +22,7 @@ def test_index():
 
     # Check if it returns the correct status code
     assert response.status_code == 200
-    assert "<title>Apps | SciLifeLab Serve</title>" in response.content.decode()
+    assert "<title>Apps | SciLifeLab Serve (beta)</title>" in response.content.decode()
 
 
 @pytest.mark.django_db
@@ -41,7 +41,7 @@ def test_home_view_class():
 
     # Check status code
     assert response.status_code == 200
-    assert "<title>Home | SciLifeLab Serve</title>" in response.content.decode()
+    assert "<title>Home | SciLifeLab Serve (beta)</title>" in response.content.decode()
 
 
 def test_about_view():
@@ -51,7 +51,7 @@ def test_about_view():
 
     # Check status code
     assert response.status_code == 200
-    assert "<title>About | SciLifeLab Serve</title>" in response.content.decode()
+    assert "<title>About | SciLifeLab Serve (beta)</title>" in response.content.decode()
 
 
 def test_teaching_view():
@@ -61,7 +61,7 @@ def test_teaching_view():
 
     # Check status code
     assert response.status_code == 200
-    assert "<title>Teaching | SciLifeLab Serve</title>" in response.content.decode()
+    assert "<title>Teaching | SciLifeLab Serve (beta)</title>" in response.content.decode()
 
 
 def test_privacy_view():
@@ -71,4 +71,4 @@ def test_privacy_view():
 
     # Check status code
     assert response.status_code == 200
-    assert "<title>Privacy policy | SciLifeLab Serve</title>" in response.content.decode()
+    assert "<title>Privacy policy | SciLifeLab Serve (beta)</title>" in response.content.decode()

portal/views.py

@@ -105,13 +105,15 @@ def get(self, request, id=0):
         published_apps, request = get_public_apps(request, id=id, get_all=False)
         published_models = PublishedModel.objects.all()
         news_objects = NewsObject.objects.all().order_by("-created_on")
+        link_all_news = False
         if published_models.count() >= 3:
             published_models = published_models[:3]
         else:
             published_models = published_models
 
         if news_objects.count() >= 3:
             news_objects = news_objects[:3]
+            link_all_news = True
         else:
             news_objects = news_objects
 

projects/tests/test_project_view.py

@@ -29,7 +29,7 @@ def test_project_overview(self):
         resp = self.get_project_page("details")
         self.assertEqual(resp.status_code, 200)
         self.assertTemplateUsed(resp, "projects/overview.html")
-        assert f"<title>{self.project_name} | SciLifeLab Serve</title>" in resp.content.decode()
+        assert f"<title>{self.project_name} | SciLifeLab Serve (beta)</title>" in resp.content.decode()
 
 
 class FrobiddenProjectViewTestCase(TestCase):

static/css/serve-elements.css

@@ -6,7 +6,6 @@
 
 .btn:focus,
 .btn:hover {
-
     box-shadow: 0 0.5rem 1rem rgba(var(--bs-body-color-rgb), .15) !important;
     text-decoration: none;
 }
@@ -158,6 +157,12 @@ h6 {
 }
 
 /* main navigation */
+
+a.navbar-brand::after,
+a.tag::after {
+    display:none;
+}
+
 .nav .nav-item .nav-link {
     color: var(--serve-teal);
     font-weight: 500;

studio/settings.py

@@ -242,6 +242,10 @@
 # then setting BigAutoField on app level (ex /projects/apps.py)
 DEFAULT_AUTO_FIELD = "django.db.models.AutoField"
 
+# Allow all clients to make requests to the OpenAPI
+CORS_URLS_REGEX = r"^/openapi/.*$"
+CORS_ALLOW_ALL_ORIGINS = True
+
 # https://www.django-rest-framework.org/api-guide/authentication/#setting-the-authentication-scheme
 # DEFAULT_VERSIONING_CLASS: NamespaceVersioning uses the URL path scheme, e.g. /v1/
 # https://www.django-rest-framework.org/api-guide/versioning/