From c9f04c6b1be04ff64536e88a35704c2038cb02b4 Mon Sep 17 00:00:00 2001
From: carlosribas <caduribas@gmail.com>
Date: Fri, 20 Sep 2024 11:40:48 +0100
Subject: [PATCH 01/24] Test kubectl commands only

---
 .gitlab-ci.yml | 46 +++++++++++++++++++++++-----------------------
 1 file changed, 23 insertions(+), 23 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 2e5d4d097..b6181d04d 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -1,29 +1,29 @@
 stages:
-  - test
+#  - test
 #  - build
   - deploy
 
-test_image:
-  image: python:3.8.15-slim
-  stage: test
-  before_script:
-    - |
-      apt-get update && apt-get install -y --no-install-recommends \
-      g++ \
-      build-essential \
-      tar \
-      git \
-      && rm -rf /var/lib/apt/lists/*
-    - python -m pip install --upgrade pip
-    - pip install -r rnacentral/requirements.txt
-    - pip install -r rnacentral/requirements_dev.txt
-    - mv rnacentral/rnacentral/unit_test_local_settings.py rnacentral/rnacentral/local_settings.py
-  script:
-    - |
-      python rnacentral/manage.py test apiv1
-      python rnacentral/manage.py test export
-      python rnacentral/manage.py test portal
-      python rnacentral/manage.py test sequence_search
+#test_image:
+#  image: python:3.8.15-slim
+#  stage: test
+#  before_script:
+#    - |
+#      apt-get update && apt-get install -y --no-install-recommends \
+#      g++ \
+#      build-essential \
+#      tar \
+#      git \
+#      && rm -rf /var/lib/apt/lists/*
+#    - python -m pip install --upgrade pip
+#    - pip install -r rnacentral/requirements.txt
+#    - pip install -r rnacentral/requirements_dev.txt
+#    - mv rnacentral/rnacentral/unit_test_local_settings.py rnacentral/rnacentral/local_settings.py
+#  script:
+#    - |
+#      python rnacentral/manage.py test apiv1
+#      python rnacentral/manage.py test export
+#      python rnacentral/manage.py test portal
+#      python rnacentral/manage.py test sequence_search
 
 #build_image:
 #  stage: build
@@ -45,6 +45,6 @@ deploy_image:
     - echo "$CI_COMMIT_BRANCH"
     - kubectl config get-contexts
     - kubectl config use-context RNAcentral/rnacentral-webcode:primary-agent
-    - kubectl config set-context --current --namespace=dev
+    - kubectl config set-context --current --namespace=prod
     - kubectl config view
     - kubectl get pods

From db7d20afd4ff371b7b7e222b28eb3d504a031765 Mon Sep 17 00:00:00 2001
From: carlosribas <caduribas@gmail.com>
Date: Fri, 20 Sep 2024 12:50:29 +0100
Subject: [PATCH 02/24] Test command to clear memcached

---
 .gitlab-ci.yml | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index b6181d04d..b306637c5 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -43,8 +43,7 @@ deploy_image:
     entrypoint: [""]
   script:
     - echo "$CI_COMMIT_BRANCH"
-    - kubectl config get-contexts
     - kubectl config use-context RNAcentral/rnacentral-webcode:primary-agent
-    - kubectl config set-context --current --namespace=prod
-    - kubectl config view
-    - kubectl get pods
+    - POD=`kubectl get pod -l app=memcached -o jsonpath="{.items[0].metadata.name}"`
+    - kubectl exec -it \$POD -- sh -c "echo flush_all | nc localhost 11211"
+#    - kubectl config set-context --current --namespace=prod

From 3d6162c9b91f22a4d5fcd041a607844b7cada0b7 Mon Sep 17 00:00:00 2001
From: carlosribas <caduribas@gmail.com>
Date: Fri, 20 Sep 2024 12:58:22 +0100
Subject: [PATCH 03/24] Change namespace

---
 .gitlab-ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index b306637c5..9017235ea 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -44,6 +44,6 @@ deploy_image:
   script:
     - echo "$CI_COMMIT_BRANCH"
     - kubectl config use-context RNAcentral/rnacentral-webcode:primary-agent
+    - kubectl config set-context --current --namespace=prod
     - POD=`kubectl get pod -l app=memcached -o jsonpath="{.items[0].metadata.name}"`
     - kubectl exec -it \$POD -- sh -c "echo flush_all | nc localhost 11211"
-#    - kubectl config set-context --current --namespace=prod

From 3bf193d37e4a680e984003ece50d13ff8fc721e1 Mon Sep 17 00:00:00 2001
From: carlosribas <caduribas@gmail.com>
Date: Fri, 20 Sep 2024 16:10:32 +0100
Subject: [PATCH 04/24] Minor change

---
 .gitlab-ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 9017235ea..c425dcce2 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -46,4 +46,4 @@ deploy_image:
     - kubectl config use-context RNAcentral/rnacentral-webcode:primary-agent
     - kubectl config set-context --current --namespace=prod
     - POD=`kubectl get pod -l app=memcached -o jsonpath="{.items[0].metadata.name}"`
-    - kubectl exec -it \$POD -- sh -c "echo flush_all | nc localhost 11211"
+    - kubectl exec -it "$POD" -- sh -c "echo flush_all | nc localhost 11211"

From c0a48f1245cef1a4825c6abaf4c5d3d72d9d52fa Mon Sep 17 00:00:00 2001
From: carlosribas <caduribas@gmail.com>
Date: Fri, 20 Sep 2024 16:16:29 +0100
Subject: [PATCH 05/24] Remove the -it flags

---
 .gitlab-ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index c425dcce2..f73edb4de 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -46,4 +46,4 @@ deploy_image:
     - kubectl config use-context RNAcentral/rnacentral-webcode:primary-agent
     - kubectl config set-context --current --namespace=prod
     - POD=`kubectl get pod -l app=memcached -o jsonpath="{.items[0].metadata.name}"`
-    - kubectl exec -it "$POD" -- sh -c "echo flush_all | nc localhost 11211"
+    - kubectl exec "$POD" -- sh -c "echo flush_all | nc localhost 11211"

From d4054a677b7af4cb36900fde9ea938bc9838afa6 Mon Sep 17 00:00:00 2001
From: carlosribas <caduribas@gmail.com>
Date: Fri, 20 Sep 2024 16:26:57 +0100
Subject: [PATCH 06/24] Testing helm

---
 .gitlab-ci.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index f73edb4de..3fcdc98be 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -46,4 +46,6 @@ deploy_image:
     - kubectl config use-context RNAcentral/rnacentral-webcode:primary-agent
     - kubectl config set-context --current --namespace=prod
     - POD=`kubectl get pod -l app=memcached -o jsonpath="{.items[0].metadata.name}"`
-    - kubectl exec "$POD" -- sh -c "echo flush_all | nc localhost 11211"
+    - kubectl exec "$POD" -- /bin/sh -c "echo flush_all | nc localhost 11211"
+    - cd kubernetes/helm
+    - helm list --all

From c8b42c8db48ca903d4ada01f3f015e6735f03aa5 Mon Sep 17 00:00:00 2001
From: carlosribas <caduribas@gmail.com>
Date: Fri, 20 Sep 2024 16:44:07 +0100
Subject: [PATCH 07/24] Ensure the pod is ready

---
 .gitlab-ci.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 3fcdc98be..7dbb244a5 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -46,6 +46,7 @@ deploy_image:
     - kubectl config use-context RNAcentral/rnacentral-webcode:primary-agent
     - kubectl config set-context --current --namespace=prod
     - POD=`kubectl get pod -l app=memcached -o jsonpath="{.items[0].metadata.name}"`
-    - kubectl exec "$POD" -- /bin/sh -c "echo flush_all | nc localhost 11211"
+    - kubectl wait --for=condition=ready pod/"$POD" --timeout=60s
+#    - kubectl exec "$POD" -- /bin/sh -c "echo flush_all | nc localhost 11211"
     - cd kubernetes/helm
     - helm list --all

From 2da92e73d7d87a047afb7ebf26f956e102345134 Mon Sep 17 00:00:00 2001
From: carlosribas <caduribas@gmail.com>
Date: Fri, 20 Sep 2024 17:18:16 +0100
Subject: [PATCH 08/24] Install helm

---
 .gitlab-ci.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 7dbb244a5..cb82f4c2b 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -45,8 +45,8 @@ deploy_image:
     - echo "$CI_COMMIT_BRANCH"
     - kubectl config use-context RNAcentral/rnacentral-webcode:primary-agent
     - kubectl config set-context --current --namespace=prod
-    - POD=`kubectl get pod -l app=memcached -o jsonpath="{.items[0].metadata.name}"`
-    - kubectl wait --for=condition=ready pod/"$POD" --timeout=60s
+#    - POD=`kubectl get pod -l app=memcached -o jsonpath="{.items[0].metadata.name}"`
 #    - kubectl exec "$POD" -- /bin/sh -c "echo flush_all | nc localhost 11211"
     - cd kubernetes/helm
+    - curl https://raw.githubusercontent.com/helm/helm/main/scripts/get-helm-3 | bash
     - helm list --all

From 36f985744336bb6dc15bfa2e530f6c9fd4914ace Mon Sep 17 00:00:00 2001
From: carlosribas <caduribas@gmail.com>
Date: Fri, 20 Sep 2024 17:26:22 +0100
Subject: [PATCH 09/24] Install curl

---
 .gitlab-ci.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index cb82f4c2b..8eb3ec8c7 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -42,6 +42,7 @@ deploy_image:
     name: bitnami/kubectl:1.23.15
     entrypoint: [""]
   script:
+    - apt-get update && apt-get install -y curl
     - echo "$CI_COMMIT_BRANCH"
     - kubectl config use-context RNAcentral/rnacentral-webcode:primary-agent
     - kubectl config set-context --current --namespace=prod

From 77ba7653cf252e5959ba46d63ef67e3942a41d92 Mon Sep 17 00:00:00 2001
From: carlosribas <caduribas@gmail.com>
Date: Fri, 20 Sep 2024 17:33:23 +0100
Subject: [PATCH 10/24] Create the missing directory

---
 .gitlab-ci.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 8eb3ec8c7..aceb7d018 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -42,6 +42,7 @@ deploy_image:
     name: bitnami/kubectl:1.23.15
     entrypoint: [""]
   script:
+    - mkdir -p /var/lib/apt/lists/partial
     - apt-get update && apt-get install -y curl
     - echo "$CI_COMMIT_BRANCH"
     - kubectl config use-context RNAcentral/rnacentral-webcode:primary-agent

From 980a5ccb7c4a2f17e8f8ff347e14fe8ac04f1ad7 Mon Sep 17 00:00:00 2001
From: carlosribas <caduribas@gmail.com>
Date: Mon, 23 Sep 2024 11:23:30 +0100
Subject: [PATCH 11/24] Test new image

---
 .gitlab-ci.yml | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index aceb7d018..b0b143576 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -39,16 +39,14 @@ stages:
 deploy_image:
   stage: deploy
   image:
-    name: bitnami/kubectl:1.23.15
+    name: rnacentral/rnacentral-ci-cd
     entrypoint: [""]
   script:
-    - mkdir -p /var/lib/apt/lists/partial
-    - apt-get update && apt-get install -y curl
     - echo "$CI_COMMIT_BRANCH"
     - kubectl config use-context RNAcentral/rnacentral-webcode:primary-agent
     - kubectl config set-context --current --namespace=prod
 #    - POD=`kubectl get pod -l app=memcached -o jsonpath="{.items[0].metadata.name}"`
 #    - kubectl exec "$POD" -- /bin/sh -c "echo flush_all | nc localhost 11211"
+    - kubectl get pod
     - cd kubernetes/helm
-    - curl https://raw.githubusercontent.com/helm/helm/main/scripts/get-helm-3 | bash
     - helm list --all

From d134ab003c7fdb8d6d2b14d9ee7009b41b517eb5 Mon Sep 17 00:00:00 2001
From: carlosribas <caduribas@gmail.com>
Date: Mon, 23 Sep 2024 11:40:32 +0100
Subject: [PATCH 12/24] Remove entrypoint

---
 .gitlab-ci.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index b0b143576..f5cac6e2e 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -40,7 +40,6 @@ deploy_image:
   stage: deploy
   image:
     name: rnacentral/rnacentral-ci-cd
-    entrypoint: [""]
   script:
     - echo "$CI_COMMIT_BRANCH"
     - kubectl config use-context RNAcentral/rnacentral-webcode:primary-agent

From 169c72292fe20b1390fe99341e3786f83e692a84 Mon Sep 17 00:00:00 2001
From: carlosribas <caduribas@gmail.com>
Date: Mon, 23 Sep 2024 12:10:34 +0100
Subject: [PATCH 13/24] Enable debugging

---
 .gitlab-ci.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index f5cac6e2e..4d167764e 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -41,6 +41,8 @@ deploy_image:
   image:
     name: rnacentral/rnacentral-ci-cd
   script:
+    - set -x
+    - echo $SHELL
     - echo "$CI_COMMIT_BRANCH"
     - kubectl config use-context RNAcentral/rnacentral-webcode:primary-agent
     - kubectl config set-context --current --namespace=prod

From 2d360b652a43ad2813d947950c03e8f5acf8b169 Mon Sep 17 00:00:00 2001
From: carlosribas <caduribas@gmail.com>
Date: Mon, 23 Sep 2024 12:16:43 +0100
Subject: [PATCH 14/24] Remove quotes

---
 .gitlab-ci.yml | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 4d167764e..c8c585f3f 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -43,11 +43,9 @@ deploy_image:
   script:
     - set -x
     - echo $SHELL
-    - echo "$CI_COMMIT_BRANCH"
+    - echo $CI_COMMIT_BRANCH
     - kubectl config use-context RNAcentral/rnacentral-webcode:primary-agent
     - kubectl config set-context --current --namespace=prod
-#    - POD=`kubectl get pod -l app=memcached -o jsonpath="{.items[0].metadata.name}"`
-#    - kubectl exec "$POD" -- /bin/sh -c "echo flush_all | nc localhost 11211"
     - kubectl get pod
     - cd kubernetes/helm
     - helm list --all

From 32518eaf7a9c2669f9e4d69193dc7ea5f089b7e2 Mon Sep 17 00:00:00 2001
From: carlosribas <caduribas@gmail.com>
Date: Mon, 23 Sep 2024 14:41:13 +0100
Subject: [PATCH 15/24] Add dockerfile to be used by GitLab

---
 Dockerfile-CI-CD | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)
 create mode 100644 Dockerfile-CI-CD

diff --git a/Dockerfile-CI-CD b/Dockerfile-CI-CD
new file mode 100644
index 000000000..84596102d
--- /dev/null
+++ b/Dockerfile-CI-CD
@@ -0,0 +1,22 @@
+# Build container with kubectl and helm to be used by GitLab CI/CD
+
+ARG BUILDPLATFORM
+FROM ${BUILDPLATFORM}alpine:3.20
+
+ARG TARGETOS
+ARG TARGETARCH
+
+# Use kubectl version v1.23.8 and helm version v3.16.1
+RUN apk -U upgrade \
+    && apk add --no-cache ca-certificates bash git openssh curl gettext jq \
+    && wget -q https://dl.k8s.io/release/v1.23.8/bin/${TARGETOS}/${TARGETARCH}/kubectl -O /usr/local/bin/kubectl \
+    && wget -q https://get.helm.sh/helm-v3.16.1-${TARGETOS}-${TARGETARCH}.tar.gz -O - | tar -xzO ${TARGETOS}-${TARGETARCH}/helm > /usr/local/bin/helm \
+    && chmod +x /usr/local/bin/helm /usr/local/bin/kubectl \
+    && mkdir /config \
+    && chmod g+rwx /config /root \
+    && kubectl version --client \
+    && helm version
+
+WORKDIR /config
+
+CMD bash

From 092403e1407ac61a1d615656fae3461d366bb3b7 Mon Sep 17 00:00:00 2001
From: carlosribas <caduribas@gmail.com>
Date: Mon, 23 Sep 2024 15:49:33 +0100
Subject: [PATCH 16/24] Add rules

---
 .gitlab-ci.yml | 14 ++++++++++----
 1 file changed, 10 insertions(+), 4 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index c8c585f3f..05d88115c 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -41,11 +41,17 @@ deploy_image:
   image:
     name: rnacentral/rnacentral-ci-cd
   script:
-    - set -x
-    - echo $SHELL
-    - echo $CI_COMMIT_BRANCH
     - kubectl config use-context RNAcentral/rnacentral-webcode:primary-agent
     - kubectl config set-context --current --namespace=prod
-    - kubectl get pod
+    - POD=`kubectl get pod -l app=memcached -o jsonpath="{.items[0].metadata.name}"`
+    - echo $POD
+    - kubectl exec $POD -- /bin/sh -c "echo flush_all | nc localhost 11211"
     - cd kubernetes/helm
     - helm list --all
+  rules:
+    - if: $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH
+      when: always
+#      changes:
+#        - rnacentral/*
+    - if: $CI_COMMIT_BRANCH != $CI_DEFAULT_BRANCH
+      when: manual

From 046e783ce809d08143a385d177a2c81094a67ae3 Mon Sep 17 00:00:00 2001
From: carlosribas <caduribas@gmail.com>
Date: Mon, 23 Sep 2024 15:58:04 +0100
Subject: [PATCH 17/24] Add verbose logging

---
 .gitlab-ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 05d88115c..67296eaef 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -45,7 +45,7 @@ deploy_image:
     - kubectl config set-context --current --namespace=prod
     - POD=`kubectl get pod -l app=memcached -o jsonpath="{.items[0].metadata.name}"`
     - echo $POD
-    - kubectl exec $POD -- /bin/sh -c "echo flush_all | nc localhost 11211"
+    - kubectl -v=9 exec $POD -- /bin/sh -c "echo flush_all | nc localhost 11211"
     - cd kubernetes/helm
     - helm list --all
   rules:

From 3d2317799a736efcaa3b8e3af362bed2a39ea33f Mon Sep 17 00:00:00 2001
From: carlosribas <caduribas@gmail.com>
Date: Mon, 23 Sep 2024 16:23:01 +0100
Subject: [PATCH 18/24] Add namespace to the command

---
 .gitlab-ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 67296eaef..214ce2fa7 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -45,7 +45,7 @@ deploy_image:
     - kubectl config set-context --current --namespace=prod
     - POD=`kubectl get pod -l app=memcached -o jsonpath="{.items[0].metadata.name}"`
     - echo $POD
-    - kubectl -v=9 exec $POD -- /bin/sh -c "echo flush_all | nc localhost 11211"
+    - kubectl -v=9 exec $POD -n prod -- /bin/sh -c "echo flush_all | nc localhost 11211"
     - cd kubernetes/helm
     - helm list --all
   rules:

From bbec913c39ed0b2ec752c3143afc6e2f0ee74823 Mon Sep 17 00:00:00 2001
From: carlosribas <caduribas@gmail.com>
Date: Tue, 24 Sep 2024 14:32:29 +0100
Subject: [PATCH 19/24] Add storageClassName

---
 kubernetes/sitemaps-pvc.yaml      | 1 +
 kubernetes/static-volume-pvc.yaml | 1 +
 2 files changed, 2 insertions(+)

diff --git a/kubernetes/sitemaps-pvc.yaml b/kubernetes/sitemaps-pvc.yaml
index 28f3e6dab..a71baeff0 100644
--- a/kubernetes/sitemaps-pvc.yaml
+++ b/kubernetes/sitemaps-pvc.yaml
@@ -5,6 +5,7 @@ metadata:
     pvc: sitemaps
   name: sitemaps
 spec:
+  storageClassName: standard-nfs-production
   accessModes:
   - ReadWriteMany
   resources:
diff --git a/kubernetes/static-volume-pvc.yaml b/kubernetes/static-volume-pvc.yaml
index 797973bd3..e8e669284 100644
--- a/kubernetes/static-volume-pvc.yaml
+++ b/kubernetes/static-volume-pvc.yaml
@@ -5,6 +5,7 @@ metadata:
     pvc: static-volume
   name: static-volume
 spec:
+  storageClassName: standard-nfs-production
   accessModes:
   - ReadWriteMany
   resources:

From b49ffe42d93f4def7cd5e2cbba2337d98e62e9c5 Mon Sep 17 00:00:00 2001
From: carlosribas <caduribas@gmail.com>
Date: Tue, 24 Sep 2024 14:32:44 +0100
Subject: [PATCH 20/24] Add roll-update-timestamp

---
 kubernetes/helm/templates/memcached.yaml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/kubernetes/helm/templates/memcached.yaml b/kubernetes/helm/templates/memcached.yaml
index c84c0cb95..139d9276b 100644
--- a/kubernetes/helm/templates/memcached.yaml
+++ b/kubernetes/helm/templates/memcached.yaml
@@ -25,6 +25,8 @@ spec:
     metadata:
       labels:
         app: memcached
+      annotations:
+        roll-update-timestamp: "{{ now | quote }}"
     spec:
       containers:
         - image: memcached:1.6.7-alpine

From 53654e152aed2aed8fecd1c42e2da30c3d567408 Mon Sep 17 00:00:00 2001
From: carlosribas <caduribas@gmail.com>
Date: Tue, 24 Sep 2024 14:43:29 +0100
Subject: [PATCH 21/24] Test deployment

---
 .gitlab-ci.yml | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 214ce2fa7..43249460a 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -43,11 +43,10 @@ deploy_image:
   script:
     - kubectl config use-context RNAcentral/rnacentral-webcode:primary-agent
     - kubectl config set-context --current --namespace=prod
-    - POD=`kubectl get pod -l app=memcached -o jsonpath="{.items[0].metadata.name}"`
-    - echo $POD
-    - kubectl -v=9 exec $POD -n prod -- /bin/sh -c "echo flush_all | nc localhost 11211"
     - cd kubernetes/helm
-    - helm list --all
+    - helm uninstall full-prod --namespace prod
+    - sleep 10
+    - helm upgrade --install full-prod --namespace prod --set proxy=proxy-hx,database=db-fb,searchIndex=search-index-prod,rnacentralBranch=export-app,rnacentralReplicas=1 .
   rules:
     - if: $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH
       when: always

From e444d519a2348b52c469ac623f37b70fef8d9d33 Mon Sep 17 00:00:00 2001
From: carlosribas <caduribas@gmail.com>
Date: Tue, 24 Sep 2024 14:53:42 +0100
Subject: [PATCH 22/24] Bug fix

---
 kubernetes/helm/templates/memcached.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/kubernetes/helm/templates/memcached.yaml b/kubernetes/helm/templates/memcached.yaml
index 139d9276b..3d32e1d49 100644
--- a/kubernetes/helm/templates/memcached.yaml
+++ b/kubernetes/helm/templates/memcached.yaml
@@ -26,7 +26,7 @@ spec:
       labels:
         app: memcached
       annotations:
-        roll-update-timestamp: "{{ now | quote }}"
+        roll-update-timestamp: {{ now | quote }}
     spec:
       containers:
         - image: memcached:1.6.7-alpine

From 12f1008b65245c46bc859172392eec7a71275e48 Mon Sep 17 00:00:00 2001
From: carlosribas <caduribas@gmail.com>
Date: Tue, 24 Sep 2024 14:57:21 +0100
Subject: [PATCH 23/24] Remove PVC

---
 kubernetes/helm/templates/rnacentral.yaml | 10 ----------
 1 file changed, 10 deletions(-)

diff --git a/kubernetes/helm/templates/rnacentral.yaml b/kubernetes/helm/templates/rnacentral.yaml
index 9db6b74d3..eda955735 100644
--- a/kubernetes/helm/templates/rnacentral.yaml
+++ b/kubernetes/helm/templates/rnacentral.yaml
@@ -48,10 +48,6 @@ spec:
           volumeMounts:
             - name: static-volume
               mountPath: /srv/rnacentral/static
-            - name: rnacentral-species-specific-ids
-              mountPath: /srv/rnacentral/fasta
-            - name: export-results
-              mountPath: /srv/rnacentral/export
             {{- if eq .Values.sitemaps "true" }}
             - name: sitemaps
               mountPath: /srv/rnacentral/rnacentral-webcode/rnacentral/sitemaps
@@ -81,12 +77,6 @@ spec:
         - name: static-volume
           persistentVolumeClaim:
             claimName: static-volume
-        - name: rnacentral-species-specific-ids
-          persistentVolumeClaim:
-            claimName: rnacentral-species-specific-ids
-        - name: export-results
-          persistentVolumeClaim:
-            claimName: export-results
         {{- if eq .Values.sitemaps "true" }}
         - name: sitemaps
           persistentVolumeClaim:

From 7f47cf04aa337437f617fd39a69bcaf0c2a9d45d Mon Sep 17 00:00:00 2001
From: carlosribas <caduribas@gmail.com>
Date: Tue, 24 Sep 2024 15:27:30 +0100
Subject: [PATCH 24/24] Add variables

---
 .gitlab-ci.yml | 13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 43249460a..88c5f5eda 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -40,13 +40,20 @@ deploy_image:
   stage: deploy
   image:
     name: rnacentral/rnacentral-ci-cd
+  variables:
+    NAMESPACE: "prod"
+    PROXY: "proxy-hx"
+    DATABASE: "db-fb"
+    SEARCH_INDEX: "search-index-prod"
+    RNACENTRAL_BRANCH: "export-app"
+    RNACENTRAL_REPLICAS: "1"
   script:
     - kubectl config use-context RNAcentral/rnacentral-webcode:primary-agent
-    - kubectl config set-context --current --namespace=prod
+    - kubectl config set-context --current --namespace=$NAMESPACE
     - cd kubernetes/helm
-    - helm uninstall full-prod --namespace prod
+    - helm uninstall full-$NAMESPACE --namespace $NAMESPACE
     - sleep 10
-    - helm upgrade --install full-prod --namespace prod --set proxy=proxy-hx,database=db-fb,searchIndex=search-index-prod,rnacentralBranch=export-app,rnacentralReplicas=1 .
+    - helm upgrade --install full-$NAMESPACE --namespace $NAMESPACE --set proxy=$PROXY,database=$DATABASE,searchIndex=$SEARCH_INDEX,rnacentralBranch=$RNACENTRAL_BRANCH,rnacentralReplicas=$RNACENTRAL_REPLICAS .
   rules:
     - if: $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH
       when: always