feat: Upgrade to non-Bitnami MariaDB

.version/Jenkinsfile

@@ -112,7 +112,7 @@ pipeline {
 									}
 
 									codeDxVersion             = currentVersions[0]
-									mariaDBVersion            = 'v1.38.0' // currentVersions[1]
+									mariaDBVersion            = currentVersions[1]
 									// Note: v1.34.0 is the most recent TO version that the legacy K8s chart (codedx-kubernetes) supports
 									toolOrchestrationVersion  = 'v1.34.0'
 									// Note: v1.34.0 is the most recent Workflow version that the legacy K8s chart (codedx-kubernetes) supports

setup/core/README.md

@@ -43,7 +43,7 @@ This section describes the setup.ps1 script parameters, which you can specify by
 | `minioCPUReservation`                              | CPU request and limit for MinIO                            | `2` (example)                                     |
 | `workflowCPUReservation`                           | CPU request and limit for workflow controller              | `2` (example)                                     |
 |                                                    |                                                            |                                                   |
-| `codeDxEphemeralStorageReservation`                | storage request and limit for Code Dx                      | `2868Mi`                                             |
+| `codeDxEphemeralStorageReservation`                | storage request and limit for Code Dx                      | `3368Mi`                                             |
 | `dbMasterEphemeralStorageReservation`              | storage request and limit for the master database          | `2Gi` (example)                                   |
 | `dbSlaveEphemeralStorageReservation`               | storage request and limit for slave databases              | `2Gi` (example)                                   |
 | `toolServiceEphemeralStorageReservation`           | storage request and limit for the tool service             | `2Gi` (example)                                   |

setup/core/charts/codedx/Chart.yaml

@@ -17,8 +17,8 @@ sources:
 - https://hub.docker.com/r/bitnami/mariadb
 dependencies:
 - name: mariadb
-  version: 7.4.3
-  repository: https://codedx.github.io/codedx-kubernetes
+  version: 7.10.0
+  repository: https://codedx.github.io/srm-k8s
   condition: mariadb.enabled
 maintainers:
 - name: tylercamp

setup/core/charts/codedx/values.yaml

@@ -564,31 +564,39 @@ mariadb:
       maxUnavailable: 0
     config: |-
       [mysqld]
+      init_file=/docker-entrypoint-initdb.d/runalways-setup.sql
       skip-name-resolve
       explicit_defaults_for_timestamp
-      basedir=/opt/bitnami/mariadb
+      basedir=/usr
+      datadir=/mariadb/data/
       port=3306
-      socket=/opt/bitnami/mariadb/tmp/mysql.sock
-      tmpdir=/opt/bitnami/mariadb/tmp
+      socket=/usr/tmp/mysqld.sock
+      tmpdir=/usr/tmp
       max_allowed_packet=16M
       bind-address=0.0.0.0
-      pid-file=/opt/bitnami/mariadb/tmp/mysqld.pid
-      log-error=/opt/bitnami/mariadb/logs/mysqld.log
+      pid-file=/usr/tmp/mysqld.pid
       character-set-server=utf8mb4
       collation-server=utf8mb4_general_ci
       optimizer_search_depth=0
       lower_case_table_names=1
       innodb_flush_log_at_trx_commit=0
+      log_bin_trust_function_creators=1
+      expire_logs_days=5
+      server-id=1
+      log-bin=mysql-bin
 
       [client]
       port=3306
-      socket=/opt/bitnami/mariadb/tmp/mysql.sock
+      socket=/usr/tmp/mysqld.sock
 
       [manager]
       port=3306
-      socket=/opt/bitnami/mariadb/tmp/mysql.sock
-      pid-file=/opt/bitnami/mariadb/tmp/mysqld.pid
+      socket=/usr/tmp/mysqld.sock
+      pid-file=/usr/tmp/mysqld.pid
   slave:
+    extraEnvVars:
+      - name: MARIADB_ROOT_PASSWORD_FILE
+        value: /usr/secrets/mariadb-root-password
     persistence:
       # Use default storage class for master/slave PVCs
       storageClass: 
@@ -606,25 +614,30 @@ mariadb:
       [mysqld]
       skip-name-resolve
       explicit_defaults_for_timestamp
-      basedir=/opt/bitnami/mariadb
+      basedir=/usr
+      datadir=/mariadb/data/
       port=3306
-      socket=/opt/bitnami/mariadb/tmp/mysql.sock
-      tmpdir=/opt/bitnami/mariadb/tmp
+      socket=/usr/tmp/mysqld.sock
+      tmpdir=/usr/tmp
       max_allowed_packet=16M
       bind-address=0.0.0.0
-      pid-file=/opt/bitnami/mariadb/tmp/mysqld.pid
-      log-error=/opt/bitnami/mariadb/logs/mysqld.log
+      pid-file=/usr/tmp/mysqld.pid
       character-set-server=utf8mb4
       collation-server=utf8mb4_general_ci
       optimizer_search_depth=0
       lower_case_table_names=1
       innodb_flush_log_at_trx_commit=0
+      log_bin_trust_function_creators=1
+      expire_logs_days=5
+      server-id=2
+      log-bin=mysql-bin
+      relay-log=mysql-relay-bin
 
       [client]
       port=3306
-      socket=/opt/bitnami/mariadb/tmp/mysql.sock
+      socket=/usr/tmp/mysqld.sock
 
       [manager]
       port=3306
-      socket=/opt/bitnami/mariadb/tmp/mysql.sock
-      pid-file=/opt/bitnami/mariadb/tmp/mysqld.pid
+      socket=/usr/tmp/mysqld.sock
+      pid-file=/usr/tmp/mysqld.pid

setup/core/common/codedx.ps1

@@ -167,15 +167,15 @@ function New-CodeDxDeploymentValuesFile([string] $codeDxDnsName,
 	$masterDatabaseTlsConfig = ''
 	if ('' -ne $dbMasterTlsSecretName) {
 		$masterDatabaseTlsConfig = @'
-      ssl_cert=/bitnami/mariadb/tls/cert/tls.crt
-      ssl_key=/bitnami/mariadb/tls/cert/tls.key
+      ssl_cert=/mariadb/tls/cert/tls.crt
+      ssl_key=/mariadb/tls/cert/tls.key
 '@
 	}
 
 	$masterDatabaseTlsCaConfig = ''
 	if ('' -ne $dbMasterTlsCaConfigMapName) {
 		$masterDatabaseTlsCaConfig = @'
-      ssl_ca=/bitnami/mariadb/tls/ca/ca.crt
+      ssl_ca=/mariadb/tls/ca/ca.crt
 '@
 	}
 
@@ -280,39 +280,45 @@ mariadb:
       size: {10}Gi
     config: |-
       [mysqld]
+      init_file=/docker-entrypoint-initdb.d/runalways-setup.sql
       skip-name-resolve
       explicit_defaults_for_timestamp
-      basedir=/opt/bitnami/mariadb
+      basedir=/usr
+      datadir=/mariadb/data/
       port=3306
-      socket=/opt/bitnami/mariadb/tmp/mysql.sock
-      tmpdir=/opt/bitnami/mariadb/tmp
+      socket=/usr/tmp/mysqld.sock
+      tmpdir=/usr/tmp
       max_allowed_packet=16M
       bind-address=0.0.0.0
-      pid-file=/opt/bitnami/mariadb/tmp/mysqld.pid
-      log-error=/opt/bitnami/mariadb/logs/mysqld.log
+      pid-file=/usr/tmp/mysqld.pid
       character-set-server=utf8mb4
       collation-server=utf8mb4_general_ci
       optimizer_search_depth=0
       lower_case_table_names=1
       innodb_flush_log_at_trx_commit=0
       log_bin_trust_function_creators=1
       expire_logs_days=5
+      server-id=1
+      log-bin=mysql-bin
 {50}
 {51}
 
       [client]
       port=3306
-      socket=/opt/bitnami/mariadb/tmp/mysql.sock
+      socket=/usr/tmp/mysqld.sock
 
       [manager]
       port=3306
-      socket=/opt/bitnami/mariadb/tmp/mysql.sock
-      pid-file=/opt/bitnami/mariadb/tmp/mysqld.pid
+      socket=/usr/tmp/mysqld.sock
+      pid-file=/usr/tmp/mysqld.pid
     annotations: {45}
     nodeSelector: {32}
     tolerations: {35}
 {19}
   slave:
+    extraEnvVars:
+      - name: MARIADB_ROOT_PASSWORD_FILE
+        value: /usr/secrets/mariadb-root-password
     replicas: {15}
     persistence:
       storageClass: {52}
@@ -323,31 +329,34 @@ mariadb:
       [mysqld]
       skip-name-resolve
       explicit_defaults_for_timestamp
-      basedir=/opt/bitnami/mariadb
+      basedir=/usr
+      datadir=/mariadb/data/
       port=3306
-      socket=/opt/bitnami/mariadb/tmp/mysql.sock
-      tmpdir=/opt/bitnami/mariadb/tmp
+      socket=/usr/tmp/mysqld.sock
+      tmpdir=/usr/tmp
       max_allowed_packet=16M
       bind-address=0.0.0.0
-      pid-file=/opt/bitnami/mariadb/tmp/mysqld.pid
-      log-error=/opt/bitnami/mariadb/logs/mysqld.log
+      pid-file=/usr/tmp/mysqld.pid
       character-set-server=utf8mb4
       collation-server=utf8mb4_general_ci
       optimizer_search_depth=0
       lower_case_table_names=1
       innodb_flush_log_at_trx_commit=0
       log_bin_trust_function_creators=1
       expire_logs_days=5
+      server-id=2
+      log-bin=mysql-bin
+      relay-log=mysql-relay-bin
 
       [client]
       port=3306
-      socket=/opt/bitnami/mariadb/tmp/mysql.sock
+      socket=/usr/tmp/mysqld.sock
 {51}
 
       [manager]
       port=3306
-      socket=/opt/bitnami/mariadb/tmp/mysql.sock
-      pid-file=/opt/bitnami/mariadb/tmp/mysqld.pid
+      socket=/usr/tmp/mysqld.sock
+      pid-file=/usr/tmp/mysqld.pid
     annotations: {46}
     nodeSelector: {33}
     tolerations: {36}

setup/core/common/mariadb.ps1

@@ -43,7 +43,7 @@ spec:
         command: ["/bin/bash"]
         args: ["-c", "/home/sdb/restore"]
         volumeMounts:
-        - mountPath: /bitnami/mariadb
+        - mountPath: /mariadb
           name: data
         - mountPath: /home/sdb/cfg
           name: rootpwd

setup/core/common/velero.ps1

@@ -86,7 +86,7 @@ spec:
             command:
             - /bin/bash
             - -c
-            - /bitnami/mariadb/scripts/backup.sh && sleep {1}
+            - /mariadb/scripts/backup.sh && sleep {1}
             timeout: '{2}'
 '@ -f 	$codeDxNamespace, `
 		$backupLagTime, `

setup/core/setup.ps1

@@ -1,5 +1,5 @@
 <#PSScriptInfo
-.VERSION 2.17.1
+.VERSION 2.18.0
 .GUID 47733b28-676e-455d-b7e8-88362f442aa3
 .AUTHOR Black Duck
 .COPYRIGHT Copyright 2024 Black Duck Software, Inc. All rights reserved.
@@ -47,7 +47,7 @@ param (
 	[string]                 $minioCPUReservation,
 	[string]                 $workflowCPUReservation,
 
-	[string]                 $codeDxEphemeralStorageReservation = '2868Mi',
+	[string]                 $codeDxEphemeralStorageReservation = '3368Mi',
 	[string]                 $dbMasterEphemeralStorageReservation,
 	[string]                 $dbSlaveEphemeralStorageReservation,
 	[string]                 $toolServiceEphemeralStorageReservation,
@@ -66,7 +66,7 @@ param (
 	[string]                 $imagePreDelete          = 'codedx/codedx-cleanup:v1.34.0',
 
 	[string]                 $imageCodeDxTomcatInit   = 'codedx/codedx-tomcat:v2026.3.2',
-	[string]                 $imageMariaDB            = 'codedx/codedx-mariadb:v1.38.0',
+	[string]                 $imageMariaDB            = 'codedx/codedx-mariadb:v1.41.0',
 	[string]                 $imageMinio              = 'bitnami/minio:2021.4.6-debian-10-r11',
 	[string]                 $imageWorkflowController = 'codedx/codedx-workflow-controller:v2.18.0',
 	[string]                 $imageWorkflowExecutor   = 'codedx/codedx-argoexec:v2.18.0',
@@ -178,6 +178,7 @@ param (
 	[Tuple`2[string,string]] $toolNoScheduleExecuteToleration,
 
 	[switch]                 $pauseAfterGitClone,
+	[switch]                 $skipGitClone,
 
 	[switch]                 $useHelmOperator,
 	[switch]                 $useHelmController,
@@ -606,9 +607,15 @@ $repoDirectory,$oldRepoDirectory | ForEach-Object {
 	}
 }
 
-Invoke-GitClone $codedxGitRepo $codedxGitRepoBranch $repoDirectory
-if ($pauseAfterGitClone) {
-	Read-Host -Prompt 'git clone complete, press Enter to continue...' | Out-Null
+if ($skipGitClone) {
+	$localRepoRoot = join-path $PSScriptRoot '../..'
+	Write-Verbose "Copying local repo from $localRepoRoot to $repoDirectory..."
+	Copy-Item -Path $localRepoRoot -Destination $repoDirectory -Recurse -Force
+} else {
+	Invoke-GitClone $codedxGitRepo $codedxGitRepoBranch $repoDirectory
+	if ($pauseAfterGitClone) {
+		Read-Host -Prompt 'git clone complete, press Enter to continue...' | Out-Null
+	}
 }
 
 $defaultHelmRepo = 'https://codedx.github.io/codedx-kubernetes'

setup/steps/ephemeralstorage.ps1

@@ -162,7 +162,7 @@ class CodeDxEphemeralStorage : EphemeralStorageStep {
 	}
 
 	[string]GetDefault() {
-		return '2868Mi'
+		return '3368Mi'
 	}
 }