[AN-256] Update mysql version to 8.0 for unit test and local leo (#4802)

DataBiosphere · Nov 22, 2024 · eac42c2 · eac42c2
1 parent 7bb0c3b
commit eac42c2
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Showing 10 changed files with 18 additions and 25 deletions.
diff --git a/.github/workflows/unit_test.yml b/.github/workflows/unit_test.yml
@@ -21,7 +21,7 @@ jobs:
 
     services:
       mysql:
-        image: mysql/mysql-server:5.6
+        image: mysql/mysql-server:8.0
         env:
           MYSQL_ROOT_PASSWORD: leonardo-test
           MYSQL_USER: leonardo-test

diff --git a/docker/run-mysql.sh b/docker/run-mysql.sh
@@ -1,7 +1,7 @@
 #!/usr/bin/env bash
 
-# The CloudSQL console simply states "MySQL 5.6" so we may not match the minor version number
-MYSQL_VERSION=5.6
+# The CloudSQL console simply states "MySQL 8.0" so we may not match the minor version number
+MYSQL_VERSION=8.0
 start() {
 
     echo "attempting to remove old $CONTAINER container..."

diff --git a/...ute/dsde/workbench/leonardo/liquibase/changesets/20170901_cluster-createdDate-default.xml b/...ute/dsde/workbench/leonardo/liquibase/changesets/20170901_cluster-createdDate-default.xml
@@ -2,6 +2,6 @@
 <databaseChangeLog logicalFilePath="leonardo" xmlns="http://www.liquibase.org/xml/ns/dbchangelog" xmlns:ext="http://www.liquibase.org/xml/ns/dbchangelog-ext" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.liquibase.org/xml/ns/dbchangelog-ext http://www.liquibase.org/xml/ns/dbchangelog/dbchangelog-ext.xsd http://www.liquibase.org/xml/ns/dbchangelog http://www.liquibase.org/xml/ns/dbchangelog/dbchangelog-3.4.xsd">
     <changeSet logicalFilePath="leonardo" author="kumra" id="cluster-createdDate-default">
         <sql dbms="mysql">ALTER TABLE  CLUSTER
-            CHANGE createdDate createdDate TIMESTAMP(6) NOT NULL DEFAULT 0</sql>
+            CHANGE createdDate createdDate TIMESTAMP(6) NOT NULL DEFAULT "1970-01-01 00:00:01.000000"</sql>
     </changeSet>
 </databaseChangeLog>
diff --git a/.../dsde/workbench/leonardo/liquibase/changesets/20171011_cluster_destroyedDate_not_null.xml b/.../dsde/workbench/leonardo/liquibase/changesets/20171011_cluster_destroyedDate_not_null.xml
@@ -1,13 +1,8 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <databaseChangeLog logicalFilePath="leonardo" xmlns="http://www.liquibase.org/xml/ns/dbchangelog" xmlns:ext="http://www.liquibase.org/xml/ns/dbchangelog-ext" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.liquibase.org/xml/ns/dbchangelog-ext http://www.liquibase.org/xml/ns/dbchangelog/dbchangelog-ext.xsd http://www.liquibase.org/xml/ns/dbchangelog http://www.liquibase.org/xml/ns/dbchangelog/dbchangelog-3.4.xsd">
     <changeSet logicalFilePath="leonardo" author="vkumra" id="cluster_destroyeddate_not_null">
-        <addNotNullConstraint columnDataType="TIMESTAMP(6)"
-                              columnName="destroyedDate"
-                              defaultNullValue="1970-01-01 00:00:01.000000"
-                              tableName="CLUSTER"/>
-        <addDefaultValue columnDataType="TIMESTAMP(6)"
-                         columnName="destroyedDate"
-                         defaultValue="1970-01-01 00:00:01.000000"
-                         tableName="CLUSTER"/>
+        <sql>
+            ALTER TABLE CLUSTER MODIFY COLUMN destroyedDate TIMESTAMP(6) NOT NULL DEFAULT '1970-01-01 00:00:01.000000';
+        </sql>
     </changeSet>
 </databaseChangeLog>
diff --git a/...dinstitute/dsde/workbench/leonardo/liquibase/changesets/20180515_cluster_dateaccessed.xml b/...dinstitute/dsde/workbench/leonardo/liquibase/changesets/20180515_cluster_dateaccessed.xml
@@ -13,8 +13,6 @@
     </changeSet>
 
     <changeSet id="make dateAccessed not null" author="vkumra">
-        <addNotNullConstraint columnDataType="TIMESTAMP(6)"
-                              columnName="dateAccessed"
-                              tableName="CLUSTER"/>
+        <sql>ALTER TABLE CLUSTER MODIFY COLUMN dateAccessed TIMESTAMP(6) NOT NULL DEFAULT '1970-01-01 00:00:01.000000'</sql>
     </changeSet>
 </databaseChangeLog>
diff --git a/...roadinstitute/dsde/workbench/leonardo/liquibase/changesets/20200501_kubernetes_tables.xml b/...roadinstitute/dsde/workbench/leonardo/liquibase/changesets/20200501_kubernetes_tables.xml
@@ -27,13 +27,13 @@
             <column name="creator" type="VARCHAR(254)">
                 <constraints nullable="false"/>
             </column>
-            <column name="createdDate" type="TIMESTAMP(6)" defaultValue="0000-00-00 00:00:00.000000">
+            <column name="createdDate" type="TIMESTAMP(6)" defaultValue="1970-01-01 00:00:01.000000">
                 <constraints nullable="false"/>
             </column>
             <column name="destroyedDate" type="TIMESTAMP(6)" defaultValue="1970-01-01 00:00:01.000000">
                 <constraints nullable="false"/>
             </column>
-            <column name="dateAccessed" type="TIMESTAMP(6)" defaultValue="0000-00-00 00:00:00.000000">
+            <column name="dateAccessed" type="TIMESTAMP(6)" defaultValue="1970-01-01 00:00:01.000000">
                 <constraints nullable="false"/>
             </column>
             <column name="apiServerIp" type="VARCHAR(254)"/>
@@ -61,13 +61,13 @@
             <column name="creator" type="VARCHAR(254)">
                 <constraints nullable="false"/>
             </column>
-            <column name="createdDate" type="TIMESTAMP(6)" defaultValue="0000-00-00 00:00:00.000000">
+            <column name="createdDate" type="TIMESTAMP(6)" defaultValue="1970-01-01 00:00:01.000000">
                 <constraints nullable="false"/>
             </column>
             <column name="destroyedDate" type="TIMESTAMP(6)" defaultValue="1970-01-01 00:00:01.000000">
                 <constraints nullable="false"/>
             </column>
-            <column name="dateAccessed" type="TIMESTAMP(6)" defaultValue="0000-00-00 00:00:00.000000">
+            <column name="dateAccessed" type="TIMESTAMP(6)" defaultValue="1970-01-01 00:00:01.000000">
                 <constraints nullable="false"/>
             </column>
             <column name="machineType" type="VARCHAR(254)">

diff --git a/...adinstitute/dsde/workbench/leonardo/liquibase/changesets/20200520_kubernetes_refactor.xml b/...adinstitute/dsde/workbench/leonardo/liquibase/changesets/20200520_kubernetes_refactor.xml
@@ -41,13 +41,13 @@
             <column name="creator" type="VARCHAR(254)">
                 <constraints nullable="false"/>
             </column>
-            <column name="createdDate" type="TIMESTAMP(6)" defaultValue="0000-00-00 00:00:00.000000">
+            <column name="createdDate" type="TIMESTAMP(6)" defaultValue="1970-01-01 00:00:01.000000">
                 <constraints nullable="false"/>
             </column>
             <column name="destroyedDate" type="TIMESTAMP(6)" defaultValue="1970-01-01 00:00:01.000000">
                 <constraints nullable="false"/>
             </column>
-            <column name="dateAccessed" type="TIMESTAMP(6)" defaultValue="0000-00-00 00:00:00.000000">
+            <column name="dateAccessed" type="TIMESTAMP(6)" defaultValue="1970-01-01 00:00:01.000000">
                 <constraints nullable="false"/>
             </column>
             <column name="namespaceId" type="BIGINT">

diff --git a/...nstitute/dsde/workbench/leonardo/liquibase/changesets/20230911_create_app_usage_table.xml b/...nstitute/dsde/workbench/leonardo/liquibase/changesets/20230911_create_app_usage_table.xml
@@ -8,7 +8,7 @@
             <column name="appId" type="BIGINT(20)">
                 <constraints nullable="false"/>
             </column>
-            <column name="startTime" type="TIMESTAMP(6)" defaultValue="0000-00-00 00:00:00.000000">
+            <column name="startTime" type="TIMESTAMP(6)" defaultValue="1970-01-01 00:00:01.000000">
                 <constraints nullable="false"/>
             </column>
             <column name="stopTime" type="TIMESTAMP(6)" defaultValue="1970-01-01 00:00:01.000000">

diff --git a/http/src/test/resources/reference.conf b/http/src/test/resources/reference.conf
@@ -5,7 +5,7 @@
 # -e MYSQL_USER=leonardo-test \
 # -e MYSQL_PASSWORD=leonardo-test \
 # -e MYSQL_DATABASE=leotestdb \
-# -d -p 3311:3306 mysql/mysql-server:5.6
+# -d -p 3311:3306 mysql/mysql-server:8.0
 
 application {
   leoGoogleProject = "leo-project"
@@ -37,7 +37,7 @@ mysql {
   port = 3311
   db {
     driver = "com.mysql.cj.jdbc.Driver"
-    url = "jdbc:mysql://"${mysql.host}":"${mysql.port}"/leotestdb?createDatabaseIfNotExist=true&useSSL=false&rewriteBatchedStatements=true&nullNamePatternMatchesAll=true"
+    url = "jdbc:mysql://"${mysql.host}":"${mysql.port}"/leotestdb?createDatabaseIfNotExist=true&&allowPublicKeyRetrieval=true&useSSL=false&rewriteBatchedStatements=true&nullNamePatternMatchesAll=true"
     user = "leonardo-test"
     password = "leonardo-test"
     connectionTimeout = "5 seconds"  // default of 1 sec sometimes too short for docker local mysql

diff --git a/leonardo-example.conf b/leonardo-example.conf
@@ -61,7 +61,7 @@ dataproc {
 # Database connection information
 mysql {
   db {
-    url = "jdbc:mysql://YOUR_DB_HOST/leonardo?requireSSL=true&useSSL=true&rewriteBatchedStatements=true&nullNamePatternMatchesAll=true"
+    url = "jdbc:mysql://YOUR_DB_HOST/leonardo?allowPublicKeyRetrieval=true&useSSL=false&rewriteBatchedStatements=true&nullNamePatternMatchesAll=true"
     user = "USER_NAME"
     password = "PASSWORD"
   }