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[AN-257] Update mysql version to 5.7 (#4804)
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‎.github/workflows/unit_test.yml‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -21,7 +21,7 @@ jobs:
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services:
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mysql:
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image: mysql/mysql-server:5.6
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image: mysql:5.7
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env:
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MYSQL_ROOT_PASSWORD: leonardo-test
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MYSQL_USER: leonardo-test

‎docker/run-mysql.sh‎

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@@ -1,7 +1,7 @@
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#!/usr/bin/env bash
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3-
# The CloudSQL console simply states "MySQL 5.6" so we may not match the minor version number
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MYSQL_VERSION=5.6
3+
# The CloudSQL console simply states "MySQL 5.7" so we may not match the minor version number
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MYSQL_VERSION=5.7
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start() {
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echo "attempting to remove old $CONTAINER container..."
@@ -17,7 +17,7 @@ start() {
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-e MYSQL_DATABASE=leotestdb \
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-d \
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-p 3311:3306 \
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mysql/mysql-server:$MYSQL_VERSION
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mysql:$MYSQL_VERSION
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# validate mysql
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echo "running mysql validation..."

‎http/src/main/resources/org/broadinstitute/dsde/workbench/leonardo/liquibase/changesets/20170901_cluster-createdDate-default.xml‎

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@@ -1,7 +1,12 @@
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<?xml version="1.0" encoding="UTF-8" standalone="no"?>
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<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">
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<changeSet logicalFilePath="leonardo" author="kumra" id="cluster-createdDate-default">
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<validCheckSum>8:c1023fe139609a1cab82cda7caededc0</validCheckSum>
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<comment>
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Mysql 5.7+ cannot add a not null constraint with a default value simultaneously. This changeSet has been modified to reflect that; the
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validCheckSum is the checksum from when the table was not altered, but with addNotNullConstraint and addDefaultValue.
8+
</comment>
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<sql dbms="mysql">ALTER TABLE CLUSTER
5-
CHANGE createdDate createdDate TIMESTAMP(6) NOT NULL DEFAULT 0</sql>
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CHANGE createdDate createdDate TIMESTAMP(6) NOT NULL DEFAULT "1970-01-01 00:00:01.000000"</sql>
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</changeSet>
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</databaseChangeLog>

‎http/src/main/resources/org/broadinstitute/dsde/workbench/leonardo/liquibase/changesets/20171011_cluster_destroyedDate_not_null.xml‎

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@@ -1,13 +1,13 @@
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<?xml version="1.0" encoding="UTF-8" standalone="no"?>
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<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">
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<changeSet logicalFilePath="leonardo" author="vkumra" id="cluster_destroyeddate_not_null">
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<addNotNullConstraint columnDataType="TIMESTAMP(6)"
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columnName="destroyedDate"
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defaultNullValue="1970-01-01 00:00:01.000000"
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tableName="CLUSTER"/>
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<addDefaultValue columnDataType="TIMESTAMP(6)"
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columnName="destroyedDate"
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defaultValue="1970-01-01 00:00:01.000000"
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tableName="CLUSTER"/>
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<validCheckSum>8:29280ede1de44e4c3f2966c6922e9865</validCheckSum>
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<comment>
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Mysql 5.7+ changed default time stamps. This changeSet has been modified to reflect that; the
7+
validCheckSum is the checksum from when the default was 0.
8+
</comment>
9+
<sql>
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ALTER TABLE CLUSTER MODIFY COLUMN destroyedDate TIMESTAMP(6) NOT NULL DEFAULT '1970-01-01 00:00:01.000000';
11+
</sql>
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</changeSet>
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</databaseChangeLog>

‎http/src/main/resources/org/broadinstitute/dsde/workbench/leonardo/liquibase/changesets/20180515_cluster_dateaccessed.xml‎

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@@ -13,8 +13,11 @@
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</changeSet>
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<changeSet id="make dateAccessed not null" author="vkumra">
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<addNotNullConstraint columnDataType="TIMESTAMP(6)"
17-
columnName="dateAccessed"
18-
tableName="CLUSTER"/>
16+
<validCheckSum>8:5017000ff29d7873815c1bdb69895225</validCheckSum>
17+
<comment>
18+
Mysql 5.7+ cannot add a not null constraint with a default value simultaneously. This changeSet has been modified to reflect that; the
19+
validCheckSum is the checksum from when the table was not altered, but with addNotNullConstraint and addDefaultValue.
20+
</comment>
21+
<sql>ALTER TABLE CLUSTER MODIFY COLUMN dateAccessed TIMESTAMP(6) NOT NULL DEFAULT '1970-01-01 00:00:01.000000'</sql>
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</changeSet>
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</databaseChangeLog>

‎http/src/main/resources/org/broadinstitute/dsde/workbench/leonardo/liquibase/changesets/20200427_create_persistent_disk_table.xml‎

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@@ -1,6 +1,11 @@
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<?xml version="1.0" encoding="UTF-8" standalone="no"?>
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<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">
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<changeSet logicalFilePath="leonardo" author="rtitle" id="persistent-disk-table">
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<validCheckSum>8:6e2afa6af8c562abad1e253e74d79817</validCheckSum>
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<comment>
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Mysql 5.7+ changed default time stamps. This changeSet has been modified to reflect that; the
7+
validCheckSum is the checksum from when the default was not set.
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</comment>
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<createTable tableName="PERSISTENT_DISK">
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<column name="id" type="BIGINT" autoIncrement="true">
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<constraints primaryKey="true"/>
@@ -26,13 +31,13 @@
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<column name="creator" type="VARCHAR(255)">
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<constraints nullable="false"/>
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</column>
29-
<column name="createdDate" type="TIMESTAMP(6)">
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<column name="createdDate" type="TIMESTAMP(6)" defaultValue="1970-01-01 00:00:01.000000">
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<constraints nullable="false"/>
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</column>
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<column name="destroyedDate" type="TIMESTAMP(6)">
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<column name="destroyedDate" type="TIMESTAMP(6)" defaultValue="1970-01-01 00:00:01.000000">
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<constraints nullable="false"/>
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</column>
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<column name="dateAccessed" type="TIMESTAMP(6)">
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<column name="dateAccessed" type="TIMESTAMP(6)" defaultValue="1970-01-01 00:00:01.000000">
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<constraints nullable="false"/>
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</column>
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<column name="sizeGb" type="INT">

‎http/src/main/resources/org/broadinstitute/dsde/workbench/leonardo/liquibase/changesets/20200501_kubernetes_tables.xml‎

Lines changed: 14 additions & 4 deletions
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@@ -2,6 +2,11 @@
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<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">
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<changeSet logicalFilePath="leonardo" author="jcanas" id="kubernetes_cluster_table">
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<validCheckSum>8:599d13c602bc3a23e12dc577a848456f</validCheckSum>
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<comment>
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Mysql 5.7+ changed default time stamps. This changeSet has been modified to reflect that; the
8+
validCheckSum is the checksum from when the default was 0000-00-00 00:00:00.000000.
9+
</comment>
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<createTable tableName="KUBERNETES_CLUSTER">
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<column name="id" type="BIGINT" autoIncrement="true">
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<constraints primaryKey="true"/>
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<column name="creator" type="VARCHAR(254)">
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<constraints nullable="false"/>
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</column>
30-
<column name="createdDate" type="TIMESTAMP(6)" defaultValue="0000-00-00 00:00:00.000000">
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<column name="createdDate" type="TIMESTAMP(6)" defaultValue="1970-01-01 00:00:01.000000">
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<constraints nullable="false"/>
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</column>
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<column name="destroyedDate" type="TIMESTAMP(6)" defaultValue="1970-01-01 00:00:01.000000">
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<constraints nullable="false"/>
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</column>
36-
<column name="dateAccessed" type="TIMESTAMP(6)" defaultValue="0000-00-00 00:00:00.000000">
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<column name="dateAccessed" type="TIMESTAMP(6)" defaultValue="1970-01-01 00:00:01.000000">
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<constraints nullable="false"/>
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</column>
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<column name="apiServerIp" type="VARCHAR(254)"/>
@@ -45,6 +50,11 @@
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</changeSet>
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4752
<changeSet logicalFilePath="leonardo" id="nodepool_table" author="jcanas">
53+
<validCheckSum>8:854fccdae58bc9906a94269397f04ae3</validCheckSum>
54+
<comment>
55+
Mysql 5.7+ changed default time stamps. This changeSet has been modified to reflect that; the
56+
validCheckSum is the checksum from when the default was 0000-00-00 00:00:00.000000.
57+
</comment>
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<createTable tableName="NODEPOOL">
4959
<column name="id" type="BIGINT" autoIncrement="true">
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<constraints primaryKey="true"/>
@@ -61,13 +71,13 @@
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<column name="creator" type="VARCHAR(254)">
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<constraints nullable="false"/>
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</column>
64-
<column name="createdDate" type="TIMESTAMP(6)" defaultValue="0000-00-00 00:00:00.000000">
74+
<column name="createdDate" type="TIMESTAMP(6)" defaultValue="1970-01-01 00:00:01.000000">
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<constraints nullable="false"/>
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</column>
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<column name="destroyedDate" type="TIMESTAMP(6)" defaultValue="1970-01-01 00:00:01.000000">
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<constraints nullable="false"/>
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</column>
70-
<column name="dateAccessed" type="TIMESTAMP(6)" defaultValue="0000-00-00 00:00:00.000000">
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<column name="dateAccessed" type="TIMESTAMP(6)" defaultValue="1970-01-01 00:00:01.000000">
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<constraints nullable="false"/>
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</column>
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<column name="machineType" type="VARCHAR(254)">

‎http/src/main/resources/org/broadinstitute/dsde/workbench/leonardo/liquibase/changesets/20200520_kubernetes_refactor.xml‎

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@@ -19,6 +19,11 @@
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</changeSet>
2020

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<changeSet logicalFilePath="leonardo" id="kubernetes_add_app_tables" author="jcanas">
22+
<validCheckSum>8:a2cec6057088736af10dcdc3c2dd3091</validCheckSum>
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<comment>
24+
Mysql 5.7+ changed default time stamps. This changeSet has been modified to reflect that; the
25+
validCheckSum is the checksum from when the default was 0000-00-00 00:00:00.000000.
26+
</comment>
2227
<createTable tableName="APP">
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<column name="id" type="BIGINT" autoIncrement="true">
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<constraints primaryKey="true"/>
@@ -41,13 +46,13 @@
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<column name="creator" type="VARCHAR(254)">
4247
<constraints nullable="false"/>
4348
</column>
44-
<column name="createdDate" type="TIMESTAMP(6)" defaultValue="0000-00-00 00:00:00.000000">
49+
<column name="createdDate" type="TIMESTAMP(6)" defaultValue="1970-01-01 00:00:01.000000">
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<constraints nullable="false"/>
4651
</column>
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<column name="destroyedDate" type="TIMESTAMP(6)" defaultValue="1970-01-01 00:00:01.000000">
4853
<constraints nullable="false"/>
4954
</column>
50-
<column name="dateAccessed" type="TIMESTAMP(6)" defaultValue="0000-00-00 00:00:00.000000">
55+
<column name="dateAccessed" type="TIMESTAMP(6)" defaultValue="1970-01-01 00:00:01.000000">
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<constraints nullable="false"/>
5257
</column>
5358
<column name="namespaceId" type="BIGINT">

‎http/src/main/resources/org/broadinstitute/dsde/workbench/leonardo/liquibase/changesets/20230911_create_app_usage_table.xml‎

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<?xml version="1.0" encoding="UTF-8" standalone="no"?>
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<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">
33
<changeSet logicalFilePath="leonardo" author="qi" id="qi_create_app_usage_table">
4+
<validCheckSum>8:10d891c4c811215803753f8b060621be</validCheckSum>
5+
<comment>
6+
Mysql 5.7+ changed default time stamps. This changeSet has been modified to reflect that; the
7+
validCheckSum is the checksum from when the default was 0000-00-00 00:00:00.000000.
8+
</comment>
49
<createTable tableName="APP_USAGE">
510
<column name="id" type="BIGINT" autoIncrement="true">
611
<constraints primaryKey="true"/>
712
</column>
813
<column name="appId" type="BIGINT(20)">
914
<constraints nullable="false"/>
1015
</column>
11-
<column name="startTime" type="TIMESTAMP(6)" defaultValue="0000-00-00 00:00:00.000000">
16+
<column name="startTime" type="TIMESTAMP(6)" defaultValue="1970-01-01 00:00:01.000000">
1217
<constraints nullable="false"/>
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</column>
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<column name="stopTime" type="TIMESTAMP(6)" defaultValue="1970-01-01 00:00:01.000000">

‎http/src/test/resources/reference.conf‎

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@@ -37,7 +37,7 @@ mysql {
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port = 3311
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db {
3939
driver = "com.mysql.cj.jdbc.Driver"
40-
url = "jdbc:mysql://"${mysql.host}":"${mysql.port}"/leotestdb?createDatabaseIfNotExist=true&useSSL=false&rewriteBatchedStatements=true&nullNamePatternMatchesAll=true"
40+
url = "jdbc:mysql://"${mysql.host}":"${mysql.port}"/leotestdb?createDatabaseIfNotExist=true&allowPublicKeyRetrieval=true&useSSL=false&rewriteBatchedStatements=true&nullNamePatternMatchesAll=true"
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user = "leonardo-test"
4242
password = "leonardo-test"
4343
connectionTimeout = "5 seconds" // default of 1 sec sometimes too short for docker local mysql

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