DBMS updates

- MariaDB liquibase and tests.
- Re-synchronize PostgreSQL schema to other DBMS.
- Use client side datetime DATETIME(6) vs. server side TIMESTAMP.
- Test that the DBMS attribute is set on all changelogs.
- Test that the quoting strategy is set for PostgreSQL changelogs.
- Test that sequences have the same width as columns.
- Database tests by default run on all DBMS.
- Add tests to ensure schemas stay synced from now on.

build.sbt

@@ -259,6 +259,7 @@ lazy val engine = project
   .dependsOn(common % "test->test")
   .dependsOn(core % "test->test")
   .dependsOn(backend % "test->test")
+  .dependsOn(services % "test->test")
   // In the future we may have a dedicated test backend like the `TestLocalAsyncJobExecutionActor`.
   // For now, all the engine tests run on the "Local" backend, an implementation of an impl.sfs.config backend.
   .dependsOn(sfsBackend % "test->compile")

centaur/src/main/scala/centaur/CromwellConfiguration.scala

@@ -1,17 +1,19 @@
 package centaur
 
 import java.lang.ProcessBuilder.Redirect
+
 import better.files.File
+import com.typesafe.scalalogging.StrictLogging
 
-trait CromwellProcess {
+trait CromwellProcess extends StrictLogging {
   def logFile: String
-  def displayString: String
   def start(): Unit
   def stop(): Unit
   def isAlive: Boolean
   def cromwellConfiguration: CromwellConfiguration
 
   protected def runProcess(command: Array[String]): Process = {
+    logger.info(s"Running: ${command.mkString(" ")}")
     val processBuilder = new java.lang.ProcessBuilder()
       .command(command: _*)
       .redirectOutput(Redirect.appendTo(File(logFile).toJava))

centaur/src/main/scala/centaur/DockerComposeCromwellConfiguration.scala

@@ -32,8 +32,6 @@ case class DockerComposeCromwellConfiguration(dockerTag: String, dockerComposeFi
       private val stopCommand = composeCommand("down -v")
       private val rmCommand = composeCommand("rm -fsv")
 
-      override def displayString: String = startCommand.mkString(" ")
-
       private var process: Option[Process] = None
 
       override def start(): Unit = {

centaur/src/main/scala/centaur/JarCromwellConfiguration.scala

@@ -26,8 +26,6 @@ case class JarCromwellConfiguration(jar: String, conf: String, logFile: String)
 
       private var process: Option[Process] = None
 
-      override def displayString: String = command.mkString(" ")
-
       override def start(): Unit = {
         process = Option(runProcess(command))
       }

core/src/test/resources/application.conf

@@ -25,7 +25,7 @@ database-test-mysql {
   profile = "slick.jdbc.MySQLProfile$"
   db {
     driver = "com.mysql.cj.jdbc.Driver"
-    url = "jdbc:mysql://localhost:3306/cromwell_test?useSSL=false&rewriteBatchedStatements=true&serverTimezone=UTC"
+    url = "jdbc:mysql://localhost:3306/cromwell_test?useSSL=false&rewriteBatchedStatements=true&serverTimezone=UTC&useInformationSchema=true"
     url = ${?CROMWELL_BUILD_MYSQL_JDBC_URL}
     user = "cromwell"
     user = ${?CROMWELL_BUILD_MYSQL_USERNAME}
@@ -52,8 +52,8 @@ database-test-mariadb {
   # mysql --protocol=tcp -P13306 -ucromwell -ptest -e "DROP DATABASE IF EXISTS cromwell_test; CREATE DATABASE cromwell_test;"
   profile = "slick.jdbc.MySQLProfile$"
   db {
-    driver = "com.mysql.cj.jdbc.Driver"
-    url = "jdbc:mysql://localhost:13306/cromwell_test?useSSL=false&rewriteBatchedStatements=true&serverTimezone=UTC"
+    driver = "org.mariadb.jdbc.Driver"
+    url = "jdbc:mariadb://localhost:13306/cromwell_test?rewriteBatchedStatements=true"
     url = ${?CROMWELL_BUILD_MARIADB_JDBC_URL}
     user = "cromwell"
     user = ${?CROMWELL_BUILD_MARIADB_USERNAME}

database/migration/src/main/resources/changelog.xml

@@ -79,6 +79,8 @@
     <include file="changesets/enlarge_call_caching_hash_entry_id.xml" relativeToChangelogFile="true" />
     <include file="changesets/postgresql_engine_schema.xml" relativeToChangelogFile="true" />
     <include file="changesets/add_hog_group_in_workflow_store.xml" relativeToChangelogFile="true" />
+    <include file="changesets/mariadb_engine_schema.xml" relativeToChangelogFile="true" />
+    <include file="changesets/resync_engine_schema.xml" relativeToChangelogFile="true" />
     <!-- REMINDER!
       Before appending here, did you remember to include the 'objectQuotingStrategy="QUOTE_ALL_OBJECTS"' line in your changeset/xyz.xml...?
     -->

database/migration/src/main/resources/changesets/add_hog_group_in_workflow_store.xml

@@ -4,7 +4,7 @@
                    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                    xsi:schemaLocation="http://www.liquibase.org/xml/ns/dbchangelog http://www.liquibase.org/xml/ns/dbchangelog/dbchangelog-3.3.xsd">
 
-    <changeSet id="add_hog_group_in_workflow_store" author="cjllanwarne">
+    <changeSet id="add_hog_group_in_workflow_store" author="cjllanwarne" dbms="hsqldb,mysql,postgresql">
         <addColumn tableName="WORKFLOW_STORE_ENTRY">
             <column name="HOG_GROUP" type="VARCHAR(100)">
                 <constraints nullable="true" />