Merge 8706b0e into b7fd8d4

src/main/resources/org/broadinstitute/dsde/sam/liquibase/changesets/initial_schema.xml

@@ -37,7 +37,7 @@
 
     <changeSet logicalFilePath="dummy" author="dvoet" id="user_table">
         <createTable tableName="SAM_USER">
-            <column autoIncrement="true" name="id" type="BIGINT">
+            <column name="id" type="VARCHAR">
                 <constraints primaryKey="true"/>
             </column>
             <column name="email" type="VARCHAR">
@@ -51,7 +51,7 @@
 
     <changeSet logicalFilePath="dummy" author="dvoet" id="pet_service_account_table">
         <createTable tableName="SAM_PET_SERVICE_ACCOUNT">
-            <column name="user_id" type="BIGINT">
+            <column name="user_id" type="VARCHAR">
                 <constraints primaryKey="true" foreignKeyName="FK_SPSA_USER" referencedTableName="SAM_USER" referencedColumnNames="id"/>
             </column>
             <column name="project" type="VARCHAR">
@@ -77,7 +77,7 @@
             <column name="member_group_id" type="BIGINT">
                 <constraints foreignKeyName="FK_SGM_MEMBER_GROUP" referencedTableName="SAM_GROUP" referencedColumnNames="id"/>
             </column>
-            <column name="member_user_id" type="BIGINT">
+            <column name="member_user_id" type="VARCHAR">
                 <constraints foreignKeyName="FK_SGM_MEMBER_USER" referencedTableName="SAM_USER" referencedColumnNames="id"/>
             </column>
         </createTable>

src/main/scala/org/broadinstitute/dsde/workbench/sam/db/DatabaseKey.scala

@@ -0,0 +1,7 @@
+package org.broadinstitute.dsde.workbench.sam.db
+
+trait DatabaseKey {
+  val value: Long
+
+  override def toString: String = value.toString
+}

src/main/scala/org/broadinstitute/dsde/workbench/sam/db/DbReference.scala

@@ -43,7 +43,7 @@ object DbReference extends LazyLogging {
     }
   }
 
-  private def init(liquibaseConfig: LiquibaseConfig): DbReference = {
+  def init(liquibaseConfig: LiquibaseConfig): DbReference = {
     DBs.setupAll()
     if (liquibaseConfig.initWithLiquibase)
       initWithLiquibase(liquibaseConfig)
@@ -57,7 +57,6 @@ object DbReference extends LazyLogging {
 }
 
 case class DbReference() {
-
   def inReadOnlyTransaction[A](f: DBSession => A): A = {
     DB.readOnly[A] { implicit session =>
       f(session)

src/main/scala/org/broadinstitute/dsde/workbench/sam/db/SamParameterBinderFactory.scala

@@ -0,0 +1,14 @@
+package org.broadinstitute.dsde.workbench.sam.db
+
+import org.broadinstitute.dsde.workbench.model.ValueObject
+import scalikejdbc.ParameterBinderFactory
+
+object SamParameterBinderFactory {
+  implicit def databaseKeyPbf[T <: DatabaseKey]: ParameterBinderFactory[T] = ParameterBinderFactory[T] {
+    value => (stmt, idx) => stmt.setLong(idx, value.value)
+  }
+
+  implicit def valueObjectPbf[T <: ValueObject]: ParameterBinderFactory[T] = ParameterBinderFactory[T] {
+    value => (stmt, idx) => stmt.setString(idx, value.value)
+  }
+}

src/main/scala/org/broadinstitute/dsde/workbench/sam/db/SamTypeBinders.scala

@@ -0,0 +1,111 @@
+package org.broadinstitute.dsde.workbench.sam.db
+
+import java.sql.ResultSet
+
+import org.broadinstitute.dsde.workbench.model.google.GoogleProject
+import org.broadinstitute.dsde.workbench.model.{GoogleSubjectId, WorkbenchEmail, WorkbenchGroupName, WorkbenchUserId}
+import org.broadinstitute.dsde.workbench.sam.db.tables._
+import org.broadinstitute.dsde.workbench.sam.model._
+import scalikejdbc.TypeBinder
+
+object SamTypeBinders {
+  implicit val accessInstructionsPKTypeBinder: TypeBinder[AccessInstructionsPK] = new TypeBinder[AccessInstructionsPK] {
+    def apply(rs: ResultSet, label: String): AccessInstructionsPK = AccessInstructionsPK(rs.getLong(label))
+    def apply(rs: ResultSet, index: Int): AccessInstructionsPK = AccessInstructionsPK(rs.getLong(index))
+  }
+
+  implicit val groupMemberPKTypeBinder: TypeBinder[GroupMemberPK] = new TypeBinder[GroupMemberPK] {
+    def apply(rs: ResultSet, label: String): GroupMemberPK = GroupMemberPK(rs.getLong(label))
+    def apply(rs: ResultSet, index: Int): GroupMemberPK = GroupMemberPK(rs.getLong(index))
+  }
+
+  implicit val groupPKTypeBinder: TypeBinder[GroupPK] = new TypeBinder[GroupPK] {
+    def apply(rs: ResultSet, label: String): GroupPK = GroupPK(rs.getLong(label))
+    def apply(rs: ResultSet, index: Int): GroupPK = GroupPK(rs.getLong(index))
+  }
+
+  implicit val policyPKTypeBinder: TypeBinder[PolicyPK] = new TypeBinder[PolicyPK] {
+    def apply(rs: ResultSet, label: String): PolicyPK = PolicyPK(rs.getLong(label))
+    def apply(rs: ResultSet, index: Int): PolicyPK = PolicyPK(rs.getLong(index))
+  }
+
+  implicit val policyNameTypeBinder: TypeBinder[AccessPolicyName] = new TypeBinder[AccessPolicyName] {
+    def apply(rs: ResultSet, label: String): AccessPolicyName = AccessPolicyName(rs.getString(label))
+    def apply(rs: ResultSet, index: Int): AccessPolicyName = AccessPolicyName(rs.getString(index))
+  }
+
+  implicit val resourceActionPatternPKTypeBinder: TypeBinder[ResourceActionPatternPK] = new TypeBinder[ResourceActionPatternPK] {
+    def apply(rs: ResultSet, label: String): ResourceActionPatternPK = ResourceActionPatternPK(rs.getLong(label))
+    def apply(rs: ResultSet, index: Int): ResourceActionPatternPK = ResourceActionPatternPK(rs.getLong(index))
+  }
+
+  implicit val resourceActionPatternNameTypeBinder: TypeBinder[ResourceActionPatternName] = new TypeBinder[ResourceActionPatternName] {
+    def apply(rs: ResultSet, label: String): ResourceActionPatternName = ResourceActionPatternName(rs.getString(label))
+    def apply(rs: ResultSet, index: Int): ResourceActionPatternName = ResourceActionPatternName(rs.getString(index))
+  }
+
+  implicit val resourceActionPKTypeBinder: TypeBinder[ResourceActionPK] = new TypeBinder[ResourceActionPK] {
+    def apply(rs: ResultSet, label: String): ResourceActionPK = ResourceActionPK(rs.getLong(label))
+    def apply(rs: ResultSet, index: Int): ResourceActionPK = ResourceActionPK(rs.getLong(index))
+  }
+
+  implicit val resourceActionNameTypeBinder: TypeBinder[ResourceAction] = new TypeBinder[ResourceAction] {
+    def apply(rs: ResultSet, label: String): ResourceAction = ResourceAction(rs.getString(label))
+    def apply(rs: ResultSet, index: Int): ResourceAction = ResourceAction(rs.getString(index))
+  }
+
+  implicit val resourceRolePKTypeBinder: TypeBinder[ResourceRolePK] = new TypeBinder[ResourceRolePK] {
+    def apply(rs: ResultSet, label: String): ResourceRolePK = ResourceRolePK(rs.getLong(label))
+    def apply(rs: ResultSet, index: Int): ResourceRolePK = ResourceRolePK(rs.getLong(index))
+  }
+
+  implicit val resourceRoleNameTypeBinder: TypeBinder[ResourceRoleName] = new TypeBinder[ResourceRoleName] {
+    def apply(rs: ResultSet, label: String): ResourceRoleName = ResourceRoleName(rs.getString(label))
+    def apply(rs: ResultSet, index: Int): ResourceRoleName = ResourceRoleName(rs.getString(index))
+  }
+
+  implicit val resourcePKTypeBinder: TypeBinder[ResourcePK] = new TypeBinder[ResourcePK] {
+    def apply(rs: ResultSet, label: String): ResourcePK = ResourcePK(rs.getLong(label))
+    def apply(rs: ResultSet, index: Int): ResourcePK = ResourcePK(rs.getLong(index))
+  }
+
+  implicit val resourceIdTypeBinder: TypeBinder[ResourceId] = new TypeBinder[ResourceId] {
+    def apply(rs: ResultSet, label: String): ResourceId = ResourceId(rs.getString(label))
+    def apply(rs: ResultSet, index: Int): ResourceId = ResourceId(rs.getString(index))
+  }
+
+  implicit val resourceTypePKTypeBinder: TypeBinder[ResourceTypePK] = new TypeBinder[ResourceTypePK] {
+    def apply(rs: ResultSet, label: String): ResourceTypePK = ResourceTypePK(rs.getLong(label))
+    def apply(rs: ResultSet, index: Int): ResourceTypePK = ResourceTypePK(rs.getLong(index))
+  }
+
+  implicit val resourceTypeNameTypeBinder: TypeBinder[ResourceTypeName] = new TypeBinder[ResourceTypeName] {
+    def apply(rs: ResultSet, label: String): ResourceTypeName = ResourceTypeName(rs.getString(label))
+    def apply(rs: ResultSet, index: Int): ResourceTypeName = ResourceTypeName(rs.getString(index))
+  }
+
+  implicit val workbenchGroupNameTypeBinder: TypeBinder[WorkbenchGroupName] = new TypeBinder[WorkbenchGroupName] {
+    def apply(rs: ResultSet, label: String): WorkbenchGroupName = WorkbenchGroupName(rs.getString(label))
+    def apply(rs: ResultSet, index: Int): WorkbenchGroupName = WorkbenchGroupName(rs.getString(index))
+  }
+
+  implicit val workbenchEmailTypeBinder: TypeBinder[WorkbenchEmail] = new TypeBinder[WorkbenchEmail] {
+    def apply(rs: ResultSet, label: String): WorkbenchEmail = WorkbenchEmail(rs.getString(label))
+    def apply(rs: ResultSet, index: Int): WorkbenchEmail = WorkbenchEmail(rs.getString(index))
+  }
+
+  implicit val googleProjectTypeBinder: TypeBinder[GoogleProject] = new TypeBinder[GoogleProject] {
+    def apply(rs: ResultSet, label: String): GoogleProject = GoogleProject(rs.getString(label))
+    def apply(rs: ResultSet, index: Int): GoogleProject = GoogleProject(rs.getString(index))
+  }
+
+  implicit val googleSubjectIdTypeBinder: TypeBinder[GoogleSubjectId] = new TypeBinder[GoogleSubjectId] {
+    def apply(rs: ResultSet, label: String): GoogleSubjectId = GoogleSubjectId(rs.getString(label))
+    def apply(rs: ResultSet, index: Int): GoogleSubjectId = GoogleSubjectId(rs.getString(index))
+  }
+
+  implicit val workbenchUserIdTypeBinder: TypeBinder[WorkbenchUserId] = new TypeBinder[WorkbenchUserId] {
+    def apply(rs: ResultSet, label: String): WorkbenchUserId = WorkbenchUserId(rs.getString(label))
+    def apply(rs: ResultSet, index: Int): WorkbenchUserId = WorkbenchUserId(rs.getString(index))
+  }
+}

src/main/scala/org/broadinstitute/dsde/workbench/sam/db/tables/AccessInstructionsTable.scala

@@ -0,0 +1,20 @@
+package org.broadinstitute.dsde.workbench.sam.db.tables
+
+import org.broadinstitute.dsde.workbench.sam.db.{DatabaseKey, SamTypeBinders}
+import scalikejdbc._
+
+final case class AccessInstructionsPK(value: Long) extends DatabaseKey
+final case class AccessInstructionsRecord(id: AccessInstructionsPK,
+                                          groupId: GroupPK,
+                                          instructions: String)
+
+object AccessInstructionsTable extends SQLSyntaxSupport[AccessInstructionsRecord] {
+  override def tableName: String = "SAM_ACCESS_INSTRUCTIONS"
+
+  import SamTypeBinders._
+  def apply(e: ResultName[AccessInstructionsRecord])(rs: WrappedResultSet): AccessInstructionsRecord = AccessInstructionsRecord(
+    rs.get(e.id),
+    rs.get(e.groupId),
+    rs.get(e.instructions)
+  )
+}

src/main/scala/org/broadinstitute/dsde/workbench/sam/db/tables/AuthDomainTable.scala

@@ -0,0 +1,17 @@
+package org.broadinstitute.dsde.workbench.sam.db.tables
+
+import scalikejdbc._
+import org.broadinstitute.dsde.workbench.sam.db.SamTypeBinders
+
+final case class AuthDomainRecord(resourceId: ResourcePK,
+                                  groupId: GroupPK)
+
+object AuthDomainTable extends SQLSyntaxSupport[AuthDomainRecord] {
+  override def tableName: String = "SAM_RESOURCE_AUTH_DOMAIN"
+
+  import SamTypeBinders._
+  def apply(e: ResultName[AuthDomainRecord])(rs: WrappedResultSet): AuthDomainRecord = AuthDomainRecord(
+    rs.get(e.resourceId),
+    rs.get(e.groupId)
+  )
+}

src/main/scala/org/broadinstitute/dsde/workbench/sam/db/tables/GroupMemberTable.scala

@@ -0,0 +1,28 @@
+package org.broadinstitute.dsde.workbench.sam.db.tables
+
+import org.broadinstitute.dsde.workbench.model.WorkbenchUserId
+import org.broadinstitute.dsde.workbench.sam.db.{DatabaseKey, SamTypeBinders}
+import scalikejdbc._
+
+final case class GroupMemberPK(value: Long) extends DatabaseKey
+final case class GroupMemberRecord(id: GroupMemberPK,
+                                   groupId: GroupPK,
+                                   memberUserId: Option[WorkbenchUserId],
+                                   memberGroupId: Option[GroupPK])
+
+object GroupMemberTable extends SQLSyntaxSupport[GroupMemberRecord] {
+  override def tableName: String = "SAM_GROUP_MEMBER"
+
+  import SamTypeBinders._
+  def apply(e: ResultName[GroupMemberRecord])(rs: WrappedResultSet): GroupMemberRecord = GroupMemberRecord(
+    rs.get(e.id),
+    rs.get(e.groupId),
+    rs.get(e.memberUserId),
+    rs.get(e.memberGroupId)
+  )
+
+  def apply(m: SyntaxProvider[GroupMemberRecord])(rs: WrappedResultSet): GroupMemberRecord = apply(m.resultName)(rs)
+
+  def opt(m: SyntaxProvider[GroupMemberRecord])(rs: WrappedResultSet): Option[GroupMemberRecord] =
+    rs.longOpt(m.resultName.id).map(_ => GroupMemberTable(m)(rs))
+}

src/main/scala/org/broadinstitute/dsde/workbench/sam/db/tables/GroupTable.scala

@@ -0,0 +1,32 @@
+package org.broadinstitute.dsde.workbench.sam.db.tables
+
+import java.time.Instant
+
+import org.broadinstitute.dsde.workbench.model.{WorkbenchEmail, WorkbenchGroupName}
+import org.broadinstitute.dsde.workbench.sam.db.{DatabaseKey, SamTypeBinders}
+import scalikejdbc._
+
+final case class GroupPK(value: Long) extends DatabaseKey
+final case class GroupRecord(id: GroupPK,
+                             name: WorkbenchGroupName,
+                             email: WorkbenchEmail,
+                             updatedDate: Option[Instant],
+                             synchronizedDate: Option[Instant])
+
+object GroupTable extends SQLSyntaxSupport[GroupRecord] {
+  override def tableName: String = "SAM_GROUP"
+
+  import SamTypeBinders._
+  def apply(e: ResultName[GroupRecord])(rs: WrappedResultSet): GroupRecord = GroupRecord(
+    rs.get(e.id),
+    rs.get(e.name),
+    rs.get(e.email),
+    rs.get(e.updatedDate),
+    rs.get(e.synchronizedDate)
+  )
+
+  def apply(o: SyntaxProvider[GroupRecord])(rs: WrappedResultSet): GroupRecord = apply(o.resultName)(rs)
+
+  def opt(m: SyntaxProvider[GroupRecord])(rs: WrappedResultSet): Option[GroupRecord] =
+    rs.longOpt(m.resultName.id).map(_ => GroupTable(m)(rs))
+}

src/main/scala/org/broadinstitute/dsde/workbench/sam/db/tables/PetServiceAccountTable.scala

@@ -0,0 +1,23 @@
+package org.broadinstitute.dsde.workbench.sam.db.tables
+
+import org.broadinstitute.dsde.workbench.model.google.GoogleProject
+import org.broadinstitute.dsde.workbench.model.{GoogleSubjectId, WorkbenchEmail, WorkbenchUserId}
+import org.broadinstitute.dsde.workbench.sam.db.SamTypeBinders
+import scalikejdbc._
+
+final case class PetServiceAccountRecord(userId: WorkbenchUserId,
+                                         project: GoogleProject,
+                                         googleSubjectId: GoogleSubjectId,
+                                         email: WorkbenchEmail)
+
+object PetServiceAccountTable extends SQLSyntaxSupport[PetServiceAccountRecord] {
+  override def tableName: String = "SAM_PET_SERVICE_ACCOUNT"
+
+  import SamTypeBinders._
+  def apply(e: ResultName[PetServiceAccountRecord])(rs: WrappedResultSet): PetServiceAccountRecord = PetServiceAccountRecord(
+    rs.get(e.userId),
+    rs.get(e.project),
+    rs.get(e.googleSubjectId),
+    rs.get(e.email)
+  )
+}

src/main/scala/org/broadinstitute/dsde/workbench/sam/db/tables/PolicyActionTable.scala

@@ -0,0 +1,17 @@
+package org.broadinstitute.dsde.workbench.sam.db.tables
+
+import scalikejdbc._
+import org.broadinstitute.dsde.workbench.sam.db.SamTypeBinders
+
+final case class PolicyActionRecord(policyId: PolicyPK,
+                                    actionId: ResourceActionPK)
+
+object PolicyActionTable extends SQLSyntaxSupport[PolicyActionRecord] {
+  override def tableName: String = "SAM_POLICY_ACTION"
+
+  import SamTypeBinders._
+  def apply(e: ResultName[PolicyActionRecord])(rs: WrappedResultSet): PolicyActionRecord = PolicyActionRecord(
+    rs.get(e.policyId),
+    rs.get(e.actionId)
+  )
+}

src/main/scala/org/broadinstitute/dsde/workbench/sam/db/tables/PolicyRoleTable.scala

@@ -0,0 +1,17 @@
+package org.broadinstitute.dsde.workbench.sam.db.tables
+
+import scalikejdbc._
+import org.broadinstitute.dsde.workbench.sam.db.SamTypeBinders
+
+final case class PolicyRoleRecord(policyId: PolicyPK,
+                                  roleId: ResourceRolePK)
+
+object PolicyRoleTable extends SQLSyntaxSupport[PolicyRoleRecord] {
+  override def tableName: String = "SAM_POLICY_ROLE"
+
+  import SamTypeBinders._
+  def apply(e: ResultName[PolicyRoleRecord])(rs: WrappedResultSet): PolicyRoleRecord = PolicyRoleRecord(
+    rs.get(e.policyId),
+    rs.get(e.roleId)
+  )
+}

src/main/scala/org/broadinstitute/dsde/workbench/sam/db/tables/PolicyTable.scala

@@ -0,0 +1,23 @@
+package org.broadinstitute.dsde.workbench.sam.db.tables
+
+import org.broadinstitute.dsde.workbench.sam.db.{DatabaseKey, SamTypeBinders}
+import org.broadinstitute.dsde.workbench.sam.model.AccessPolicyName
+import scalikejdbc._
+
+final case class PolicyPK(value: Long) extends DatabaseKey
+final case class PolicyRecord(id: PolicyPK,
+                              resourceId: ResourcePK,
+                              groupId: GroupPK,
+                              name: AccessPolicyName)
+
+object PolicyTable extends SQLSyntaxSupport[PolicyRecord] {
+  override def tableName: String = "SAM_RESOURCE_POLICY"
+
+  import SamTypeBinders._
+  def apply(e: ResultName[PolicyRecord])(rs: WrappedResultSet): PolicyRecord = PolicyRecord(
+    rs.get(e.id),
+    rs.get(e.resourceId),
+    rs.get(e.groupId),
+    rs.get(e.name)
+  )
+}

src/main/scala/org/broadinstitute/dsde/workbench/sam/db/tables/ResourceActionPatternTable.scala

@@ -0,0 +1,22 @@
+package org.broadinstitute.dsde.workbench.sam.db.tables
+
+import org.broadinstitute.dsde.workbench.model.ValueObject
+import org.broadinstitute.dsde.workbench.sam.db.{DatabaseKey, SamTypeBinders}
+import scalikejdbc._
+
+final case class ResourceActionPatternPK(value: Long) extends DatabaseKey
+final case class ResourceActionPatternName(value: String) extends ValueObject
+final case class ResourceActionPatternRecord(id: ResourceActionPatternPK,
+                                             resourceTypeId: ResourceTypePK,
+                                             actionPattern: ResourceActionPatternName)
+
+object ResourceActionPatternTable extends SQLSyntaxSupport[ResourceActionPatternRecord] {
+  override def tableName: String = "SAM_ACTION_PATTERN"
+
+  import SamTypeBinders._
+  def apply(e: ResultName[ResourceActionPatternRecord])(rs: WrappedResultSet): ResourceActionPatternRecord = ResourceActionPatternRecord(
+    rs.get(e.id),
+    rs.get(e.resourceTypeId),
+    rs.get(e.actionPattern)
+  )
+}