Rework env (#833)

* more config - remove unused standard_db config option - replace all occurences of foo and bar - simplify tel/env folder structure * Refactor tel * rename classes and fix path * move env creation - has to be refactored at a later point * add missing imports * fix db path * build improvements * use sbt shell in docker image * play 2.7 (#812) * closes #808, closes #802, closes #803 (#810) * closes #808 * Cleaner solution for passing env variables * closes #802 * closes #803 * fix some play 2.7 migration issues (#813) * now pulled as webjar from npm * Closes #809 (#814) * closes #809 * Updated reformat submodule * akka 2.5.20 * sbt build improvements (#815) * extracted some bits to project/Settings.scala * removed unused dependencies * Setting version to 1.1.11 * Setting version to 1.1.12-SNAPSHOT * update scalatest (#822) * set next version * simplify json parsing code (#825) * add missing module name (#826) * remove Env * stop using a mutable map * use shared ivy cache * reformat imports * remove more occurrences of mutable map * remove unnecessary implicit * Remove scalafmt flag * fix hostname missing * remove unused imports * #824, db logic for jobs moved out of controllers
proteinevolution · Jun 18, 2019 · a0fd35e · a0fd35e
1 parent 37fd516
commit a0fd35e
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Showing 35 changed files with 128 additions and 397 deletions.
diff --git a/app/controllers/Application.scala b/app/controllers/Application.scala
@@ -20,7 +20,6 @@ import java.net.InetAddress
 
 import de.proteinevolution.auth.UserSessions
 import de.proteinevolution.base.controllers.ToolkitController
-import de.proteinevolution.tel.env.Env
 import de.proteinevolution.tools.ToolConfig
 import javax.inject.{ Inject, Singleton }
 import org.webjars.play.WebJarsUtil
@@ -35,7 +34,6 @@ final class Application @Inject()(
     toolConfig: ToolConfig,
     userSessions: UserSessions,
     cc: ControllerComponents,
-    env: Env,
     environment: Environment,
     assetsFinder: AssetsFinder,
     config: Configuration
@@ -44,7 +42,6 @@ final class Application @Inject()(
     with Logging {
 
   def index(message: String = ""): Action[AnyContent] = Action.async { implicit request =>
-    configEnv(request)
     userSessions.getUser.map { user =>
       logger.info(InetAddress.getLocalHost.getHostName + "\n" + user.toString)
       Ok(
@@ -79,20 +76,4 @@ final class Application @Inject()(
     )
   }
 
-  private def configEnv(request: Request[AnyContent]): Unit = {
-
-    env.configure(s"HOSTNAME", config.get[String]("host_name"))
-
-    environment.mode match {
-
-      case play.api.Mode.Prod =>
-        val port = "9000"
-        env.configure("PORT", port)
-
-      case _ =>
-        val port = request.host.slice(request.host.indexOf(":") + 1, request.host.length)
-        env.configure("PORT", port)
-    }
-  }
-
 }
diff --git a/app/modules/TELEnvProvider.scala b/app/modules/TELEnvProvider.scala
diff --git a/app/modules/TELModule.scala b/app/modules/TELModule.scala
@@ -17,15 +17,13 @@
 package modules
 
 import com.google.inject.AbstractModule
-import de.proteinevolution.tel.env.Env
 import de.proteinevolution.tel.param.Params
 import com.google.inject.name.Names
 import de.proteinevolution.tel.{ ParamCollectorProvider, RunscriptPathProvider, WrapperPathProvider }
 
 class TELModule extends AbstractModule {
 
   override def configure(): Unit = {
-    bind(classOf[Env]).toProvider(classOf[TELEnvProvider]).asEagerSingleton()
     bind(classOf[Params]).toProvider(classOf[ParamCollectorProvider]).asEagerSingleton()
     bind(classOf[String])
       .annotatedWith(Names.named("runscriptPath"))

diff --git a/build.sbt b/build.sbt
@@ -211,6 +211,7 @@ javaOptions += "-Dplay.editor=http://localhost:63342/api/file/?file=%s&line=%s"
 fork in Test := true
 logLevel in Test := Level.Info
 
+
 scalacOptions in Test ++= Seq("-Yrangepos")
 testOptions in Test += Tests.Argument(TestFrameworks.ScalaTest, "-oD")
 JsEngineKeys.engineType := JsEngineKeys.EngineType.Node

diff --git a/conf/application.conf b/conf/application.conf
@@ -5,6 +5,8 @@ include "blacklist"
 #Name of the node where the Toolkit is running
 host_name = "olt"
 host_name = ${?CONFIGURED_HOSTNAME} # beware that $HOSTNAME is a shell variable and cannot be directly used
+port = 1234
+port = ${?CONFIGURED_PORT}
 
 akka {
   jvm-exit-on-fatal-error = false
@@ -140,6 +142,8 @@ play.mailer {
   tls = ${?MAIL_TLS}
   user = ${?MAIL_USER}
   password = ${?MAIL_PWD}
+  # custom attribute
+  template_host = "http://localhost:1234"
 }
 
 play.application.loader = ToolkitAppLoader
@@ -149,11 +153,11 @@ play.allowGlobalApplication = true
 ####################################################################################
 
 # geoIP
-maxmind_db = "/root/GeoLite2-City.mmdb"
+maxmind_db = "/root/data/GeoLite2-City.mmdb"
 maxmind_db = ${?MAXMIND_DB}
 
 # mongo address with auth for local docker
-mongodb.uri = "mongodb://root:rootPassXX@174.18.0.3:27017/tkplay_dev?authenticationDatabase=admin"
+mongodb.uri = "mongodb://mongodb:27017/tkplay_dev"
 mongodb.uri = ${?MONGODB_URI}
 
 modeller_key = ""
@@ -172,11 +176,7 @@ bioprogs_root = "/root/Toolkit/bioprogs"
 
 # Set the full path to this file in application-ext.conf
 # The SGE nodes will need the full path to source this file.
-environment = "tel/env/environment.sh"
-
-helper_scripts = ${bioprogs_root}"/helpers"
-
-perl_lib = ${bioprogs_root}"/lib"
+environment = "/root/Toolkit/tel/env/environment.sh"
 
 # Decide whether to submit jobs to the cluster system (sge) or to run them locally (local).
 # However, qstat-related functions (e.g. cluster load calculation) will not work in this mode.
@@ -193,6 +193,30 @@ sge_nodes = "'*'"
 # play.mailer.password = ""
 # modeller_key = ""
 # mongodb.uri = ""
+# environment = "" !! absolute path !!
 
 # include extending file with secrets
 include "application-ext"
+
+tel.env {
+  HOSTNAME = ${host_name}
+  PORT = ${port}
+  BIOPROGSROOT = ${bioprogs_root}
+  DATABASES = ${db_root}
+  SGENODES = ${sge_nodes}
+  SUBMITMODE = ${submit_mode}
+
+  HHSUITE  = ${db_root}/hh-suite
+  UNICLUST = ${db_root}/hhblits/uniclust30
+  STANDARD = ${db_root}/standard
+  CIF      = ${db_root}/pdb/mmcif/70
+  CIFALL   = ${db_root}/pdb/mmcif/all
+  HHOMP    = ${db_root}/hhomp/db
+  HHBLITS  = ${db_root}/hhblits/
+  SCOPE    = ${db_root}/hh-suite/scope70/pdbEn
+  ECOD     = ${db_root}/hh-suite/ECOD/pdb
+
+  ENVIRONMENT = ${environment}
+  HELPER = ${bioprogs_root}"/helpers"
+  PERLLIB  = ${bioprogs_root}"/lib"
+}
diff --git a/conf/tel.conf b/conf/tel.conf
@@ -1,7 +1,7 @@
 # Configures the tel module of the Toolkit
 play.modules.enabled += "modules.TELModule"
 
-tel.env = "tel/env" # must be reconfigured in different environments
+tel.env = "tel/env"
 tel.params = "tel/paramspec/PARAMS"
 tel.types = "tel/types"
 tel.runscripts = "tel/runscripts/"

diff --git a/docker-compose.yml b/docker-compose.yml
@@ -8,47 +8,34 @@ services:
     environment:
       - SUBMIT_MODE=LOCAL
       - SBT_OPTS=-Xms2G -Xmx4G -Xss2M
-    stdin_open: true
-    tty: true
+    #    stdin_open: true
+    #    tty: true
     ports:
       - 1234:1234
       - 8080:8080
     volumes:
       - .:/toolkit
+    #      Uncommenting following 3 lines will speed up sbt boot time significatnly providing you have GeoIP built locally
+    #      - ~/.ivy2:/root/.ivy2
+    #      - ~/.sbt:/root/.sbt
+    #      - ~/.coursier:/root/.coursier
     links:
       - mongodb
     depends_on:
       - mongodb
-    networks:
-      tk-network:
-        ipv4_address: 174.18.0.2
 
   # The container for the MongoDB Database
   mongodb:
     image: mongo:4.0
     container_name: tk-mongodb
     environment:
-    - MONGO_DATA_DIR=/data/db
-    - MONGO_LOG_DIR=/data/log
-    - MONGO_INITDB_ROOT_USERNAME=root
-    - MONGO_INITDB_ROOT_PASSWORD=rootPassXX
+      - MONGO_DATA_DIR=/data/db
+      - MONGO_LOG_DIR=/data/log
     volumes:
       - mongodb:/data/db
     ports:
       - 27017:27017
-    command: mongod --auth
-    networks:
-      tk-network:
-        ipv4_address: 174.18.0.3
+    command: mongod
 
 volumes:
   mongodb:
-
-networks:
-  tk-network:
-    name: tk-network
-    driver: bridge
-    ipam:
-      driver: default
-      config:
-      - subnet: 174.18.0.1/24
diff --git a/modules/auth/src/main/scala/de/proteinevolution/auth/controllers/AuthController.scala b/modules/auth/src/main/scala/de/proteinevolution/auth/controllers/AuthController.scala
@@ -26,12 +26,11 @@ import de.proteinevolution.auth.models.MailTemplate._
 import de.proteinevolution.auth.models.Session.ChangeSessionID
 import de.proteinevolution.auth.models.{FormDefinitions, JSONTemplate}
 import de.proteinevolution.base.controllers.ToolkitController
-import de.proteinevolution.tel.env.Env
-import de.proteinevolution.user.{User, UserToken}
+import de.proteinevolution.user.{ User, UserToken }
 import io.circe.syntax._
-import javax.inject.{Inject, Singleton}
-import play.api.Logging
 import play.api.cache.{NamedCache, SyncCacheApi}
+import javax.inject.{ Inject, Singleton }
+import play.api.{ Configuration, Logging }
 import play.api.libs.mailer.MailerClient
 import play.api.mvc.{Action, AnyContent, ControllerComponents}
 import reactivemongo.bson.{BSONDateTime, BSONDocument}
@@ -45,7 +44,7 @@ class AuthController @Inject()(
     cc: ControllerComponents,
     @NamedCache("wsActorCache") wsActorCache: SyncCacheApi,
     environment: play.Environment,
-    env: Env
+    config: Configuration,
 )(implicit ec: ExecutionContext, mailerClient: MailerClient)
     extends ToolkitController(cc)
     with JSONTemplate
@@ -194,7 +193,7 @@ class AuthController @Inject()(
                         // All done. User is registered, now send the welcome eMail
                         registeredUser.userToken match {
                           case Some(token) =>
-                            val eMail = NewUserWelcomeMail(registeredUser, token.token, environment, env)
+                            val eMail = NewUserWelcomeMail(registeredUser, token.token, environment, config)
                             eMail.send
                             Ok(signedUp)
                           case None => Ok(tokenMismatch())
@@ -249,7 +248,7 @@ class AuthController @Inject()(
                     case Some(registeredUser) =>
                       // All done. User is registered, now send the welcome eMail
                       val eMail =
-                        ResetPasswordMail(registeredUser, token.token, environment: play.Environment, env: Env)
+                        ResetPasswordMail(registeredUser, token.token, environment: play.Environment, config)
                       eMail.send
                       Ok(passwordRequestSent)
                     case None =>
@@ -299,7 +298,7 @@ class AuthController @Inject()(
                       .map {
                         case Some(updatedUser) =>
                           // All done. Now send the eMail to notify the user that the password has been changed
-                          val eMail = PasswordChangedMail(updatedUser, environment: play.Environment, env: Env)
+                          val eMail = PasswordChangedMail(updatedUser, environment, config)
                           eMail.send
                           Ok(passwordChanged(updatedUser))
                         case None =>
@@ -350,7 +349,7 @@ class AuthController @Inject()(
                   userSessions.modifyUserWithCache(selector, modifier).map {
                     case Some(updatedUser) =>
                       // All done. Now send the eMail
-                      val eMail = ChangePasswordMail(updatedUser, token.token, environment: play.Environment, env: Env)
+                      val eMail = ChangePasswordMail(updatedUser, token.token, environment: play.Environment, config)
                       eMail.send
                       // Everything is ok, let the user know that they are logged in now
                       Ok(passwordChanged(updatedUser))