Merge pull request #136 from overture-stack/rc/0.16.0

release 0.16.0
remove facebook
remove stub commands
dms ui branding image and text
skip waiting ego ui container to stop
pass sso providers to dms ui
create assets directory in the wrapper script
upgrade ego ui, ego, dms-ui, arranger

pom.xml

@@ -10,7 +10,7 @@
 	</parent>
 	<groupId>bio.overture</groupId>
 	<artifactId>dms</artifactId>
-  	<version>0.15.1</version>
+  	<version>0.16.0</version>
 	<name>dms</name>
 	<description>Overture Data Management System</description>
 

src/main/bin/dms-docker

@@ -112,6 +112,10 @@ function provisionConfig {
 		mkdir -p $DMS_HOME
 	fi
 
+	if [ ! -d $DMS_HOME/assets ];then
+		mkdir -p $DMS_HOME/assets
+	fi
+
 	if [ ! -f $DMS_CONFIG_FILE ];then
 		genLatestConfig $DMS_CONFIG_FILE
 	fi
@@ -171,7 +175,7 @@ function main {
 		docker_opts="$docker_opts -p 5005:5005"
 		set -x
 	fi
-	docker_opts="$docker_opts -e DOCKER_RUNAS=true"
+	docker_opts="$docker_opts -e DOCKER_RUNAS=true -e DMS_HOME_HOST_PATH=$DMS_HOME"
 	# create dms-swarm-network if it doesn't exist, this is important for first run
 	# since the dms uses that in its run options
 	found_network=$(docker network ls --filter name=${NETWORK_NAME} --format="{{ .Name }}")

src/main/java/bio/overture/dms/cli/command/DmsCommand.java

@@ -16,7 +16,6 @@
     mixinStandardHelpOptions = true,
     versionProvider = VersionProvider.class,
     subcommands = {
-      SummaryCommand.class,
       ConfigCommand.class,
       ClusterCommand.class,
       BashCompletionCommand.class

src/main/java/bio/overture/dms/cli/command/cluster/ClusterCommand.java

@@ -9,12 +9,8 @@
     mixinStandardHelpOptions = true,
     versionProvider = VersionProvider.class,
     subcommands = {
-      ClusterApplyCommand.class,
-      ClusterDestroyCommand.class,
-      ClusterGetCommand.class,
-      ClusterRestartCommand.class,
       ClusterStartCommand.class,
       ClusterStopCommand.class,
-      ClusterStatusCommand.class
+      ClusterDestroyCommand.class,
     })
 public class ClusterCommand {}

src/main/java/bio/overture/dms/cli/command/cluster/ClusterDestroyCommand.java

@@ -24,7 +24,7 @@
     name = "destroy",
     mixinStandardHelpOptions = true,
     versionProvider = VersionProvider.class,
-    description = "Destroy the cluster")
+    description = "Destroy the cluster and ALL the data")
 public class ClusterDestroyCommand implements Callable<Integer> {
 
   /** Dependencies */
@@ -34,14 +34,6 @@ public class ClusterDestroyCommand implements Callable<Integer> {
   private final DmsComposeManager dmsComposeManager;
   private final DmsConfigStore dmsConfigStore;
 
-  /** CLI Options */
-  @CommandLine.Option(
-      names = {"-v", "--volumes"},
-      required = false,
-      showDefaultValue = ALWAYS,
-      description = "Additionally destroy volumes")
-  private boolean destroyVolumes = false;
-
   @CommandLine.Option(
       names = {"-f", "--force"},
       required = false,
@@ -67,9 +59,13 @@ public Integer call() throws Exception {
     val result = dmsConfigStore.findStoredConfig();
     if (result.isPresent()) {
       t.printStatusLn(
-          "Starting cluster destruction: force=%s  destroyVolumes=%s", force, destroyVolumes);
-      val resolvedDestroyVolumes = resolveDestroyVolumes();
-      dmsComposeManager.destroy(result.get(), resolvedDestroyVolumes);
+          "Starting cluster destruction: force=%s", force);
+      val isConfirmed = confirmVolumesDeletion();
+      if (!isConfirmed) {
+        t.printStatusLn("Cluster destruction canceled.");
+        return 2;
+      }
+      dmsComposeManager.destroy(result.get(), true);
       t.printStatusLn("Finished cluster destruction");
       return 0;
     }
@@ -78,11 +74,11 @@ public Integer call() throws Exception {
     return 1;
   }
 
-  private boolean resolveDestroyVolumes() {
-    boolean askQuestion = !force && destroyVolumes;
-    boolean resolvedDestroyVolumes = force && destroyVolumes;
+  private boolean confirmVolumesDeletion() {
+    boolean askQuestion = !force;
+    boolean confirmedVolumeDestruction = force;
     if (askQuestion) {
-      resolvedDestroyVolumes =
+      confirmedVolumeDestruction =
           questionFactory
               .newSingleQuestion(
                   WARNING,
@@ -91,13 +87,10 @@ private boolean resolveDestroyVolumes() {
                   true,
                   false)
               .getAnswer();
-      if (!resolvedDestroyVolumes) {
-        t.printStatus("Volumes will NOT be destroyed!");
-      }
     }
-    if (resolvedDestroyVolumes) {
+    if (confirmedVolumeDestruction) {
       t.printStatus("Forcefully destroying all volumes!");
     }
-    return resolvedDestroyVolumes;
+    return confirmedVolumeDestruction;
   }
 }

src/main/java/bio/overture/dms/cli/command/cluster/ClusterStartCommand.java

@@ -1,25 +1,49 @@
 package bio.overture.dms.cli.command.cluster;
 
+import bio.overture.dms.cli.DmsConfigStore;
+import bio.overture.dms.cli.terminal.Terminal;
 import bio.overture.dms.cli.util.VersionProvider;
+import bio.overture.dms.compose.deployment.DmsComposeManager;
 import java.util.concurrent.Callable;
+import lombok.NonNull;
+import lombok.val;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Component;
 import picocli.CommandLine.Command;
-import picocli.CommandLine.Option;
 
+@Component
 @Command(
     name = "start",
     mixinStandardHelpOptions = true,
     versionProvider = VersionProvider.class,
-    description = "Start an existing cluster")
+    description = "Deploy a configuration to the cluster")
 public class ClusterStartCommand implements Callable<Integer> {
 
-  @Option(
-      names = {"--skip-ego-init"},
-      required = false,
-      description = "Skip Ego initialization")
-  private boolean skipEgoInit = false;
+  private final Terminal t;
+  private final DmsComposeManager dmsComposeManager;
+  private final DmsConfigStore dmsConfigStore;
+
+  @Autowired
+  public ClusterStartCommand(
+      @NonNull Terminal terminal,
+      @NonNull DmsComposeManager dmsComposeManager,
+      @NonNull DmsConfigStore dmsConfigStore) {
+    this.dmsComposeManager = dmsComposeManager;
+    this.t = terminal;
+    this.dmsConfigStore = dmsConfigStore;
+  }
 
   @Override
   public Integer call() throws Exception {
-    return 0;
+    val result = dmsConfigStore.findStoredConfig();
+    if (result.isPresent()) {
+      t.printStatusLn("Starting deployment...");
+      dmsComposeManager.deploy(result.get());
+      t.printStatusLn("Deployment completed successfully");
+      return 0;
+    }
+
+    t.printErrorLn("Could not find DMS configuration: %s", dmsConfigStore.getDmsConfigFilePath());
+    return 1;
   }
 }

src/main/java/bio/overture/dms/cli/command/cluster/ClusterStopCommand.java

@@ -1,18 +1,54 @@
 package bio.overture.dms.cli.command.cluster;
 
+import bio.overture.dms.cli.DmsConfigStore;
+import bio.overture.dms.cli.terminal.Terminal;
 import bio.overture.dms.cli.util.VersionProvider;
 import java.util.concurrent.Callable;
+
+import bio.overture.dms.compose.deployment.DmsComposeManager;
+import lombok.Builder;
+import lombok.NonNull;
+import lombok.val;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Component;
 import picocli.CommandLine.Command;
 
+@Component
 @Command(
     name = "stop",
     mixinStandardHelpOptions = true,
     versionProvider = VersionProvider.class,
-    description = "Stop a running cluster")
+    description = "Stop a running cluster, without deleting data volumes")
 public class ClusterStopCommand implements Callable<Integer> {
 
+  /** Dependencies */
+  private final Terminal t;
+
+  private final DmsComposeManager dmsComposeManager;
+  private final DmsConfigStore dmsConfigStore;
+
+  @Builder
+  @Autowired
+  public ClusterStopCommand(
+      @NonNull Terminal terminal,
+      @NonNull DmsComposeManager dmsComposeManager,
+      @NonNull DmsConfigStore dmsConfigStore) {
+    this.t = terminal;
+    this.dmsComposeManager = dmsComposeManager;
+    this.dmsConfigStore = dmsConfigStore;
+  }
+
   @Override
   public Integer call() throws Exception {
-    return 0;
+    val result = dmsConfigStore.findStoredConfig();
+    if (result.isPresent()) {
+      t.printStatusLn(
+          "Stopping cluster..");
+      dmsComposeManager.destroy(result.get(), false);
+      t.printStatusLn("Finished stopping cluster");
+      return 0;
+    }
+    t.printErrorLn("Could not find DMS configuration: %s", dmsConfigStore.getDmsConfigFilePath());
+    return 1;
   }
 }

src/main/java/bio/overture/dms/cli/command/config/ConfigBuildCommand.java

@@ -52,7 +52,7 @@ public ConfigBuildCommand(
   public Integer call() throws Exception {
     t.printStatusLn("Starting interactive configuration");
     // TODO: Fix this so that the storedDmsConfig is input into the buildDmsConfig method
-    dmsConfigStore.apply(storedDmsConfig -> dmsQuestionnaire.buildDmsConfig());
+    dmsConfigStore.apply(dmsQuestionnaire::buildDmsConfig);
     t.printStatusLn("Wrote config file to %s", dmsConfigStore.getDmsConfigFilePath());
     return 0;
   }

src/main/java/bio/overture/dms/cli/command/config/ConfigCommand.java

@@ -9,13 +9,7 @@
     mixinStandardHelpOptions = true,
     versionProvider = VersionProvider.class,
     subcommands = {
-      ConfigCheckCommand.class,
       ConfigBuildCommand.class,
       ConfigGetCommand.class,
-      ConfigSetCommand.class,
-      ConfigDeleteCommand.class,
-      ConfigStatusCommand.class,
-      ConfigUpgradeCommand.class,
-      ConfigVersionCommand.class
     })
 public class ConfigCommand {}

src/main/java/bio/overture/dms/cli/question/QuestionFactory.java

@@ -13,6 +13,8 @@
 import static java.util.Objects.isNull;
 
 import bio.overture.dms.cli.model.enums.QuestionProfiles;
+import bio.overture.dms.cli.question.validation.EmailValidator;
+import bio.overture.dms.cli.question.validation.FileValidator;
 import bio.overture.dms.cli.question.validation.QuestionValidator;
 import bio.overture.dms.cli.question.validation.UrlQuestionValidator;
 import bio.overture.dms.cli.terminal.UrlInputReader;
@@ -43,6 +45,10 @@ public class QuestionFactory {
 
   private static final UrlQuestionValidator URL_QUESTION_VALIDATOR = new UrlQuestionValidator();
 
+  private static final EmailValidator EMAIL_VALIDATOR = new EmailValidator();
+
+  private static final FileValidator FILE_VALIDATOR = new FileValidator();
+
   /** Dependencies */
   private final TextIO textIO;
 
@@ -85,6 +91,18 @@ public SingleQuestion<URL> newUrlSingleQuestion(
         URL.class, question, optional, defaultValue, URL_QUESTION_VALIDATOR);
   }
 
+  public SingleQuestion<String> newEmailQuestion(
+      @NonNull String question, boolean optional, String defaultVal) {
+    return newDefaultSingleQuestion(
+        String.class, question, optional, defaultVal, EMAIL_VALIDATOR);
+  }
+
+  public SingleQuestion<String> newFileQuestion(
+      @NonNull String question, boolean optional) {
+    return newDefaultSingleQuestion(
+        String.class, question, optional, null, FILE_VALIDATOR);
+  }
+
   public SingleQuestion<String> newPasswordQuestion(@NonNull String question) {
     return new SingleQuestion<>(question, buildPasswordInputReader());
   }

src/main/java/bio/overture/dms/cli/question/validation/EmailValidator.java

@@ -0,0 +1,18 @@
+package bio.overture.dms.cli.question.validation;
+
+import java.util.List;
+import java.util.regex.Pattern;
+
+public class EmailValidator implements QuestionValidator<String> {
+
+  public static final Pattern VALID_EMAIL_ADDRESS_REGEX =
+      Pattern.compile("^[A-Z0-9._%+-]+@[A-Z0-9.-]+\\.[A-Z]{2,6}$", Pattern.CASE_INSENSITIVE);
+
+  @Override
+  public List<String> getErrorMessages(String val) {
+    if (VALID_EMAIL_ADDRESS_REGEX.matcher(val).matches()) {
+      return null;
+    }
+    return List.of("The provided value is not a valid email");
+  }
+}

src/main/java/bio/overture/dms/cli/question/validation/FileValidator.java

@@ -0,0 +1,20 @@
+package bio.overture.dms.cli.question.validation;
+
+import lombok.val;
+
+import java.io.File;
+import java.util.List;
+
+public class FileValidator implements QuestionValidator<String> {
+
+  @Override
+  public List<String> getErrorMessages(String path) {
+    try {
+      val fileExists = new File(path).exists();
+      if (fileExists) return null;
+      return List.of("File not found");
+    } catch (Exception e) {
+      return List.of("Couldn't check the provided file");
+    }
+  }
+}

src/main/java/bio/overture/dms/cli/question/validation/UrlQuestionValidator.java

@@ -24,6 +24,6 @@ public List<String> getErrorMessages(URL url) {
       errors.add(
           format("The url protocol '%s' is not one of ['http', 'https']", url.getProtocol()));
     }
-    return null;
+    return errors.size() == 0 ? null : errors;
   }
 }