Merge pull request #154 from DataBiosphere/ps/fix-stairctl

PF-3004: Fix stairctl so it runs again, other updates

.gitignore

@@ -44,3 +44,6 @@ pom.xml
 
 ### Jenv directory-local version setting
 .java-version
+
+### Spring Shell
+spring-shell.log

STAIRCTL.md

@@ -17,8 +17,7 @@ In the short-term, you can:
 - run StairCtl: `java -jar stairctl/build/libs/stairctl-VERSION.jar`
 
 ## Command Summary
-StairCtl will be getting new capabilities frequently, so this document may not be an up-to-date
-reference of the available commands. You can use the `help` command to get a list of the
+You can use the `help` command to get a list of the
 commands and use `help "<command>"` to get more detailed help.
 
 ```
@@ -49,6 +48,11 @@ Stairway Commands
         list stairways: List stairway instances
 ```
 
+### Using Spring Shell
+StairCtl is built using [Spring Shell](https://docs.spring.io/spring-shell/reference/index.html), 
+so it can be used as an interactive shell or to run a single command.
+As an interactive shell, it supports history operations and tab completion.
+
 ## Connecting to a Stairway
 The most complex part of using StairCtl is connecting to a Stairway; that is, providing the
 information for connecting to a Stairway database.
@@ -60,15 +64,16 @@ connect [--username string]  [--password string]  [--dbname string]  [--host str
 ```
 
 This table shows the precedence and defaults for each part of the input. Switches override
-environment variables, which override the default. 
+environment variables, which override the default. If you've run the stairway tests locally,
+the default settings will connect to the local stairway database used by these tests.
 
-| **Option** | **Environment Variable** | **Default** |
-|:---|:---|:---|
-| `-u, -U, --username`| STAIRCTL_USERNAME | stairwayuser |
-| `-w, --password` | STAIRCTL_PASSWORD | starwaypw |
-| `-h, --host` | STAIRCTL_HOST | 127.0.0.1 |
-| `-p, --port` | STAIRCTL_PORT | 5432 |
-| `-d, --dbname` | STAIRCTL_DBNAME | stairwaylib |
+| **Option**           | **Environment Variable** | **Default** |
+|:---------------------|:---|:---|
+| `-u, -U, --username` | STAIRCTL_USERNAME | stairwayuser |
+| `-w, --password`     | STAIRCTL_PASSWORD | starwaypw |
+| `-H, --host`         | STAIRCTL_HOST | 127.0.0.1 |
+| `-p, --port`         | STAIRCTL_PORT | 5432 |
+| `-d, --dbname`       | STAIRCTL_DBNAME | stairwaylib |
 
 ### `disconnect` command
 You can disconnect from a Stairway with the `disconnect` command. It takes no options.
@@ -276,7 +281,7 @@ This section provides a few capabilities of StairCtl.
 ### Unrecoverable Flight
 We have had cases where a service is unable to start, because a Stairway
 flight is not recoverable. The Stairway `recoverAndStart` call fails and
-the service is unable start.
+the service is unable to start.
 
 This problem can be addressed by locating the stuck flight, perhaps using the `list flights` and
 `get flight` commands. Then forcing the flight into the "dismal failure" state, so that it will

buildSrc/build.gradle

@@ -11,5 +11,5 @@ repositories {
 dependencies {
     implementation group: 'com.diffplug.spotless', name: 'spotless-plugin-gradle', version: '6.25.0'
     implementation group: 'com.srcclr.gradle', name: 'com.srcclr.gradle.gradle.plugin', version: '3.1.12'
-    implementation group: 'org.apache.commons', name: 'commons-compress', version: '1.25.0'
+    implementation group: 'org.apache.commons', name: 'commons-compress', version: '1.26.0'
 }

buildSrc/src/main/groovy/stairway.java-conventions.gradle

@@ -3,7 +3,6 @@ plugins {
     id 'idea'
     id 'jacoco'
     id 'java'
-    id 'java-library'
     id 'com.diffplug.spotless'
 }
 
@@ -14,7 +13,7 @@ repositories {
 
 dependencies {
     // For logging
-    implementation group: 'org.slf4j', name: 'slf4j-api', version: '1.7.36'
+    implementation group: 'org.slf4j', name: 'slf4j-api', version: '2.0.13'
 
     // Database
     runtimeOnly group: 'org.postgresql', name: 'postgresql', version: '42.7.2'

stairctl/build.gradle

@@ -19,7 +19,7 @@ dependencies {
     implementation group: 'org.apache.commons', name: 'commons-lang3'
 
     // Spring
-    implementation group: 'org.springframework.boot', name: 'spring-boot-starter'
+    implementation group: 'org.springframework.boot', name: 'spring-boot'
     // Spring Boot and Spring Shell versions should stay in sync
     implementation group: 'org.springframework.shell', name: 'spring-shell-starter', version: '3.3.1'
 }

stairctl/src/main/java/bio/terra/stairctl/Application.java

@@ -4,11 +4,9 @@
 import org.springframework.boot.SpringApplication;
 import org.springframework.boot.autoconfigure.SpringBootApplication;
 import org.springframework.context.annotation.Bean;
-import org.springframework.context.annotation.ComponentScan;
 import org.springframework.shell.jline.PromptProvider;
 
 @SpringBootApplication
-@ComponentScan(basePackages = {"bio.terra.stairctl"})
 public class Application {
 
   public static void main(String[] args) {

stairctl/src/main/java/bio/terra/stairctl/ConnectParams.java

@@ -1,71 +1,23 @@
 package bio.terra.stairctl;
 
-import java.util.Optional;
+import java.util.Objects;
 
 // Container for DB connection parameters. It provides defaulting from another instance
 // of ConnectParams so that we can easily apply the incoming configuration.
-public class ConnectParams {
-  private String username;
-  private String password;
-  private String host;
-  private String port;
-  private String dbname;
-
-  public String getUsername() {
-    return username;
-  }
-
-  public ConnectParams username(String username) {
-    this.username = username;
-    return this;
-  }
-
-  public String getPassword() {
-    return password;
-  }
-
-  public ConnectParams password(String password) {
-    this.password = password;
-    return this;
-  }
-
-  public String getHost() {
-    return host;
-  }
-
-  public ConnectParams host(String host) {
-    this.host = host;
-    return this;
-  }
-
-  public String getPort() {
-    return port;
-  }
-
-  public ConnectParams port(String port) {
-    this.port = port;
-    return this;
-  }
-
-  public String getDbname() {
-    return dbname;
-  }
-
-  public ConnectParams dbname(String dbname) {
-    this.dbname = dbname;
-    return this;
-  }
+public record ConnectParams(
+    String username, String password, String host, String port, String dbname) {
 
   public String makeUri() {
     return String.format("jdbc:postgresql://%s:%s/%s", host, port, dbname);
   }
 
   // Fill in any null parameters with those from the provided defaults
-  public void applyDefaults(ConnectParams defaults) {
-    username = Optional.ofNullable(username).orElse(defaults.getUsername());
-    password = Optional.ofNullable(password).orElse(defaults.getPassword());
-    host = Optional.ofNullable(host).orElse(defaults.getHost());
-    port = Optional.ofNullable(port).orElse(defaults.getPort());
-    dbname = Optional.ofNullable(dbname).orElse(defaults.getDbname());
+  public ConnectParams withDefaults(ConnectParams defaults) {
+    return new ConnectParams(
+        Objects.requireNonNullElseGet(username, defaults::username),
+        Objects.requireNonNullElseGet(password, defaults::password),
+        Objects.requireNonNullElseGet(host, defaults::host),
+        Objects.requireNonNullElseGet(port, defaults::port),
+        Objects.requireNonNullElseGet(dbname, defaults::dbname));
   }
 }

stairctl/src/main/java/bio/terra/stairctl/StairwayService.java

@@ -1,5 +1,6 @@
 package bio.terra.stairctl;
 
+import bio.terra.stairctl.commands.Output;
 import bio.terra.stairctl.configuration.StairwayConfiguration;
 import bio.terra.stairway.Control;
 import bio.terra.stairway.Stairway;
@@ -13,28 +14,26 @@
 import org.apache.commons.dbcp2.PoolingDataSource;
 import org.apache.commons.pool2.ObjectPool;
 import org.apache.commons.pool2.impl.GenericObjectPool;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Component;
 
 @Component
 public class StairwayService {
-  private static final Logger logger = LoggerFactory.getLogger(StairwayService.class);
-
   private final StairwayConfiguration stairwayConfiguration;
+  private final Output output;
   private Stairway stairway;
   private Control control;
   private ConnectParams currentConnectParams;
 
   @Autowired
-  public StairwayService(StairwayConfiguration stairwayConfiguration) {
+  public StairwayService(StairwayConfiguration stairwayConfiguration, Output output) {
     this.stairwayConfiguration = stairwayConfiguration;
+    this.output = output;
   }
 
   public void connectStairway(ConnectParams connectParams) {
     // Fill in the defaults from the configuration
-    connectParams.applyDefaults(stairwayConfiguration.makeConnectParams());
+    connectParams = connectParams.withDefaults(stairwayConfiguration.makeConnectParams());
     DataSource dataSource = configureDataSource(connectParams);
 
     try {
@@ -53,10 +52,10 @@ public void connectStairway(ConnectParams connectParams) {
 
       control = stairway.getControl();
       currentConnectParams = connectParams;
-      System.out.println("Connected to Stairway");
+      output.println("Connected to Stairway");
     } catch (Exception ex) {
-      System.err.println("Failed to connect to Stairway or database: " + ex.getMessage());
-      logger.error("Failed to connect to Stairway", ex);
+      output.error(
+          "Failed to connect to Stairway or database using connection: " + connectParams, ex);
     }
   }
 
@@ -84,8 +83,8 @@ public boolean isConnected() {
 
   private DataSource configureDataSource(ConnectParams connectParams) {
     Properties props = new Properties();
-    props.setProperty("user", connectParams.getUsername());
-    props.setProperty("password", connectParams.getPassword());
+    props.setProperty("user", connectParams.username());
+    props.setProperty("password", connectParams.password());
     ConnectionFactory connectionFactory =
         new DriverManagerConnectionFactory(connectParams.makeUri(), props);
     PoolableConnectionFactory poolableConnectionFactory =

stairctl/src/main/java/bio/terra/stairctl/commands/ConnectCommands.java

@@ -10,10 +10,12 @@
 @ShellComponent
 public class ConnectCommands {
   private final StairwayService stairwayService;
+  private final Output output;
 
   @Autowired
-  public ConnectCommands(StairwayService stairwayService) {
+  public ConnectCommands(StairwayService stairwayService, Output output) {
     this.stairwayService = stairwayService;
+    this.output = output;
   }
 
   @ShellMethod(value = "Connect to a Stairway database", key = "connect")
@@ -31,47 +33,41 @@ public void connect(
               defaultValue = ShellOption.NULL)
           String dbname,
       @ShellOption(
-              value = {"-h", "--host"},
+              value = {"-H", "--host"},
               defaultValue = ShellOption.NULL)
           String host,
       @ShellOption(
               value = {"-p", "--port"},
               defaultValue = ShellOption.NULL)
-          String port)
-      throws Exception {
+          String port) {
 
-    ConnectParams connectParams =
-        new ConnectParams()
-            .username(username)
-            .password(password)
-            .dbname(dbname)
-            .host(host)
-            .port(port);
+    ConnectParams connectParams = new ConnectParams(username, password, host, port, dbname);
 
     disconnectIfConnected();
     stairwayService.connectStairway(connectParams);
-    System.out.println("Connected to Stairway on database " + connectParams.getDbname());
+    output.println(
+        "Connected to Stairway on database " + stairwayService.getCurrentConnectParams().dbname());
   }
 
   @ShellMethod(value = "Disconnect from a Stairway database", key = "disconnect")
-  public void disconnect() throws Exception {
+  public void disconnect() {
     disconnectIfConnected();
   }
 
   @ShellMethod(value = "Show the current connection", key = "show connection")
-  public void showConnection() throws Exception {
+  public void showConnection() {
     if (!stairwayService.isConnected()) {
-      System.out.println("Not connected to a Stairway");
+      output.println("Not connected to a Stairway");
     } else {
-      Output.showConnection(stairwayService.getCurrentConnectParams());
+      output.showConnection(stairwayService.getCurrentConnectParams());
     }
   }
 
   private void disconnectIfConnected() {
     if (stairwayService.isConnected()) {
-      System.out.println(
+      output.println(
           "Disconnecting from Stairway on database "
-              + stairwayService.getCurrentConnectParams().getDbname());
+              + stairwayService.getCurrentConnectParams().dbname());
       stairwayService.disconnectStairway();
     }
   }