AJ-1219: Convert application.properties to YAML (#324)

Convert application.properties to YAML

In keeping with DSP standardizing on YAML, this converts the two props files in WDS to YML format.

It was tested by diffing the properties before/after conversion and visually inspecting the results using the following testing mechanism which was temporarily introduced to support this verification:
```
DUMP_PROPERTIES=true ./gradlew bootRun
```

That tool can be found in the deletion commit if it's lost in the squash/merge commit: 5743b05

Additionally, the following properties were not referred to from anywhere else in https://github.com/DataBiosphere, so they are removed.
* `sam.healthcheck.pingTTL`
* `twds.clientId`

Finally, an outdated comment referring to data.sql is removed from the configuration property.

service/src/main/java/org/databiosphere/workspacedataservice/SentryInitializer.java

@@ -1,6 +1,8 @@
 package org.databiosphere.workspacedataservice;
 
 import io.sentry.Sentry;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.SmartInitializingSingleton;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.context.annotation.Bean;
@@ -13,8 +15,8 @@
 
 @Configuration
 @PropertySource("classpath:git.properties")
-@PropertySource("classpath:application.properties")
 public class SentryInitializer  {
+	private static final Logger LOGGER = LoggerFactory.getLogger(SentryInitializer.class);
 
 	@Value("${sentry.dsn}")
 	String dsn;
@@ -42,6 +44,7 @@ public class SentryInitializer  {
 	@Bean
 	public SmartInitializingSingleton initialize() {
 		String env = urlToEnv(samurl);
+
 		return () ->
         Sentry.init(options -> {
 				options.setEnvironment(env);
@@ -53,7 +56,6 @@ public SmartInitializingSingleton initialize() {
 			});
 	}
 
-
 	/**
 	 * Extracts an environment (e.g. "dev" or "prod") from a Sam url.
 	 * Looks for ".dsde-${env} and returns ${env} if found.

service/src/main/resources/application.yml

@@ -0,0 +1,124 @@
+# These values are used more than once, so we'll set them here with appropriate defaults
+env:
+  wds:
+    db:
+      host: ${WDS_DB_HOST:localhost}
+      port: ${WDS_DB_PORT:5432}
+      name: ${WDS_DB_NAME:wds}
+      password: ${WDS_DB_PASSWORD:wds}
+      user: ${WDS_DB_USER:wds}
+      # When running on Azure in k8s with workload identity set ADDITIONAL_JDBC_URL_PARAMS to
+      # sslmode=require&authenticationPluginClassName=com.azure.identity.extensions.jdbc.postgresql.AzurePostgresqlAuthenticationPlugin
+      additionalUrlParams: ${ADDITIONAL_JDBC_URL_PARAMS:}
+
+management:
+  endpoint:
+    info:
+      enabled: true
+    health:
+      enabled: true
+      show-details: ALWAYS
+      probes:
+        enabled: true
+      group:
+        liveness:
+          include: livenessState,db
+  endpoints:
+    enabled-by-default: false
+    web:
+      exposure.include: info,health
+      base-path: /
+      path-mapping:
+        info: version
+        health: status
+  # additional keys to expose in the actuator info endpoint:
+  info:
+    env:
+      enabled: true
+
+info:
+  app:
+    chart-version: ${HELM_CHART:unknown}
+    image: ${WDS_IMAGE:unknown}
+
+spring:
+  cache:
+    jcache:
+      config: classpath:ehcache.xml
+
+  datasource:
+    hikari:
+      jdbc-url: jdbc:postgresql://${env.wds.db.host}:${env.wds.db.port}/${env.wds.db.name}?reWriteBatchedInserts=true&${env.wds.db.additionalUrlParams}
+      username: ${env.wds.db.user}
+      password: ${env.wds.db.password}
+      maximum-pool-size: 7
+      minimum-idle: 7
+  servlet:
+    multipart.max-request-size: 5GB
+    multipart.max-file-size: 5GB
+  sql:
+    init:
+      mode: never
+  # Run Liquibase instead
+  liquibase:
+    change-log: classpath:liquibase/changelog.yaml
+#   # activate the "local" profile to turn on CORS response headers,
+#   # which may be necessary for local development.
+#   profiles:
+#     active: local
+
+# set hikari logging to DEBUG or even TRACE to troubleshoot connection pool issues
+logging:
+  level:
+    com.zaxxer.hikari.HikariConfig: INFO
+    com.zaxxer.hikari: INFO
+
+server:
+  error:
+    include-stacktrace: never
+    include-message: always
+
+twds:
+  write.batch.size: 5000
+  streaming.fetch.size: 5000
+  instance:
+    # Workspace Id for launching instance
+    workspace-id: ${WORKSPACE_ID:}
+    source-workspace-id: ${SOURCE_WORKSPACE_ID:}
+  # short-lived credentials to use during cloning
+  startup-token: ${STARTUP_TOKEN:}
+
+  pg_dump:
+    path: ${PGDUMP_PATH:/usr/bin/pg_dump}
+    psqlPath: ${PSQL_PATH:/usr/bin/psql}
+    port: ${env.wds.db.port}
+    user: ${env.wds.db.user}
+    dbName: ${env.wds.db.name}
+    password: ${env.wds.db.password}
+    host: ${env.wds.db.host}
+    # When running on Azure in k8s with workload identity set PGDUMP_USE_AZURE_IDENTITY to true
+    useAzureIdentity: ${PGDUMP_USE_AZURE_IDENTITY:true}
+
+sentry:
+  dsn: https://[email protected]/4504299946835968
+  samurl: ${SAM_URL:}
+  mrg: ${LZ_MRG:}
+  releasename: ${RELEASE_NAME:}
+
+sam:
+  retry:
+    maxAttempts: 5
+    backoff:
+      delay: 500
+      multiplier: 1.5
+
+api:
+  retry:
+    maxAttempts: 10
+    backoff:
+      delay: 150
+      multiplier: 1.5
+
+datarepourl: ${DATA_REPO_URL:}
+workspacemanagerurl: ${WORKSPACE_MANAGER_URL:}
+leoUrl: ${LEONARDO_URL:}

service/src/test/resources/application-mock-sam.properties → service/src/test/resources/application-mock-sam.yml

@@ -2,5 +2,7 @@
 # Sam client underneath that dao. In order for SamConfig to create the HttpSamDao,
 # we need a valid workspace id.
 # This is the example uuid from https://en.wikipedia.org/wiki/Universally_unique_identifier
-twds.instance.workspace-id=123e4567-e89b-12d3-a456-426614174000
+twds:
+  instance:
+    workspace-id: 123e4567-e89b-12d3-a456-426614174000