WX-1122 Enable Azure ApplicationInsights

.gitignore

@@ -55,3 +55,4 @@ tesk_application.conf
 **/venv/
 exome_germline_single_sample_v1.3/
 **/*.pyc
+applicationinsights.log

CHANGELOG.md

@@ -4,7 +4,12 @@
 
 ### HTTPFilesystem Improvements
 
- * WDL `size` engine function now works for HTTP files. 
+WDL `size` engine function now works for HTTP files. 
+
+### Azure Instrumentation Support
+Cromwell can now send logs and process information to Azure Application Insights. To enable, set environment 
+variable `APPLICATIONINSIGHTS_CONNECTION_STRING` to your connection string. [See here for information.](https://learn.microsoft.com/en-us/azure/azure-monitor/app/sdk-connection-string)
+
 
 ## 85 Release Notes
 

project/Dependencies.scala

@@ -12,6 +12,7 @@ object Dependencies {
   // https://github.com/sbt/sbt/issues/4531
   private val azureStorageBlobNioV = "12.0.0-beta.19"
   private val azureIdentitySdkV = "1.9.0-beta.2"
+  private val azureAppInsightsV = "3.4.12"
   private val betterFilesV = "3.9.1"
   private val jsonSmartV = "2.4.10"
   /*
@@ -210,7 +211,8 @@ object Dependencies {
     "com.azure" % "azure-core-management" % "1.7.1",
     "com.fasterxml.jackson.dataformat" % "jackson-dataformat-xml" % jacksonV,
     "com.azure.resourcemanager" % "azure-resourcemanager" % "2.18.0",
-    "net.minidev" % "json-smart" % jsonSmartV
+    "net.minidev" % "json-smart" % jsonSmartV,
+    "com.microsoft.azure" % "applicationinsights-runtime-attach" % azureAppInsightsV,
   )
 
   val wsmDependencies: List[ModuleID] = List(

server/src/main/resources/applicationinsights.json

@@ -0,0 +1,7 @@
+{
+  "instrumentation": {
+    "jdbc": {
+      "enabled": false
+    }
+  }
+}

server/src/main/scala/cromwell/CromwellEntryPoint.scala

@@ -9,6 +9,7 @@ import cats.data.Validated._
 import cats.effect.{ContextShift, IO}
 import cats.syntax.apply._
 import cats.syntax.validated._
+import com.microsoft.applicationinsights.attach.ApplicationInsights
 import com.typesafe.config.{Config, ConfigFactory}
 import common.exception.MessageAggregation
 import common.validation.ErrorOr._
@@ -45,6 +46,11 @@ object CromwellEntryPoint extends GracefulStopSupport {
   private val dnsCacheTtl = config.getOrElse("system.dns-cache-ttl", 3 minutes)
   java.security.Security.setProperty("networkaddress.cache.ttl", dnsCacheTtl.toSeconds.toString)
 
+  // The presence of this env var tells us that the user is trying to send instrumentation data and
+  // logs to Azure Application Insights. If it's present, we'll attach the ApplicationInsights agent.
+  // To configure the behavior of this agent, see server/src/main/resources/applicationinsights.json
+  private lazy val useAzureInstrumentation = sys.env.contains("APPLICATIONINSIGHTS_CONNECTION_STRING")
+
   /**
     * Run Cromwell in server mode.
     */
@@ -140,8 +146,17 @@ object CromwellEntryPoint extends GracefulStopSupport {
     *
     * Also copies variables from config/system/environment/defaults over to the system properties.
     * Fixes issue where users are trying to specify Java properties as environment variables.
+    *
+    * Also also enables Azure log handling when appropriate
     */
   private def initLogging(command: Command): Unit = {
+
+    // Enable Azure instrumentation and log-slurping if desired. Running ApplicationInsights.attach()
+    // without checking for the presence of the relevant env var doesn't cause any failures, but does
+    // print an error that would be confusing for non-Azure users.
+    if (useAzureInstrumentation)
+      ApplicationInsights.attach()
+
     val logbackSetting = command match {
       case Server => "STANDARD"
       case Submit => "PRETTY"