Update Cromwell to 87 and parse prerelease tags as customized (#822)

Author: BMurri

src/deploy-cromwell-on-azure/Configuration.cs

@@ -107,7 +107,7 @@ public static Configuration BuildConfiguration(string[] args)
 
             if (System.IO.File.Exists(configFilename))
             {
-                configBuilder.AddJsonFile(configFilename);
+                configBuilder.AddJsonFile(System.IO.Path.GetFullPath(configFilename));
             }
 
             var configurationSource = configBuilder.AddCommandLine(args).Build();

src/deploy-cromwell-on-azure/Deployer.cs

@@ -1003,8 +1003,8 @@ private Dictionary<string, string> ConfigureSettings(string managedIdentityClien
             UpdateSetting(settings, defaults, "CromwellImageName",
                 value: string.IsNullOrWhiteSpace(configuration.CromwellImageName) ? (string.IsNullOrWhiteSpace(configuration.CromwellVersion) ? null : configuration.CromwellVersion) : configuration.CromwellImageName,
                 ConvertValue: string.IsNullOrWhiteSpace(configuration.CromwellImageName) ? (v => installedVersion is null ? $"broadinstitute/cromwell:{v}" : $"{GetCromwellImageNameWithoutTag(settings["CromwellImageName"])}:{v}") : null,
-                ignoreDefaults: ImageNameIgnoreDefaults(settings, defaults, "CromwellImageName", configuration.CromwellVersion is null && configuration.CromwellImageName is null, installedVersion,
-                    tag => GetCromwellImageTag(settings["CromwellImageName"]) <= GetCromwellImageTag(defaults["CromwellImageName"]))); // There's not a good way to detect customization of this property, so default to forced upgrade to the new default.
+                ignoreDefaults: ImageNameIgnoreDefaults(settings, defaults, "CromwellImageName", configuration.CromwellVersion is null && configuration.CromwellImageName is null, installedVersion, tagKey: nameof(configuration.CromwellVersion),
+                    IsInstalledNotCustomized: tag => GetCromwellImageTag(settings["CromwellImageName"]) <= GetCromwellImageTag(defaults["CromwellImageName"]))); // There's not a good way to detect customization of this property, so default to forced upgrade to the new default.
 
             UpdateSetting(settings, defaults, "TesImageName", configuration.TesImageName, ignoreDefaults: ImageNameIgnoreDefaults(settings, defaults, "TesImageName", configuration.TesImageName is null, installedVersion));
             UpdateSetting(settings, defaults, "TriggerServiceImageName", configuration.TriggerServiceImageName, ignoreDefaults: ImageNameIgnoreDefaults(settings, defaults, "TriggerServiceImageName", configuration.TriggerServiceImageName is null, installedVersion));
@@ -1050,7 +1050,7 @@ static string GetCromwellImageNameWithoutTag(string imageName)
                 => imageName?[..(imageName.LastIndexOf(':'))] ?? null;
 
             static int GetCromwellImageTag(string imageName)
-                => int.TryParse(imageName?[(imageName.LastIndexOf(':') + 1)..] ?? string.Empty, System.Globalization.NumberStyles.Integer, System.Globalization.NumberFormatInfo.InvariantInfo, out var tag) ? tag : 0;
+                => int.TryParse(imageName?[(imageName.LastIndexOf(':') + 1)..] ?? string.Empty, System.Globalization.NumberStyles.Integer, System.Globalization.NumberFormatInfo.InvariantInfo, out var tag) ? tag : int.MaxValue;
         }
 
         /// <summary>
@@ -1062,9 +1062,10 @@ static int GetCromwellImageTag(string imageName)
         /// <param name="valueIsNull">True if configuration value to set is null. See <see cref="UpdateSetting{T}(Dictionary{string, string}, Dictionary{string, string}, string, T, Func{T, string}, string, bool?)"/>'s "value" parameter.</param>
         /// <param name="installedVersion">A <see cref="Version"/> of the current configuration, or null if this is not an update.</param>
         /// <param name="IsInstalledNotCustomized">A <see cref="Predicate{T}"/> where the parameter is the image tag of the currently configured image. Only called if the rest of the image name is identical to the default. Return False if the value is considered customized, otherwise True.</param>
+        /// <param name="tagKey">Configuration key of tag to use in warning if <paramref name="key"/> is not correct.</param>
         /// <returns>false if current setting should be ignored, null otherwise.</returns>
         /// <remarks>This method provides a value for the "ignoreDefaults" parameter to <see cref="UpdateSetting{T}(Dictionary{string, string}, Dictionary{string, string}, string, T, Func{T, string}, string, bool?)"/> for use with container image names.</remarks>
-        private static bool? ImageNameIgnoreDefaults(Dictionary<string, string> settings, Dictionary<string, string> defaults, string key, bool valueIsNull, Version installedVersion, Predicate<string> IsInstalledNotCustomized = default)
+        private static bool? ImageNameIgnoreDefaults(Dictionary<string, string> settings, Dictionary<string, string> defaults, string key, bool valueIsNull, Version installedVersion, Predicate<string> IsInstalledNotCustomized = default, string tagKey = default)
         {
             if (installedVersion is null || !valueIsNull)
             {
@@ -1106,7 +1107,8 @@ static int GetCromwellImageTag(string imageName)
 
             if (result is null && !sameVersionUpgrade)
             {
-                ConsoleEx.WriteLine($"Warning: CromwellOnAzure is being upgraded, but {key} was customized, and is not being upgraded, which might not be what you want. (To remove the customization of {key}, set it to the empty string.)", ConsoleColor.Yellow);
+                var configKey = installed.StartsWith(defaultPath + ":") ? tagKey ?? key : key;
+                ConsoleEx.WriteLine($"Warning: CromwellOnAzure is being upgraded, but {configKey} was customized, and is not being upgraded, which might not be what you want. (To remove the customization of {configKey}, set it to the empty string.)", ConsoleColor.Yellow);
             }
 
             return result;
@@ -2258,6 +2260,7 @@ void ValidateHelmInstall(string helmPath, string featureName)
 
             if (!configuration.ManualHelmDeployment)
             {
+                configuration.HelmBinaryPath = configuration.HelmBinaryPath is null ? null : Environment.ExpandEnvironmentVariables(configuration.HelmBinaryPath);
                 ValidateHelmInstall(configuration.HelmBinaryPath, nameof(configuration.HelmBinaryPath));
             }
 

src/deploy-cromwell-on-azure/scripts/env-03-external-images.txt

@@ -1 +1 @@
-CromwellImageName=broadinstitute/cromwell:86
+CromwellImageName=broadinstitute/cromwell:87