Merge pull request #131 from OHDSI/dev_Validation

Validation

.gitignore

@@ -346,3 +346,4 @@ ETL-LambdaBuilder.Rproj
 sources/Presentation/org.ohdsi.cdm.presentation.lambdabuilder/aws-lambda-tools-defaults.json
 sources/Presentation/org.ohdsi.cdm.presentation.lambdamerge/aws-lambda-tools-defaults.json
 /sources/Tests/RunLocal/App.config
+/sources/RunValidation/App.config

sources/Framework/org.ohdsi.cdm.framework/Common/Enums/Vendor.cs

@@ -25,6 +25,19 @@ public override string ToString()
             return this.Name;
         }
 
+        public override bool Equals(object? obj)
+        {
+            if (obj is not Vendor other || other == null)
+                return false;
+
+            return this.Name == other.Name;
+        }
+
+        public override int GetHashCode()
+        {
+            return HashCode.Combine(this.Name);
+        }
+
         #endregion
     }
 }

sources/Framework/org.ohdsi.cdm.framework/Common/Utility/EtlLibrary.cs

@@ -3,6 +3,7 @@
 using org.ohdsi.cdm.framework.common.Enums;
 using org.ohdsi.cdm.framework.common.Extensions;
 using org.ohdsi.cdm.framework.Common.Base;
+using System.Linq;
 using System.Reflection;
 
 namespace org.ohdsi.cdm.framework.common.Utility
@@ -128,6 +129,7 @@ public static Vendor CreateVendorInstance(string etlLibraryPath, string name)
                 {
                     Console.WriteLine("CreateVendorInstance | assembly: " + assembly.GetName().Name);
                     Console.WriteLine("CreateVendorInstance | vendorType: " + vendorType);
+                    Console.WriteLine();
 
                     return Activator.CreateInstance(vendorType) as Vendor;
                 }

sources/RunValidation/Program.cs

@@ -0,0 +1,98 @@
+using CommandLine.Text;
+using CommandLine;
+using org.ohdsi.cdm.framework.common.Enums;
+using org.ohdsi.cdm.framework.common.Utility;
+using System.Configuration;
+using org.ohdsi.cdm.framework.common.Omop;
+
+namespace RunValidation
+{
+    internal class Program
+    {
+        internal class Options
+        {
+            [Option('v', "vendor", Required = true, HelpText = "Vendor name.")]
+            public required string Vendor { get; set; }
+
+            [Option('b', "buildingId", Required = true, HelpText = "Building ID.")]
+            public required int BuildingId { get; set; }
+
+            [Option('e', "etlLibraryPath", Default = "", HelpText = "(Optional) Path to a folder containing an external ETL .dll")]
+            public string EtlLibraryPath { get; set; } = "";
+
+            [Option('l', "localTmpPath", Default = "C:\\_tmp", HelpText = "(Optional) Path to local folder to contain intermediary data")]
+            public string LocalTmpPath { get; set; } = "C:\\_tmp";
+
+            [Option('c', "chunks", Separator = ',', HelpText = "(Optional) Comma-separated list of chunk IDs to process. All of them, if omitted.")]
+            public IEnumerable<int> Chunks { get; set; } = new List<int>();
+
+            [Option('p', "personId", Default = null, HelpText = "(Optional) If specified, the usual check changes to finding SliceId for the given PersonId within the first specified ChunkId.")]
+            public long? PersonId { get; set; } = null;
+
+            [Usage(ApplicationAlias = "RunValidation")]
+            public static IEnumerable<Example> Examples
+            {
+                get
+                {
+                    yield return new Example("Process all chunks of a vendor", new Options 
+                        { Vendor = "VendorName", BuildingId = 123});
+                    yield return new Example("Process all vendor's chunks from an external .dll", new Options 
+                        { Vendor = "ExternalVendorName", BuildingId = 123, EtlLibraryPath = "C:\\PathToExternalDllFolder"});
+                    yield return new Example("Process specified chunks of a vendor", new Options 
+                        { Vendor = "VendorName", BuildingId = 123, Chunks = new List<int> { 1, 2, 3 } });
+                    yield return new Example("Get SliceId within the given vendor's chunk containing the given PersonId", new Options
+                    { Vendor = "VendorName", BuildingId = 123, Chunks = new List<int> { 1 }, PersonId = 123 });
+                }
+            }
+        }
+
+        private static string _awsAccessKeyId => ConfigurationManager.AppSettings["awsAccessKeyId"] ?? throw new NullReferenceException("awsAccessKeyId");
+        private static string _awsSecretAccessKey => ConfigurationManager.AppSettings["awsSecretAccessKey"] ?? throw new NullReferenceException("awsSecretAccessKey");
+        private static string _bucket => ConfigurationManager.AppSettings["bucket"] ?? throw new NullReferenceException("bucket");
+        private static string _cdmFolder => ConfigurationManager.AppSettings["cdmFolder"] ?? "cdmCSV";
+
+        static void Main(string[] args)
+        {
+            Parser.Default.ParseArguments<Options>(args)
+                .WithParsed(RunWithOptions)
+                .WithNotParsed(HandleParseError);
+
+            GC.Collect(GC.MaxGeneration, GCCollectionMode.Aggressive, true, true);
+            Console.ReadLine();
+        }
+
+        static void RunWithOptions(Options opts)
+        {
+            var chunks = opts.Chunks.ToList() ?? new List<int>();
+
+            Console.WriteLine("Options:");
+            //Console.WriteLine($"Keys: {_awsAccessKeyId} - {_awsSecretAccessKey}");
+            Console.WriteLine($"Bucket - folder: {_bucket} - {_cdmFolder}");
+
+            Console.WriteLine($"Vendor: {opts.Vendor}");
+            Console.WriteLine($"Building ID: {opts.BuildingId}");
+            Console.WriteLine($"Chunks: {string.Join(", ", chunks)}");
+            Console.WriteLine($"EtlLibraryPath: {opts.EtlLibraryPath}");
+            Console.WriteLine($"LocalTmpPath: {opts.LocalTmpPath}");
+            Console.WriteLine($"Current directory: {Directory.GetCurrentDirectory()}");
+            Console.WriteLine($"PersonId: {opts.PersonId.ToString() ?? ""}");
+            Console.WriteLine();
+
+            Vendor vendor = EtlLibrary.CreateVendorInstance(opts.EtlLibraryPath, opts.Vendor);            
+            var validation = new Validation(_awsAccessKeyId, _awsSecretAccessKey, _bucket, opts.LocalTmpPath, _cdmFolder);
+            if (opts.PersonId.HasValue)
+                validation.ValidatePersonIdInSlice(vendor, opts.BuildingId, opts.Chunks.First(), opts.PersonId.Value);
+            else
+                validation.ValidateBuildingId(vendor, opts.BuildingId, chunks);
+        }
+
+        static void HandleParseError(IEnumerable<Error> errs)
+        {
+            Console.WriteLine("Failed to parse command-line arguments.");
+            foreach (var error in errs)
+            {
+                Console.WriteLine(error.ToString());
+            }            
+        }
+    }
+}

sources/RunValidation/RunValidation.csproj

@@ -0,0 +1,20 @@
+<Project Sdk="Microsoft.NET.Sdk">
+
+  <PropertyGroup>
+    <OutputType>Exe</OutputType>
+    <TargetFramework>net8.0-windows</TargetFramework>
+    <ImplicitUsings>enable</ImplicitUsings>
+    <Nullable>enable</Nullable>
+  </PropertyGroup>
+
+  <ItemGroup>
+    <PackageReference Include="CommandLineParser" Version="2.9.1" />
+    <PackageReference Include="Spectre.Console" Version="0.49.1" />
+  </ItemGroup>
+
+  <ItemGroup>
+    <ProjectReference Include="..\Framework\org.ohdsi.cdm.framework\org.ohdsi.cdm.framework.csproj" />
+    <ProjectReference Include="..\Presentation\org.ohdsi.cdm.presentation.lambdabuilder\org.ohdsi.cdm.presentation.lambdabuilder.csproj" />
+  </ItemGroup>
+
+</Project>