Add PhotosynthesisType and start SSH work

modified:   Core.Tests/Core.Tests.csproj
	modified:   Core.Tests/Parsers/FluxnetSiteCsvParserTests.cs
	new file:   Core.Tests/Remote/PiscalSshClientTests.cs
	modified:   Core/Core.csproj
	modified:   Core/DAL/LeafWebContext.cs
	modified:   Core/DAL/LeafWebInitializer.cs
	modified:   Core/Models/LeafInput.cs
	new file:   Core/Models/PhotosynthesisType.cs

	new file:   Core/Remote/IPiscalClient.cs

Get Piscal

Core.Tests/Core.Tests.csproj

@@ -48,6 +48,7 @@
     <Compile Include="Parsers\FluxnetSiteCsvParserTests.cs" />
     <Compile Include="Properties\AssemblyInfo.cs" />
     <Compile Include="Parsers\LeafInputCsvParserTests.cs" />
+    <Compile Include="Remote\PiscalSshClientTests.cs" />
   </ItemGroup>
   <ItemGroup>
     <Content Include="Parsers\LeafInputData\LeafInput-valid.csv">

Core.Tests/Parsers/FluxnetSiteCsvParserTests.cs

@@ -1,4 +1,5 @@
 using System;
+using System.IO;
 using System.Linq;
 using System.Text.RegularExpressions;
 using LeafWeb.Core.Parsers;
@@ -34,6 +35,17 @@ namespace LeafWeb.Core.Tests.Parsers
 			}
 		}
 
+		[Test]
+		public void Parse_Find_Misencoded_Characters_test()
+		{
+			var fileInfo = new FileInfo(@"C:\Users\poprhythm\Documents\code\LeafWeb\Core\DAL\InitialData\fluxnet_site_list_all_October2015_with_joins_corrected.csv");
+			var parser = new FluxnetSiteCsvParser(fileInfo);
+			foreach (var fns in parser.Parse().Where(f => Regex.IsMatch(f.SiteName, @"[^\x00-\x7F]") || f.SiteName.Contains("?")))
+			{
+				Console.WriteLine($"{fns.FluxnetId} / {fns.SiteName}");
+			}
+		}
+
 		[Test]
 		public void Parse_Find_Duplicate_Ids()
 		{

Core.Tests/Remote/PiscalSshClientTests.cs

@@ -0,0 +1,17 @@
+using LeafWeb.Core.Models;
+using NUnit.Framework;
+
+namespace LeafWeb.Core.Tests.Remote
+{
+	[TestFixture]
+	public class PiscalSshClientTests
+	{
+		[Test]
+		public void Client()
+		{
+			var leafInputFile = new LeafInputFile {Filename = "blah", Id = 1};
+			var client = new PiscalSshClient();
+			client.SubmitLeafInputFile(leafInputFile);
+		}
+	}
+}

Core/Core.csproj

@@ -67,6 +67,8 @@
     <Compile Include="DAL\DataService.cs" />
     <Compile Include="DAL\LeafWebContext.cs" />
     <Compile Include="DAL\LeafWebInitializer.cs" />
+    <Compile Include="Models\PhotosynthesisType.cs" />
+    <Compile Include="Remote\IPiscalClient.cs" />
     <Compile Include="Models\CntrlComparison.cs" />
     <Compile Include="Models\CntrlComparisonFittingInfo.cs" />
     <Compile Include="Models\CntrlComparisonPhotosyntheticInfo.cs" />

Core/DAL/LeafWebContext.cs

@@ -10,6 +10,7 @@ namespace LeafWeb.Core.DAL
 		public DbSet<LeafInputFile> LeafInputFiles { get; set; }
 		public DbSet<LeafInputStatus> LeafInputStatus { get; set; }
 		public DbSet<FluxnetSite> FluxnetSites { get; set; }
+		public DbSet<PhotosynthesisType> PhotosynthesisTypes { get; set; }
 
 		protected override void OnModelCreating(DbModelBuilder modelBuilder)
 		{

Core/DAL/LeafWebInitializer.cs

@@ -1,5 +1,6 @@
 using System.Data.Entity;
 using System.Linq;
+using LeafWeb.Core.Models;
 using LeafWeb.Core.Parsers;
 using LeafWeb.Core.Utility;
 
@@ -18,6 +19,16 @@ namespace LeafWeb.Core.DAL
 
 			// add to context
 			fluxnetSites.ForEach(s => context.FluxnetSites.Add(s));
+			
+			var photosynthesisTypes = new []
+			{
+				new PhotosynthesisType {Id = "C3_photosynthesis_leafweb", Name = "C3 Photosynthesis"},
+				new PhotosynthesisType {Id = "C4_photosynthesis_leafweb", Name = "C4 Photosynthesis"},
+				new PhotosynthesisType {Id = "CAM_photosynthesis_leafweb", Name = "CAM Photosynthesis"}
+			};
+
+			context.PhotosynthesisTypes.AddRange(photosynthesisTypes);
+
 			context.SaveChanges();
 
 			base.Seed(context);

Core/Models/LeafInput.cs

@@ -23,6 +23,8 @@ namespace LeafWeb.Core.Models
 		[Required(ErrorMessage = "")]
 		public string SiteId { get; set; }
 
+		public virtual PhotosynthesisType Photosynthesis { get; set; }
+
 		[DataType(DataType.Date)]
 		[Required]
 		public DateTime Created { get; set; }

Core/Models/PhotosynthesisType.cs

@@ -0,0 +1,14 @@
+using System.ComponentModel.DataAnnotations;
+using System.ComponentModel.DataAnnotations.Schema;
+
+namespace LeafWeb.Core.Models
+{
+	public class PhotosynthesisType
+	{
+		[Key]
+		[DatabaseGenerated(DatabaseGeneratedOption.None)]
+		public string Id { get; set; }
+
+		public string Name { get; set; }
+	}
+}

Core/Remote/IPiscalClient.cs

@@ -0,0 +1,59 @@
+using System;
+using System.IO;
+using System.Text;
+using LeafWeb.Core.Models;
+using Renci.SshNet;
+
+namespace LeafWeb.Core
+{
+	public interface IPiscalClient
+	{
+		void SubmitLeafInputFile(LeafInputFile file);
+		void RetrieveLeafInputResult();
+	}
+
+	public class PiscalSshClient : IPiscalClient
+	{
+		private SshClient GetSshClient()
+		{
+			return new SshClient("40.76.47.173", "piscaladmin", "password");
+		}
+		private ScpClient GetScpClient()
+		{
+			return new ScpClient("40.76.47.173", "piscaladmin", "password");
+		}
+
+		public void SubmitLeafInputFile(LeafInputFile file)
+		{
+			using (var scp = GetScpClient())
+			using (var stream = new MemoryStream(file.Contents))
+			{
+				scp.Connect();
+				scp.Upload(stream, file.Filename);
+			}
+
+			using (var ssh = GetSshClient())
+			{
+				ssh.Connect();
+				var cmd = ssh.CreateCommand("ps");
+				cmd.Execute();
+				//var extendedData = Encoding.ASCII.GetString(cmd.ExtendedOutputStream.ToArray());
+				var extendedData = new StreamReader(cmd.ExtendedOutputStream, Encoding.ASCII).ReadToEnd();
+				ssh.Disconnect();
+
+				Console.Write(cmd.Result);
+				Console.Write(extendedData);
+				//Assert.AreEqual("12345\n", cmd.Result);
+				//Assert.AreEqual("654321\n", extendedData);
+			}
+			// copy file
+
+			// begin processing
+		}
+
+		public void RetrieveLeafInputResult()
+		{
+			throw new System.NotImplementedException();
+		}
+	}
+}