Leaf Input Parsing complete

2015-11-20 11:39:23 -05:00
parent 750b2aee7b
commit 1fb73b9f76
26 changed files with 1294 additions and 1 deletions
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="utf-8"?>
+<configuration>
+  <configSections>
+    <!-- For more information on Entity Framework configuration, visit http://go.microsoft.com/fwlink/?LinkID=237468 -->
+    <section name="entityFramework" type="System.Data.Entity.Internal.ConfigFile.EntityFrameworkSection, EntityFramework, Version=6.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089" requirePermission="false" />
+  </configSections>
+  <entityFramework>
+    <defaultConnectionFactory type="System.Data.Entity.Infrastructure.SqlConnectionFactory, EntityFramework" />
+    <providers>
+      <provider invariantName="System.Data.SqlClient" type="System.Data.Entity.SqlServer.SqlProviderServices, EntityFramework.SqlServer" />
+    </providers>
+  </entityFramework>
+</configuration>
@@ -0,0 +1,84 @@
+<?xml version="1.0" encoding="utf-8"?>
+<Project ToolsVersion="4.0" DefaultTargets="Build" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
+  <Import Project="$(MSBuildExtensionsPath)\$(MSBuildToolsVersion)\Microsoft.Common.props" Condition="Exists('$(MSBuildExtensionsPath)\$(MSBuildToolsVersion)\Microsoft.Common.props')" />
+  <PropertyGroup>
+    <Configuration Condition=" '$(Configuration)' == '' ">Debug</Configuration>
+    <Platform Condition=" '$(Platform)' == '' ">AnyCPU</Platform>
+    <ProjectGuid>{25BAED75-7E75-4D11-90D9-358472054DF6}</ProjectGuid>
+    <OutputType>Library</OutputType>
+    <AppDesignerFolder>Properties</AppDesignerFolder>
+    <RootNamespace>LeafWeb.Core</RootNamespace>
+    <AssemblyName>Core</AssemblyName>
+    <TargetFrameworkVersion>v4.5</TargetFrameworkVersion>
+    <FileAlignment>512</FileAlignment>
+  </PropertyGroup>
+  <PropertyGroup Condition=" '$(Configuration)|$(Platform)' == 'Debug|AnyCPU' ">
+    <DebugSymbols>true</DebugSymbols>
+    <DebugType>full</DebugType>
+    <Optimize>false</Optimize>
+    <OutputPath>bin\Debug\</OutputPath>
+    <DefineConstants>DEBUG;TRACE</DefineConstants>
+    <ErrorReport>prompt</ErrorReport>
+    <WarningLevel>4</WarningLevel>
+  </PropertyGroup>
+  <PropertyGroup Condition=" '$(Configuration)|$(Platform)' == 'Release|AnyCPU' ">
+    <DebugType>pdbonly</DebugType>
+    <Optimize>true</Optimize>
+    <OutputPath>bin\Release\</OutputPath>
+    <DefineConstants>TRACE</DefineConstants>
+    <ErrorReport>prompt</ErrorReport>
+    <WarningLevel>4</WarningLevel>
+  </PropertyGroup>
+  <ItemGroup>
+    <Reference Include="CsvHelper, Version=2.0.0.0, Culture=neutral, PublicKeyToken=8c4959082be5c823, processorArchitecture=MSIL">
+      <HintPath>..\packages\CsvHelper.2.13.2.0\lib\net40-client\CsvHelper.dll</HintPath>
+      <Private>True</Private>
+    </Reference>
+    <Reference Include="EntityFramework, Version=6.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089, processorArchitecture=MSIL">
+      <HintPath>..\packages\EntityFramework.6.1.3\lib\net45\EntityFramework.dll</HintPath>
+      <Private>True</Private>
+    </Reference>
+    <Reference Include="EntityFramework.SqlServer, Version=6.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089, processorArchitecture=MSIL">
+      <HintPath>..\packages\EntityFramework.6.1.3\lib\net45\EntityFramework.SqlServer.dll</HintPath>
+      <Private>True</Private>
+    </Reference>
+    <Reference Include="Fasterflect, Version=2.1.3.0, Culture=neutral, PublicKeyToken=38d18473284c1ca7, processorArchitecture=MSIL">
+      <HintPath>..\packages\fasterflect.2.1.3\lib\net40\Fasterflect.dll</HintPath>
+      <Private>True</Private>
+    </Reference>
+    <Reference Include="System" />
+    <Reference Include="System.ComponentModel.DataAnnotations" />
+    <Reference Include="System.Core" />
+    <Reference Include="System.Xml.Linq" />
+    <Reference Include="System.Data.DataSetExtensions" />
+    <Reference Include="Microsoft.CSharp" />
+    <Reference Include="System.Data" />
+    <Reference Include="System.Xml" />
+  </ItemGroup>
+  <ItemGroup>
+    <Compile Include="Models\LeafInput.cs" />
+    <Compile Include="Models\LeafInputData.cs" />
+    <Compile Include="Models\LeafInputFile.cs" />
+    <Compile Include="Models\LeafInputPhotosynthetic.cs" />
+    <Compile Include="Models\LeafInputSite.cs" />
+    <Compile Include="Properties\AssemblyInfo.cs" />
+    <Compile Include="Services\ParseInfoAttribute.cs" />
+    <Compile Include="Services\LeafInputCsvParser.cs" />
+    <Compile Include="Services\ParsedObjectFactory.cs" />
+    <Compile Include="Services\ParseException.cs" />
+    <Compile Include="Utility\StringExtensions.cs" />
+  </ItemGroup>
+  <ItemGroup>
+    <None Include="App.config" />
+    <None Include="packages.config" />
+  </ItemGroup>
+  <ItemGroup />
+  <Import Project="$(MSBuildToolsPath)\Microsoft.CSharp.targets" />
+  <!-- To modify your build process, add your task inside one of the targets below and uncomment it. 
+       Other similar extension points exist, see Microsoft.Common.targets.
+  <Target Name="BeforeBuild">
+  </Target>
+  <Target Name="AfterBuild">
+  </Target>
+  -->
+</Project>
@@ -0,0 +1,54 @@
+using System.Collections.Generic;
+using System.ComponentModel.DataAnnotations;
+using LeafWeb.Core.Services;
+
+namespace LeafWeb.Core.Models
+{
+	/// <summary>
+	/// Descriptive information about the investigator, 
+	/// contact information, the site,the sample leaf and its general environmental condition
+	/// </summary>
+	public class LeafInput
+	{
+		[Key]
+		public string LeafInputId { get; set; }
+
+		public string FileName { get; set; }
+
+		[ParseInfo(1, exampleValue: "First and last name")]
+		public string InvestigatorName { get; set; }
+
+		[ParseInfo(2, exampleValue: "Your email / mail addresses")]
+		public string ContactInformation { get; set; }
+
+		[ParseInfo(3, alternateTitle: "Site name in full", exampleValue: "Your site's identifier / name")]
+		public string SiteName { get; set; }
+
+		[ParseInfo(4, exampleValue: "Mixed forest / grasslands / croplands/ etc")]
+		public string VegetationType { get; set; }
+
+		[ParseInfo(5, exampleValue: "Soil type at your site")]
+		public string SoilType { get; set; }
+
+		[ParseInfo(6, exampleValue: "List of major species at the site")]
+		public string MajorSpecies { get; set; }
+
+		[ParseInfo(7, 
+			alternateTitle: "Sample leaf light environment",
+			exampleValue: "The general light environment in which the leaf is in (e.g. heavily shaded from above)")]
+		public string SampleLeafLightEnv { get; set; }
+
+		[ParseInfo(8, exampleValue: "Indicate whether there is water stress at the time of sampling")]
+		public string WaterStressAssessment { get; set; }
+
+		[ParseInfo(9, exampleValue: "For example - Licor-6400")]
+		public string InstrumentUsed { get; set; }
+
+		[ParseInfo(10, exampleValue: "Any extra information you feel would be helpful to put the sampled leaf in context")]
+		public string ExtraInfo { get; set; }
+
+		public virtual LeafInputSite Site { get; set; }
+		public virtual LeafInputPhotosynthetic Photosynthetic { get; set; }
+		public virtual IEnumerable<LeafInputData> Data { get; set; }
+	}
+}
@@ -0,0 +1,145 @@
+using System.ComponentModel.DataAnnotations;
+using LeafWeb.Core.Services;
+
+namespace LeafWeb.Core.Models
+{
+    /// <summary>
+	/// A/Ci data for a variety of analyses, including photosynthesis, stomatal conductance, internal conductance, water use efficiency.
+    /// </summary>
+    public class LeafInputData
+    {
+		public int ListOrder { get; set; }
+
+		/// <summary>the data point No.</summary>
+		[ParseInfo(1, units: "no unit")]
+		public double? Obs { get; set; }
+
+		/// <summary>clock time</summary>
+		[StringLength(8)]
+		[ParseInfo(2, units: "hh:mm:ss")]
+		public string HHMMSS { get; set; }
+
+		/// <summary>number of seconds since file opened</summary>
+		[ParseInfo(3, units: "seconds")]
+		public double? FTime { get; set; }
+
+		/// <summary>photosynthetic rate</summary>
+		[ParseInfo(4, units: "umol/m2/s")]
+		public double? Photo { get; set; }
+
+		/// <summary>adjusted photosynthetic rate (leakage corrected)</summary>
+		/// <remarks>required</remarks>
+		[ParseInfo(5, alternateTitle: "!AdjPhoto", units: "umol/m2/s")]
+		public double? AdjPhoto { get; set; }
+
+		/// <summary>stomatal conductance</summary>
+		/// <remarks>required</remarks>
+		[ParseInfo(6, alternateTitle: "!StomCond", units: "mol/m2/s")]
+		public double? StomCond { get; set; }
+
+		/// <summary>intercellular CO2 concentration (umol CO2 / mol moist air)</summary>
+		[ParseInfo(7, alternateTitle: "!Ci", units: "umol/mol")]
+		public double? Ci { get; set; }
+
+		/// <summary>transpiration rate</summary>
+		/// <remarks>must provide</remarks>
+		[ParseInfo(8, alternateTitle: "!Trmmol", units:"mmol/m2/s")]
+		public double? Trmmol { get; set; }
+
+		/// <summary>water vapor pressure deficit based on leaf temperature, must provide</summary>
+		[ParseInfo(9, alternateTitle: "!VpdL", units: "KPa")]
+		public double? VpdL { get; set; }
+
+		/// <summary>leaf area</summary>
+		[ParseInfo(10, units:"cm2")]
+		public double? Area { get; set; }
+
+		/// <summary>estimate of the ratio of stomatal conductances of one side of the leaf to the other</summary>
+		[ParseInfo(11, units: "NA")]
+		public double? StmRat { get; set; }
+
+		/// <summary>total boundary layer conductance</summary>
+		[ParseInfo(12, units: "mol/m2/s")]
+		public double? BLCond { get; set; }
+
+		/// <summary>temperature in sample cell</summary>
+		[ParseInfo(13, units: "oC")]
+		public double? Tair { get; set; }
+
+		/// <summary>temperature of leaf thermocouple</summary>
+		/// <remarks>required</remarks>
+		[ParseInfo(14, alternateTitle: "!Tleaf", units: "oC")]
+		public double? Tleaf { get; set; }
+
+		/// <summary>IRGA Block temperature</summary>
+		[ParseInfo(15, units: "oC")]
+		public double? TBlk { get; set; }
+
+		/// <summary>reference CO2 concentration</summary>
+		[ParseInfo(16, units: "umol/mol")]
+		public double? CO2R { get; set; }
+
+		/// <summary>Sample CO2 concentration</summary>
+		[ParseInfo(17, units: "umol/mol")]
+		public double? CO2S { get; set; }
+
+		/// <summary>reference cell water vapor concentration</summary>
+		[ParseInfo(18, units: "mmol/mol")]
+		public double? H2OR { get; set; }
+
+		/// <summary>sample cell water vapor concentration</summary>
+		[ParseInfo(19, units: "mmol/mol")]
+		public double? H2OS { get; set; }
+
+		/// <summary>(%) Reference cell relative humidity</summary>
+		[ParseInfo(20)]
+		public double? RH_R { get; set; }
+
+		/// <summary>(%) sample cell relative humidity</summary>
+		[ParseInfo(21)]
+		public double? RH_S { get; set; }
+
+		/// <summary>(umol/s) molar flow rate of air entering the leaf chamber</summary>
+		[ParseInfo(22)]
+		public double? Flow { get; set; }
+
+		/// <summary> PAR measured by the in-chamber quantum sensor</summary>
+		/// <remarks>required</remarks>
+		[ParseInfo(23, alternateTitle: "!PARi", units: "umol/m2/s")]
+		public double? PARi { get; set; }
+
+		/// <summary>PAR measured by the external quantum sensor</summary>
+		[ParseInfo(24, units: "umol/m2/s")]
+		public double? PARo { get; set; }
+
+		/// <summary>atmospheric pressure</summary>
+		[ParseInfo(25, units: "KPa")]
+		public double? Press { get; set; }
+
+		/// <summary>sample CO2 offset</summary>
+		[ParseInfo(26, units: "umol/mol")]
+		public double? CsMch { get; set; }
+
+		/// <summary>sample H2O offset</summary>
+		[ParseInfo(27, units: "mmol/mol")]
+		public double? HsMch { get; set; }
+
+		/// <summary>a stability indicator as a decimal value</summary>
+		[ParseInfo(28, units: "NA")]
+		public double? StableF { get; set; }
+
+		/// <summary>status flag</summary>
+		[ParseInfo(29, units: "NA")]
+		public string Status { get; set; }
+
+		/// <summary>DeltaF/Fm, the fraction of absorbed PSII photons that are used in photochemistry</summary>
+		[ParseInfo(30, units: "NA")]
+		public double? PhiPS2 { get; set; }
+
+		/// <summary>atmospheric O2 partial pressure</summary>
+		[ParseInfo(31, units: "Pa")]
+		public double? OxygenPress { get; set; }
+
+		public virtual LeafInput LeafInput { get; set; }
+    }
+}
@@ -0,0 +1,11 @@
+using System.ComponentModel.DataAnnotations;
+
+namespace LeafWeb.Core.Models
+{
+	public class LeafInputFile
+	{
+		[Key]
+		public string LeafInputId { get; set; }
+		public byte[] File { get; set; }
+	}
+}
@@ -0,0 +1,41 @@
+using LeafWeb.Core.Services;
+
+namespace LeafWeb.Core.Models
+{
+	/// <summary>
+	/// Photosynthetic parameters of Leaf Input
+	/// </summary>
+	public class LeafInputPhotosynthetic
+	{
+		/// <summary>chloroplastic CO2 photocompensation point</summary>
+		/// <remarks>must be positive</remarks>
+		[ParseInfo(1, alternateTitle:"Gamma*", units: "Pa")]
+		public double GammaStar { get; set; }
+
+		/// <summary>Michaelis-Menten constant for RuBP carboxylation</summary>
+		/// <remarks>must be positive</remarks>
+		[ParseInfo(2, units: "Pa")]
+		public double Kc { get; set; }
+
+		/// <summary>Michaelis-Menten constant for RuBP oxygenation</summary>
+		/// <remarks>must be positive</remarks>
+		[ParseInfo(3, units: "Pa")]
+		public double Ko { get; set; }
+
+		/// <summary>the fraction of glycolate carbon not returned to the chloroplast</summary>
+		/// <remarks>must be between 0~1 if provided</remarks>
+		[ParseInfo(4)]
+		public double Alpha { get; set; }
+
+		/// <summary>dark respiration</summary>
+		/// <remarks>must be positive if provided</remarks>
+		[ParseInfo(5, units: "umol/m2/s")]
+		public double Rd { get; set; }
+
+		/// <summary>internal (also known as mesophyll) conductance</summary>
+		[ParseInfo(6, units: "umol/m2/s/Pa")]
+		public double gi { get; set; }
+
+		public virtual LeafInput LeafInput { get; set; }
+	}
+}
@@ -0,0 +1,96 @@
+using LeafWeb.Core.Services;
+
+namespace LeafWeb.Core.Models
+{
+	/// <summary>
+	/// Contains info about the site such as elevation, canopy height, site ID, etc
+    /// </summary>
+    public class LeafInputSite
+    {
+		/// <summary>Site identifier</summary>
+		/// <remarks>do not leave blank between letters</remarks>
+		[ParseInfo(1)]
+		public string SiteID { get; set; }
+
+		/// <summary>Site latitude, northern hermisphere positive</summary>
+		[ParseInfo(2, units:"degrees")]
+		public double? Latitude { get; set; }
+
+		/// <summary>Site longitude, east positive</summary>
+		[ParseInfo(3, units: "degrees")]
+		public double? Longitude { get; set; }
+
+		/// <summary>site elevation</summary>
+		[ParseInfo(4, units: "m")]
+		public double? Elevation { get; set; }
+
+		/// <summary>the year when the A/Ci data is taken</summary>
+		[ParseInfo(5, units: "year")]
+		public int? SampleYear { get; set; }
+
+		/// <summary>the day of year (since 1 Jan) when the A/Ci data is taken</summary>
+		[ParseInfo(6, units: "day")]
+		public int? SampleDayOfYear { get; set; }
+
+		/// <summary>the approximate start day (since 1 Jan) of growing season</summary>
+		[ParseInfo(7, units: "day")]
+		public int? GrowSeasonStart { get; set; }
+
+		/// <summary>the approximate end day (since 1 Jan) of growing season</summary>
+		[ParseInfo(8, units: "day")]
+		public int? GrowSeasonEnd { get; set; }
+
+		/// <summary>stand age since the last disturbance</summary>
+		[ParseInfo(9, units: "year")]
+		public double? StandAge { get; set; }
+
+		/// <summary>the height of the canopy</summary>
+		[ParseInfo(10, units: "m")]
+		public double? CanopyHeight { get; set; }
+
+		/// <summary>the leaf area index in the middle of growing season</summary>
+		[ParseInfo(11, units: "m2/m2")]
+		public double? LeafAreaIndex { get; set; }
+
+		/// <summary>the species of the leaf sample</summary>
+		/// <remarks>don't leave blank between letters</remarks>
+		[ParseInfo(12, units: "dimensionless")]
+		public string SpeciesSampled { get; set; }
+
+		/// <summary>the average time interval between two consecutive A/Ci data points</summary>
+		[ParseInfo(13, alternateTitle: "AveTimeResolution", units: "minutes")]
+		public double? AverageTimeResolution { get; set; }
+
+		/// <summary>the height at which the leaf is located</summary>
+		[ParseInfo(14, units: "m")]
+		public double? SampleHeight { get; set; }
+
+		/// <summary>the age of the leaf</summary>
+		[ParseInfo(15, units: "day")]
+		public int? LeafAge { get; set; }
+
+		/// <summary>specific leaf area of the sample</summary>
+		[ParseInfo(16, units: "cm2/g")]
+		public double? SpecificLeafArea { get; set; }
+
+		/// <summary>dry leaf nitrogen content of the sample</summary>
+		[ParseInfo(17, units: "%")]
+		public double? LfNitrogenContent { get; set; }
+
+		/// <summary>dry leaf carbon content of the sample</summary>
+		[ParseInfo(18, units: "%")]
+		public double? LfCarbonContent { get; set; }
+
+		/// <summary>dry leaf phosphorus content of the sample</summary>
+		[ParseInfo(19, units: "%")]
+		public double? LfPhosphContent { get; set; }
+
+		// WoodPorosity
+
+		// SapWoodDensity
+
+		// DataType,TissueArea,TissueMass,Fo'_or_Fo,Fm'_or_Fm,Fs,MeasLight
+
+		public virtual LeafInput LeafInput { get; set; }
+	}
+}
@@ -0,0 +1,36 @@
+using System.Reflection;
+using System.Runtime.CompilerServices;
+using System.Runtime.InteropServices;
+
+// General Information about an assembly is controlled through the following 
+// set of attributes. Change these attribute values to modify the information
+// associated with an assembly.
+[assembly: AssemblyTitle("Core")]
+[assembly: AssemblyDescription("")]
+[assembly: AssemblyConfiguration("")]
+[assembly: AssemblyCompany("")]
+[assembly: AssemblyProduct("Core")]
+[assembly: AssemblyCopyright("Copyright ©  2015")]
+[assembly: AssemblyTrademark("")]
+[assembly: AssemblyCulture("")]
+
+// Setting ComVisible to false makes the types in this assembly not visible 
+// to COM components.  If you need to access a type in this assembly from 
+// COM, set the ComVisible attribute to true on that type.
+[assembly: ComVisible(false)]
+
+// The following GUID is for the ID of the typelib if this project is exposed to COM
+[assembly: Guid("678132a7-2bfc-426b-a14a-761822c06bd5")]
+
+// Version information for an assembly consists of the following four values:
+//
+//      Major Version
+//      Minor Version 
+//      Build Number
+//      Revision
+//
+// You can specify all the values or you can default the Build and Revision Numbers 
+// by using the '*' as shown below:
+// [assembly: AssemblyVersion("1.0.*")]
+[assembly: AssemblyVersion("1.0.0.0")]
+[assembly: AssemblyFileVersion("1.0.0.0")]
@@ -0,0 +1,155 @@
+using System;
+using System.Collections.Generic;
+using System.IO;
+using CsvHelper;
+using CsvHelper.Configuration;
+using LeafWeb.Core.Models;
+
+namespace LeafWeb.Core.Services
+{
+	public class LeafInputCsvParser : IDisposable
+	{
+		private readonly FileSystemInfo _csvFile;
+		private readonly StreamReader _reader;
+		private readonly CsvReader _csv;
+		
+		public LeafInputCsvParser(FileSystemInfo csvFile)
+		{
+			_csvFile = csvFile;
+			if (!csvFile.Exists)
+				throw new FileNotFoundException("Cannot find file '" + csvFile.Name + "'");
+
+			_reader = File.OpenText(csvFile.FullName);
+			var csvConfiguration = new CsvConfiguration {HasHeaderRecord = false};
+			_csv = new CsvReader(_reader, csvConfiguration);
+		}
+
+		public LeafInput Parse()
+		{
+			// First 10 lines
+			var leafInput = ParseLeafInput();
+			leafInput.FileName = _csvFile.Name;
+
+			// Next 3 (Header, Units, and Values)
+			leafInput.Site = ParseLeafInputSite();
+
+			// Next 3 (Header, Units, and Values)
+			leafInput.Photosynthetic = ParseLeafInputPhotosynthetic();
+
+			// Remaining lines (Header, Units, and Data)
+			leafInput.Data = ParseLeafInputData();
+			
+			return leafInput;
+		}
+
+		private LeafInput ParseLeafInput()
+		{
+			var items = new List<string>();
+			for (var i = 0; i < 10; i++)
+			{
+				if (!_csv.Read())
+					throw new ParseException("Could not read line number " + _csv.Row);
+
+				string field;
+				if (!_csv.TryGetField(0, out field))
+					throw new ParseException("Could not read first field on line number " + _csv.Row);
+				items.Add(field);
+			}
+			return ParsedObjectFactory<LeafInput>.Create(items.ToArray());
+		}
+
+		private string[] GetNextCsvRowValues()
+		{
+			// get values from row
+			if (!_csv.Read())
+				return null;
+
+			// put all the values from this row into an array
+			var values = new List<string>();
+			var index = 0;
+			string value;
+			while (_csv.TryGetField(index, out value))
+			{
+				values.Add(value);
+				index++;
+			}
+			return values.ToArray();
+		}
+
+		private LeafInputSite ParseLeafInputSite()
+		{
+			var titles = GetNextCsvRowValues();
+			if (titles == null)
+				throw new ParseException("Could not read site header row on line number " + _csv.Row);
+			var units = GetNextCsvRowValues();
+			if (units == null)
+				throw new ParseException("Could not read site units row on line number " + _csv.Row);
+			var values = GetNextCsvRowValues();
+			if (values == null)
+				throw new ParseException("Could not read site value row on line number " + _csv.Row);
+		
+			var items = new List<Tuple<string, string>>();
+			for (var i = 0; i < titles.Length && i < values.Length; i++)
+			{
+				var item = Tuple.Create(titles[i], values[i]);
+				items.Add(item);
+			}
+			return ParsedObjectFactory<LeafInputSite>.Create(items.ToArray());
+		}
+
+		private LeafInputPhotosynthetic ParseLeafInputPhotosynthetic()
+		{
+			var titles = GetNextCsvRowValues();
+			if (titles == null)
+				throw new ParseException("Could not read photosynthetic header row on line number " + _csv.Row);
+			var units = GetNextCsvRowValues();
+			if (units == null)
+				throw new ParseException("Could not read photosynthetic units row on line number " + _csv.Row);
+			var values = GetNextCsvRowValues();
+			if (values == null)
+				throw new ParseException("Could not read photosynthetic value row on line number " + _csv.Row);
+		
+			var items = new List<Tuple<string, string>>();
+			for (var i = 0; i < titles.Length && i < values.Length; i++)
+			{
+				var item = Tuple.Create(titles[i], values[i]);
+				items.Add(item);
+			}
+			return ParsedObjectFactory<LeafInputPhotosynthetic>.Create(items.ToArray());
+		}
+
+		private LeafInputData[] ParseLeafInputData()
+		{
+			var titles = GetNextCsvRowValues();
+			if (titles == null)
+				throw new ParseException("Could not read data header row on line number " + _csv.Row);
+			var units = GetNextCsvRowValues();
+			if (units == null)
+				throw new ParseException("Could not read data units row on line number " + _csv.Row);
+
+			var valueArrays = new List<string[]>();
+			while (true)
+			{
+				var values = GetNextCsvRowValues();
+				if (values == null)
+					break;
+				valueArrays.Add(values);
+			}
+			return ParsedObjectFactory<LeafInputData>.Create(titles, valueArrays.ToArray());
+		}
+
+		public void Dispose()
+		{
+			_reader.Dispose();
+		}
+
+		public static void ExportCsv(string filename, IEnumerable<LeafInput> leafInputs)
+		{
+			using (var textWriter = new StreamWriter(filename))
+			{
+				var csv = new CsvWriter(textWriter);
+				csv.WriteRecords(leafInputs);
+			}
+		}
+	}
+}
@@ -0,0 +1,12 @@
+using System;
+
+namespace LeafWeb.Core.Services
+{
+	public class ParseException : Exception
+	{
+		public ParseException(string message)
+			: base(message)
+		{
+		}
+	}
+}
@@ -0,0 +1,46 @@
+using System;
+using System.Linq;
+using System.Runtime.CompilerServices;
+using LeafWeb.Core.Utility;
+
+namespace LeafWeb.Core.Services
+{
+	[AttributeUsage(AttributeTargets.Property, AllowMultiple = false, Inherited = true)]
+	public class ParseInfoAttribute : Attribute
+	{
+		public int Position { get; private set; }
+		public string Units { get; private set; }
+		public string Title { get; private set; }
+		public string AlterateTitle { get; private set; }
+		public string ExampleValue { get; private set; }
+		public string[] FieldNames
+		{
+			get
+			{
+				var fieldNames = new[] {Title, Title.SplitCamelCase()};
+				if (!string.IsNullOrEmpty(AlterateTitle))
+					fieldNames = fieldNames.Concat(new[] { AlterateTitle }).ToArray();
+				return fieldNames;
+			}
+		}
+
+		public ParseInfoAttribute(int position, [CallerMemberName]string title = null, string units = null, string alternateTitle = null, string exampleValue = null)
+		{
+			AlterateTitle = alternateTitle;
+			ExampleValue = exampleValue;
+			Title = title;
+			Position = position;
+			Units = units;
+		}
+		
+		public bool IsTitleMatch(string title)
+		{
+			return FieldNames.Any(t => string.Compare(title, t, StringComparison.InvariantCultureIgnoreCase) == 0);
+		}
+
+		public bool IsPositionMatch(int index)
+		{
+			return Position == index;
+		}
+	}
+}
@@ -0,0 +1,159 @@
+using System;
+using System.Linq;
+using System.Reflection;
+using Fasterflect;
+
+namespace LeafWeb.Core.Services
+{
+	public static class ParsedObjectFactory<T> where T : new()
+	{
+		private static PropertyInfo[] GetProperties()
+		{
+			var propertyInfos = typeof(T).Properties();
+			return propertyInfos.Where(p => p.HasAttribute<ParseInfoAttribute>()).ToArray();
+		}
+
+		/// <summary>
+		/// Create an object type T filling properties from the given title values
+		/// </summary>
+		/// <param name="titleValues">Colon separated title: values</param>
+		public static T Create(string[] titleValues)
+		{
+			var properties = GetProperties();
+			var obj = new T();
+			// take each of the 
+			for (var index = 0; index < titleValues.Length; index++)
+			{
+				PropertyInfo property = null;
+				string value = null;
+
+				var lineNumber = index + 1;
+				var row = titleValues[index];
+				var split = row.Split(':');
+				if (split.Length > 1)
+				{
+					// handles case for "Title : Value"
+					var title = split[0].Trim();
+					value = split[1].Trim();
+					property =
+						properties
+						.FirstOrDefault(p => p.Attribute<ParseInfoAttribute>().IsTitleMatch(title));
+				}
+				if (property == null)
+				{
+					// handles case for row number, i.e. "Value"
+					value = row.Trim();
+					property =
+						properties
+						.FirstOrDefault(p => p.Attribute<ParseInfoAttribute>().IsPositionMatch(lineNumber));
+				}
+
+				if (property != null)
+				{
+					object convertedVal;
+					if (!TryConvertValue(property, value, out convertedVal))
+						throw new ParseException(string.Format("Cannot convert value '{0}' for {1} at line number {2}", value, property.Name, lineNumber));
+					property.Set(obj, convertedVal);
+				}
+			}
+			return obj;
+		}
+
+		public static T[] Create(string[] titles, string[][] valueArrays)
+		{
+			var properties = GetProperties();
+			var objs = new T[valueArrays.Length];
+
+			for (var vIndex = 0; vIndex < valueArrays.Length; vIndex++)
+			{
+				var obj = new T();
+				var values = valueArrays[vIndex];
+				for (var tIndex = 0; tIndex < titles.Length; tIndex++)
+				{
+					var title = titles[tIndex];
+					var value = values[tIndex];
+					var position = tIndex + 1;
+
+					if (IsMissingValue(value))
+						continue;
+
+					var property = MatchProperty(properties, title, position);
+
+					if (property != null)
+					{
+						object convertedVal;
+						if (!TryConvertValue(property, value, out convertedVal))
+							throw new ParseException(string.Format("Cannot convert value '{0}' for {1} in position {2}", value, property.Name, position));
+						property.Set(obj, convertedVal);
+					}
+				}
+				objs[vIndex] = obj;
+			}
+			return objs;
+		}
+
+		public static T Create(Tuple<string, string>[] titleValues)
+		{
+			var properties = GetProperties();
+			var obj = new T();
+
+			for (var index = 0; index < titleValues.Length; index++)
+			{
+				var item = titleValues[index];
+				var position = index + 1;
+				var title = item.Item1.Trim();
+				var value = item.Item2.Trim();
+
+				if (IsMissingValue(value))
+					continue;
+
+				var property = MatchProperty(properties, title, position);
+
+				if (property != null)
+				{
+					object convertedVal;
+					if (!TryConvertValue(property, value, out convertedVal))
+						throw new ParseException(string.Format("Cannot convert value '{0}' for {1} in position {2}", value, property.Name, position));
+					property.Set(obj, convertedVal);
+				}
+			}
+			return obj;
+		}
+
+		private static bool IsMissingValue(string value)
+		{
+			return string.IsNullOrEmpty(value) || value == "NA" || value == "-9999";
+		}
+
+		private static PropertyInfo MatchProperty(PropertyInfo[] properties, string title, int position)
+		{
+			var property =
+				properties
+				.FirstOrDefault(p => p.Attribute<ParseInfoAttribute>().IsTitleMatch(title));
+
+			if (property == null)
+			{
+				property =
+					properties
+					.FirstOrDefault(p => p.Attribute<ParseInfoAttribute>().IsPositionMatch(position));
+			}
+			return property;
+		}
+
+		private static bool TryConvertValue(PropertyInfo property, object value, out object convertedValue)
+		{
+			try
+			{
+				// http://stackoverflow.com/questions/3531318/convert-changetype-fails-on-nullable-types
+				var t = Nullable.GetUnderlyingType(property.PropertyType) ?? property.PropertyType;
+				convertedValue = Convert.ChangeType(value, t);
+			}
+			catch (Exception)
+			{
+				convertedValue = null;
+				return false;
+			}
+			return true;
+		}
+	}
+}
@@ -0,0 +1,17 @@
+using System;
+using System.Globalization;
+using System.Linq;
+
+namespace LeafWeb.Core.Utility
+{
+	public static class StringExtensions
+	{
+		public static string SplitCamelCase(this string str)
+		{
+			return str.Aggregate(
+				String.Empty,
+				(current, c) =>
+				current + (Char.IsUpper(c) && current.Length > 0 ? " " + c : c.ToString(CultureInfo.InvariantCulture)));
+		}
+	}
+}
@@ -0,0 +1,6 @@
+<?xml version="1.0" encoding="utf-8"?>
+<packages>
+  <package id="CsvHelper" version="2.13.2.0" targetFramework="net45" />
+  <package id="EntityFramework" version="6.1.3" targetFramework="net45" />
+  <package id="fasterflect" version="2.1.3" targetFramework="net45" />
+</packages>