zaaReloaded2/zaaReloaded2/Importer/ZaaImporter/LaurisItem.cs

/* LabItem.cs
 * part of zaaReloaded2
 * 
 * Copyright 2015-2017 Daniel Kraus
 * 
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 * 
 *     http://www.apache.org/licenses/LICENSE-2.0
 * 
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */
using System;
using System.Globalization;
using System.Text.RegularExpressions;
using zaaReloaded2.LabModel;

namespace zaaReloaded2.Importer.ZaaImporter
{
    /// <summary>
    /// Represents a single laboratory item (e.g., sodium or creatinine).
    /// </summary>
    public class LaurisItem : LabItem
    {
        #region Properties

        /// <summary>
        /// The original Lauris string from which this lab item was created.
        /// </summary>
        public string LaurisText { get; private set; }

        /// <summary>
        /// The original name of this item as known by Lauris
        /// </summary>
        public string OriginalName { get; private set; }

        #endregion

        #region Constructors

        /// <summary>
        /// Creates an empty LabItem object.
        /// </summary>
        public LaurisItem() : base() { }

        public LaurisItem(string laurisString)
            : this()
        {
            LaurisText = laurisString;
            ParseLauris();
            DetectMaterial();
        }

        /// <summary>
        /// Creates a LabItem object from a given Lauris output, using
        /// a <see cref="ParameterDictionary"/> too look up additional
        /// properties (canonical name, material type, whether or not
        /// to always print the reference interval).
        /// </summary>
        /// <param name="laurisString">Lauris output to parse.</param>
        /// <param name="parameterDictionary">ParameterDictionary that is used
        /// to look up the canonical name, material type, and whether or
        /// not to always print the reference interval</param>
        public LaurisItem(string laurisString,
                Thesaurus.Parameters parameterDictionary,
                Thesaurus.Units unitDictionary)
            : this(laurisString)
        {
            if (parameterDictionary != null)
            {
                Name = parameterDictionary.GetCanonicalName(OriginalName);
                AlwaysPrintLimits = parameterDictionary.GetForceReferenceDisplay(OriginalName);
                IsBlacklisted = parameterDictionary.GetIsBlacklisted(OriginalName);
                Material = parameterDictionary.GetMaterial(OriginalName, Material);
                PreferredPrecision = parameterDictionary.GetPrecision(OriginalName);
            }
            if (unitDictionary != null)
            {
                Unit = unitDictionary.TranslateLaurisUnit(Unit);
            }
        }

        #endregion

        #region Private methods

        /// <summary>
        /// Parses the original Lauris string contained in
        /// <see cref="LaurisText"/>.
        /// </summary>
        void ParseLauris()
        {
            // Examples of Lauris output strings:
            // "Natrium: 139 [135 - 145] mmol/l"
            // "HDL - Cholesterin: 45 [>= 35] mg/dl"
            // "GOT (ASAT): 303.0 [<= 50] U/l; "
            // "Niedermol. Heparin (Anti-Xa): 0.99 U/ml;"
            // "HBs-Antigen: neg. ;"
            // "Erythrozyten (U): + [negativ]"
            Match match;
            Logger.Debug("ParseLauris: {0}", LaurisText);
            if (_numericalRegex.IsMatch(LaurisText))
            {
                Logger.Debug("ParseLauris: Numerical match");
                match = _numericalRegex.Match(LaurisText);
                ParseLimits(match);
                Value = match.Groups["value"].Value.Trim().Replace(',', '.');
            }
            else
            {
                Logger.Debug("ParseLauris: Not a numerical match");
                match = _categoricalRegex.Match(LaurisText);
                Normal = match.Groups["normal"].Value.Trim();
                Value = match.Groups["value"].Value.Trim();
            }
            if (match != null)
            {
                OriginalName = match.Groups["name"].Value.Trim();
                Name = OriginalName;
                Unit = match.Groups["unit"].Value.Trim();
                Logger.Debug("ParseLauris: Match: {0}, {1}", Name, Unit);
            }
            else
            {
                Logger.Debug("ParseLauris: No match: \"{0}\"", LaurisText);
            }
        }

        /// <summary>
        /// Parses a string containing value limits. The string must be like
        /// "[3.5 - 5]", "[>= 50]", or "[&lt;= 100]".
        /// </summary>
        /// <param name="match">Match object that should contain a group "limits".</param>
        void ParseLimits(Match match)
        {
            if (match.Groups["limits"].Success)
            {
                Logger.Debug("ParseLimits: Has limits: {0}", match.Groups["limits"].Value);
                Match limitMatch = _limitRegex.Match(match.Groups["limits"].Value);
                if (limitMatch.Groups["limit1"].Success && limitMatch.Groups["limit2"].Success)
                {
                    Logger.Debug("ParseLimits: Upper and lower limit detected");
                    // Use InvariantCulture because Lauris always outputs dots as decimal separator
                    // Only in rare cases, a comma sneaks in...
                    LowerLimit = Double.Parse(limitMatch.Groups["limit1"].Value.Replace(',', '.'),
                        CultureInfo.InvariantCulture);
                    UpperLimit = Double.Parse(limitMatch.Groups["limit2"].Value.Replace(',', '.'),
                        CultureInfo.InvariantCulture);
                }
                else
                {
                    Logger.Debug("ParseLimits: Single limit detected");
                    switch (limitMatch.Groups["operator"].Value.Trim())
                    {
                        case "<=":
                            UpperLimit = Double.Parse(limitMatch.Groups["limit2"].Value.Replace(',', '.'),
                                CultureInfo.InvariantCulture);
                            break;
                        case ">=":
                            LowerLimit = Double.Parse(limitMatch.Groups["limit2"].Value.Replace(',', '.'),
                                CultureInfo.InvariantCulture);
                            break;
                        case "":
                            // NOOP for special cases such as "[s. Bem.]" which occurs in NT-proBNP
                            // Fixes exception ID 65ca8575.
                            break;
                        default:
                            string unknown = match.Groups["limits"].Value;
                            Logger.Fatal("ParseLimits: Unknown operator \"{0}\"", unknown);
                            throw new InvalidOperationException(String.Format("Unknown operator in {0}",unknown));
                    }
                }
            }
        }

        /// <summary>
        /// Parses the original Lauris name for a material abbreviation.
        /// This may be misleading in certain cases, e.g. "Sammelmenge (U)"
        /// appears to be spot urine ("U"), but is collected urine instead
        /// ("SU"). Therefore, in the constructor that takes the thesaurus
        /// parameters, the material is looked up in the Parameters thesaurus.
        /// ("Sammelmenge (U)" is contained in the Parameters thesaurus.)
        /// </summary>
        /// <example>
        /// Gesamt-Eiweiss (SU), Albumin (SU)/die, Gesamt-Eiweiss (PU)
        /// </example>
        void DetectMaterial()
        {
            // The material is encoded in the original name of the item
            // that was produced by Lauris (eg. "Natrium (PU)" for spot
            // urine).
            Match m = _materialRegex.Match(OriginalName);
            if (m.Success)
            {
                switch (m.Groups["material"].Value.ToUpper())
                {
                    case "SU":
                        Material = LabModel.Material.SU;
                        break;
                    case "PU":
                        Material = LabModel.Material.U;
                        break;
                }
            }
        }

        #endregion

        #region Fields

        static readonly Regex _numericalRegex = new Regex(
            @"(?<name>[^:]+):\s*(?<value>([\<\>]\s)?[\d,.]+)\s*(?<limits>\[[^\]]+])?\s*(?<unit>[^;]+)?");
        static readonly Regex _categoricalRegex = new Regex(
            @"(?<name>[^:]+):\s*(?<value>[^[;]+)\s*(\[(?<normal>[^\]]+)])?");
        static readonly Regex _limitRegex = new Regex(@"\[(?<limit1>[-\d,.]+)?\s*(?<operator>\S+)\s*(?<limit2>[-\d,.]+)?]");
        static readonly Regex _materialRegex = new Regex(@"\((?<material>(SU|PU))\)");

        #endregion

        #region Class logger

        private static NLog.Logger Logger { get { return _logger.Value; } }

        private static readonly Lazy<NLog.Logger> _logger = new Lazy<NLog.Logger>(() => NLog.LogManager.GetCurrentClassLogger());

        #endregion
    }
}