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FlatErikkFlatErikk
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initial push for smm functionalities #980 
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‎BExIS++.sln‎

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Microsoft Visual Studio Solution File, Format Version 12.00
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# Visual Studio Version 17
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VisualStudioVersion = 17.9.34723.18
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# Visual Studio Version 18
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VisualStudioVersion = 18.2.11415.280
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MinimumVisualStudioVersion = 10.0.40219.1
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Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "Console", "Console", "{A24A6801-2ECC-4F47-8284-8C93277D3030}"
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EndProject

‎Components/DLM/BExIS.Dlm.Entities/BExIS.Dlm.Entities.csproj‎

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<Compile Include="Party\PartyTypePair.cs" />
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<Compile Include="Party\PartyCustomGridColumns.cs" />
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<Compile Include="Properties\AssemblyInfo.cs" />
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<Compile Include="SpeciesMatching\SpeciesMatchingResult.cs" />
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</ItemGroup>
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<ItemGroup>
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<None Include="Administration\Administration.cd" />

‎Components/DLM/BExIS.Dlm.Entities/SpeciesMatching/SpeciesMatchingResult.cs‎

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using BExIS.Dlm.Entities.Data;
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using BExIS.Security.Entities.Subjects;
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using System;
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using Vaiona.Entities.Common;
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namespace BExIS.Dlm.Entities.SpeciesMatching
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{
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public class SpeciesMatchingResult : BaseEntity
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{
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// original unchanged name submitted for matching
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public virtual string OriginalName { get; set; }
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// cleaned name after preprocessing (e.g. trimming, removing special characters, etc.)
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public virtual string CleanedName { get; set; }
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// edited name after manual corrections (if any)
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public virtual string EditedName { get; set; }
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// matched name from the external source
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public virtual string MatchedName { get; set; }
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// taxonomic status of the matched name (e.g. accepted, synonym, etc.)
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public virtual string Status { get; set; }
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// type of the match (e.g. exact, fuzzy, etc.)
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public virtual string MatchType { get; set; }
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// timestamp of the match
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public virtual DateTime TimestampMatch { get; set; }
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// source of the match (e.g. Catalogue of Life, GBIF, etc.)
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public virtual string MatchSource { get; set; }
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// version of the source used for matching
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public virtual string MatchSourceVersion { get; set; }
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// indicates whether the match has been confirmed by the user
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public virtual bool ConfirmedByUser { get; set; }
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// reference to the dataset where the original name was taken from
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public virtual Dataset Dataset { get; set; }
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// reference to the specific version of the dataset
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// TODO: get this to work (maybe as a normal field instead of many-to-one relation)
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//public virtual DatasetVersion DatasetVersion { get; set; }
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// reference to the user who owns this matching result
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public virtual User Creator { get; set; }
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}
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}

‎Components/DLM/BExIS.Dlm.Orm.NH/BExIS.Dlm.Orm.NH.csproj‎

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<SubType>Designer</SubType>
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</Content>
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<Content Include="Mappings\Default\Party\PartyTypePair.hbm.xml" />
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<Content Include="Mappings\Default\SpeciesMatching\SpeciesMatchingResult.hbm.xml" />
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<Content Include="Mappings\PostgreSQL82Dialect\NativeObjects\Queries.hbm.xml">
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<CopyToOutputDirectory>PreserveNewest</CopyToOutputDirectory>
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<SubType>Designer</SubType>

‎Components/DLM/BExIS.Dlm.Orm.NH/Mappings/Default/SpeciesMatching/SpeciesMatchingResult.hbm.xml‎

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<?xml version="1.0" encoding="utf-8" ?>
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<hibernate-mapping xmlns="urn:nhibernate-mapping-2.2" assembly="BExIS.Dlm.Entities" namespace="BExIS.Dlm.Entities.SpeciesMatching">
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<class name="SpeciesMatchingResult" table="smm_species_matching_result" lazy="true">
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<id name="Id" column="id" type="Int64">
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<generator class="native"/>
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</id>
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<property name="OriginalName" column="original_name" type="string" not-null="false" />
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<property name="CleanedName" column="cleaned_name" type="string" not-null="false" />
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<property name="EditedName" column="edited_name" type="string" not-null="false" />
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<property name="MatchedName" column="matched_name" type="string" not-null="false" />
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<property name="Status" column="status" type="string" not-null="false" />
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<property name="MatchType" column="match_type" type="string" not-null="false" />
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<property name="TimestampMatch" column="timestamp_match" type="DateTime" not-null="false" />
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<property name="MatchSource" column="match_source" type="string" not-null="false" />
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<property name="MatchSourceVersion" column="match_source_version" type="string" not-null="false" />
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<property name="ConfirmedByUser" column="confirmed_by_user" type="bool" not-null="false" />
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<!-- Mapping entity associations -->
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<!--Dataset-->
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<many-to-one name="Dataset" class="BExIS.Dlm.Entities.Data.Dataset" not-null="false" column="DatasetRef" />
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<!--Creator-->
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<many-to-one name="Creator" class="BExIS.Security.Entities.Subjects.User" not-null="false" column="UserRef" />
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<!--DatasetVersion (does not work this way ... Error: refers to unmapped ...-->
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<!--
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<many-to-one class="DatasetVersion" name="DatasetVersion" column="DatasetVersionRef">
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</many-to-one>
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-->
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</class>
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</hibernate-mapping>

‎Components/DLM/BExIS.Dlm.Services/BExIS.Dlm.Services.csproj‎

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<Compile Include="Party\PartyRelationshipTypeManager.cs" />
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<Compile Include="Party\PartyTypeManager.cs" />
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<Compile Include="Properties\AssemblyInfo.cs" />
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<Compile Include="SpeciesMatching\SpeciesMatchingResultManager.cs" />
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<Compile Include="TypeSystem\DataTypeCode.cs" />
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<Compile Include="TypeSystem\DataTypeInfo.cs" />
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<Compile Include="TypeSystem\DataTypeUtility.cs" />

‎Components/DLM/BExIS.Dlm.Services/SpeciesMatching/SpeciesMatchingResultManager.cs‎

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using BExIS.Dlm.Entities.Data;
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using BExIS.Dlm.Entities.SpeciesMatching;
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using System;
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using System.Collections.Generic;
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using System.Diagnostics.Contracts;
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using System.Linq;
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using System.Text;
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using System.Threading.Tasks;
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using Vaiona.Persistence.Api;
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namespace BExIS.Dlm.Services.SpeciesMatching
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{
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public class SpeciesMatchingResultManager : IDisposable
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{
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private IUnitOfWork guow = null;
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public SpeciesMatchingResultManager()
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{
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guow = this.GetIsolatedUnitOfWork();
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this.Repo = guow.GetReadOnlyRepository<SpeciesMatchingResult>();
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}
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private bool isDisposed = false;
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~SpeciesMatchingResultManager()
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{
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Dispose(true);
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}
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public void Dispose()
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{
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Dispose(true);
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}
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protected virtual void Dispose(bool disposing)
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{
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if (!isDisposed)
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{
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if (disposing)
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{
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if (guow != null)
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guow.Dispose();
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isDisposed = true;
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}
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}
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}
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public IReadOnlyRepository<SpeciesMatchingResult> Repo { get; private set; }
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public SpeciesMatchingResult Create(SpeciesMatchingResult matchingResult)
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{
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if (matchingResult == null) throw new ArgumentNullException("Species matching result must not be null.");
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if (matchingResult.Creator == null) throw new ArgumentNullException("Creator type must not be null.");
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if (matchingResult.Dataset == null) throw new ArgumentNullException("Dataset must not be null.");
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if (matchingResult.OriginalName == null) throw new ArgumentNullException("Dataset must not be null.");
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using (IUnitOfWork uow = this.GetUnitOfWork())
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{
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try
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{
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IRepository<SpeciesMatchingResult> repo = uow.GetRepository<SpeciesMatchingResult>();
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repo.Put(matchingResult);
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uow.Commit();
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return (matchingResult);
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}
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catch (Exception ex)
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{
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throw new Exception("SpeciesMatchingResult creation failed.", ex);
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}
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}
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}
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public SpeciesMatchingResult Update(SpeciesMatchingResult matchingResult)
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{
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if (matchingResult == null) throw new ArgumentNullException("Species matching result must not be null.");
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Contract.Ensures(Contract.Result<SpeciesMatchingResult>() != null && Contract.Result<SpeciesMatchingResult>().Id >= 0);
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using (IUnitOfWork uow = this.GetUnitOfWork())
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{
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try
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{
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IRepository<SpeciesMatchingResult> repo = uow.GetRepository<SpeciesMatchingResult>();
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repo.Merge(matchingResult);
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var merged = repo.Get(matchingResult.Id);
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repo.Put(merged);
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uow.Commit();
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return (merged);
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}
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catch (Exception ex)
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{
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throw new Exception("SpeciesMatchingResult creation failed.", ex);
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}
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}
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}
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public bool Delete(long id)
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{
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if (id == 0) throw new ArgumentException("Species matching result must not be null.");
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Contract.Ensures(Contract.Result<SpeciesMatchingResult>() != null && Contract.Result<SpeciesMatchingResult>().Id >= 0);
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using (IUnitOfWork uow = this.GetUnitOfWork())
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{
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IRepository<SpeciesMatchingResult> repo = uow.GetRepository<SpeciesMatchingResult>();
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var e = repo.Get(id);
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if (e != null)
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{
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repo.Delete(e);
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uow.Commit();
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return true;
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}
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else
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{
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throw new ArgumentException(string.Format("the species matching result with the id {0} does not exist", id));
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}
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}
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}
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public bool Delete(SpeciesMatchingResult matchingResult)
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{
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if (matchingResult == null) throw new ArgumentNullException("Entity template must not be null.");
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Contract.Ensures(Contract.Result<SpeciesMatchingResult>() != null && Contract.Result<SpeciesMatchingResult>().Id >= 0);
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using (IUnitOfWork uow = this.GetUnitOfWork())
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{
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IRepository<SpeciesMatchingResult> repo = uow.GetRepository<SpeciesMatchingResult>();
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repo.Delete(matchingResult);
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uow.Commit();
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return true;
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}
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}
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}
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}

‎Components/DLM/BExIS.Dlm.Tests/BExIS.Dlm.Tests.csproj‎

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<Compile Include="Services\Party\PartyManagerTests.cs" />
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<Compile Include="Services\Party\PartyRelationshipTypeManagerTest.cs" />
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<Compile Include="Services\Party\PartyTypeManagerTests.cs" />
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<Compile Include="Services\SpeciesMatching\SpeciesMatchingResultManagerTest.cs" />
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</ItemGroup>
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<ItemGroup>
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<None Include="app.config">

‎Components/DLM/BExIS.Dlm.Tests/Services/SpeciesMatching/SpeciesMatchingResultManagerTest.cs‎

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using BExIS.App.Testing;
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using BExIS.Dlm.Entities.Data;
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using BExIS.Dlm.Entities.SpeciesMatching;
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using BExIS.Dlm.Services.Data;
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using BExIS.Dlm.Services.MetadataStructure;
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using BExIS.Dlm.Services.SpeciesMatching;
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using BExIS.Security.Services.Objects;
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using BExIS.Security.Services.Subjects;
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using BExIS.Utils.Config;
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using NUnit.Framework;
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using System;
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using System.Collections.Generic;
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using System.Linq;
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using System.Text;
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using System.Threading.Tasks;
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namespace BExIS.Dlm.Tests.Services.SpeciesMatching
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{
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internal class SpeciesMatchingResultManagerTest
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{
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private TestSetupHelper helper = null;
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[OneTimeSetUp]
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public void OneTimeSetUp()
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{
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helper = new TestSetupHelper(WebApiConfig.Register, false);
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}
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[OneTimeTearDown]
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public void OneTimeTearDown()
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{
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}
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[Test()]
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public void Create_Valid_EntityTemplate()
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{
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using (var speciesMatchingResultManager = new SpeciesMatchingResultManager())
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using (var userManager = new UserManager())
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using (var datasetManager = new DatasetManager())
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{
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//Arrange
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SpeciesMatchingResult matchingResult = new SpeciesMatchingResult();
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var user = userManager.Users.FirstOrDefault();
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var dataset = datasetManager.DatasetRepo.Get().FirstOrDefault();
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matchingResult.OriginalName = "Sunflower";
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matchingResult.CleanedName = "";
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matchingResult.EditedName = "";
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matchingResult.MatchedName = "";
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matchingResult.Status = "";
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matchingResult.MatchType = "";
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matchingResult.TimestampMatch = DateTime.Now;
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matchingResult.MatchSource = "";
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matchingResult.MatchSourceVersion = "";
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matchingResult.ConfirmedByUser = false;
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matchingResult.Dataset = dataset;
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matchingResult.Creator = user;
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//Act
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var created = speciesMatchingResultManager.Create(matchingResult);
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var fromdb = speciesMatchingResultManager.Repo.Get().LastOrDefault();
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//Assert
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Assert.IsNotNull(created);
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Assert.IsNotNull(fromdb);
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Assert.That(created.Id.Equals(fromdb.Id));
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}
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}
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}
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}

‎Console/BExIS.Web.Shell/Areas/SMM/BExIS.Modules.SMM.UI.Svelte/package-lock.json‎

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