Smm module

BExIS++.sln

@@ -1,6 +1,6 @@
 Microsoft Visual Studio Solution File, Format Version 12.00
-# Visual Studio Version 17
-VisualStudioVersion = 17.9.34723.18
+# Visual Studio Version 18
+VisualStudioVersion = 18.2.11415.280
 MinimumVisualStudioVersion = 10.0.40219.1
 Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "Console", "Console", "{A24A6801-2ECC-4F47-8284-8C93277D3030}"
 EndProject

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

@@ -124,6 +124,7 @@
     <Compile Include="Party\PartyTypePair.cs" />
     <Compile Include="Party\PartyCustomGridColumns.cs" />
     <Compile Include="Properties\AssemblyInfo.cs" />
+    <Compile Include="SpeciesMatching\SpeciesMatchingResult.cs" />
   </ItemGroup>
   <ItemGroup>
     <None Include="Administration\Administration.cd" />

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

@@ -0,0 +1,78 @@
+using BExIS.Dlm.Entities.Data;
+using BExIS.Security.Entities.Subjects;
+using System;
+using Vaiona.Entities.Common;
+
+namespace BExIS.Dlm.Entities.SpeciesMatching
+{
+    public class SpeciesMatchingResult : BaseEntity
+    {
+
+        // original unchanged name (used for matching if EditedName is empty, and for display purposes)
+        public virtual string OriginalName { get; set; }
+
+        // edited name after data cleaning + manual corrections (used for matching)
+        public virtual string EditedName { get; set; }
+
+        // matched name from the external source (the result)
+        public virtual string MatchedName { get; set; }
+
+        // taxonomic status of the matched name (e.g. accepted, synonym, etc.)
+        public virtual string Status { get; set; }
+
+        // type of the match (e.g. exact, fuzzy, etc.)
+        public virtual string MatchType { get; set; }
+
+        // taxonomic rank of the matched name (e.g. species, genus, etc.)
+        public virtual string MatchRank { get; set; }
+
+        // unique identifier of the matched name in the external source (e.g. GBIF taxon ID)
+        public virtual string MatchId { get; set; }
+
+        // authorship of the matched name
+        public virtual string MatchAuthorship { get; set; }
+
+        // accepted name if (for example) the matched name is a synonym
+        public virtual string AcceptedScientificName { get; set; }
+
+        // unique identifier of the accepted name in the external source (e.g. GBIF taxon ID)
+        public virtual string AcceptedId { get; set; }
+
+        // authorship of the accepted name
+        public virtual string AcceptedAuthorship { get; set; }
+
+        // higher classification of the matched name (e.g. kingdom, phylum, class, order, family, genus)
+        public virtual string TaxonKingdom { get; set; }
+
+        public virtual string TaxonPhylum { get; set; }
+
+        public virtual string TaxonClass { get; set; }
+
+        public virtual string TaxonOrder { get; set; }
+
+        public virtual string TaxonFamily { get; set; }
+
+        public virtual string TaxonGenus { get; set; }
+
+        // timestamp of the match (can vary by hours due to processing and queue times on different APIs)
+        public virtual DateTime TimestampMatch { get; set; }
+
+        // source of the match (e.g. Catalogue of Life, GBIF, etc.)
+        public virtual string MatchSource { get; set; }
+
+        // version of the source used for matching
+        public virtual string MatchSourceVersion { get; set; }
+
+        // indicates whether the match has been confirmed by the user
+        public virtual bool ConfirmedByUser { get; set; }
+
+        // reference to the dataset where the original name was taken from
+        public virtual Dataset Dataset { get; set; }
+
+        // VersionId + Dataset make the unique key for the matching result
+        public virtual long DatasetVersionId { get; set; }
+
+        // reference to the Matching step (or -1 if the result is not associated with a specific step)
+        public virtual long StepId { get; set; }
+    }
+}

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

@@ -239,6 +239,7 @@
       <SubType>Designer</SubType>
     </Content>
     <Content Include="Mappings\Default\Party\PartyTypePair.hbm.xml" />
+    <Content Include="Mappings\Default\SpeciesMatching\SpeciesMatchingResult.hbm.xml" />
     <Content Include="Mappings\PostgreSQL82Dialect\NativeObjects\Queries.hbm.xml">
       <CopyToOutputDirectory>PreserveNewest</CopyToOutputDirectory>
       <SubType>Designer</SubType>

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

@@ -0,0 +1,68 @@
+<?xml version="1.0" encoding="utf-8" ?>
+<hibernate-mapping xmlns="urn:nhibernate-mapping-2.2" assembly="BExIS.Dlm.Entities" namespace="BExIS.Dlm.Entities.SpeciesMatching">
+
+	<class name="SpeciesMatchingResult" table="smm_species_matching_result" lazy="true">
+		<id name="Id" column="id" type="Int64">
+			<generator class="native"/>
+		</id>
+
+		<property name="OriginalName" column="original_name" type="string" not-null="false" />
+
+		<property name="EditedName" column="edited_name" type="string" not-null="false" />
+
+		<property name="MatchedName" column="matched_name" type="string" not-null="false" />
+
+		<property name="Status" column="status" type="string" not-null="false" />
+
+		<property name="MatchType" column="match_type" type="string" not-null="false" />
+
+		<property name="MatchRank" column="match_rank" type="string" not-null="false" />
+
+		<property name="MatchId" column="match_id" type="string" not-null="false" />
+
+		<property name="MatchAuthorship" column="match_authorship" type="string" not-null="false" />
+
+		<property name="AcceptedScientificName" column="accepted_scientific_name" type="string" not-null="false" />
+
+		<property name="AcceptedId" column="accepted_id" type="string" not-null="false" />
+
+		<property name="AcceptedAuthorship" column="accepted_authorship" type="string" not-null="false" />
+
+		<property name="TaxonKingdom" column="taxon_kingdom" type="string" not-null="false" />
+
+		<property name="TaxonPhylum" column="taxon_phylum" type="string" not-null="false" />
+
+		<property name="TaxonClass" column="taxon_class" type="string" not-null="false" />
+
+		<property name="TaxonOrder" column="taxon_order" type="string" not-null="false" />
+
+		<property name="TaxonFamily" column="taxon_family" type="string" not-null="false" />
+
+		<property name="TaxonGenus" column="taxon_genus" type="string" not-null="false" />	
+
+		<property name="TimestampMatch" column="timestamp_match" type="DateTime" not-null="false" />
+
+		<property name="MatchSource" column="match_source" type="string" not-null="false" />
+
+		<property name="MatchSourceVersion" column="match_source_version" type="string" not-null="false" />
+
+		<property name="ConfirmedByUser" column="confirmed_by_user" type="bool" not-null="false" />
+
+		<property name="StepId" column="step_id" type="Int64" not-null="false" />
+
+		<!-- Mapping entity associations -->
+
+		<property name="DatasetVersionId" column="dataset_version_id" type="Int64" not-null="false" />
+
+		<!--Dataset-->
+		<many-to-one name="Dataset" class="BExIS.Dlm.Entities.Data.Dataset" not-null="false" column="DatasetRef" />
+
+		<!--DatasetVersion (does not work this way ... Error: refers to unmapped ...-->
+		<!--
+		<many-to-one class="DatasetVersion" name="DatasetVersion" column="DatasetVersionRef">
+		</many-to-one>
+		-->
+
+	</class>
+
+</hibernate-mapping>

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

@@ -166,6 +166,7 @@
     <Compile Include="Party\PartyRelationshipTypeManager.cs" />
     <Compile Include="Party\PartyTypeManager.cs" />
     <Compile Include="Properties\AssemblyInfo.cs" />
+    <Compile Include="SpeciesMatching\SpeciesMatchingResultManager.cs" />
     <Compile Include="TypeSystem\DataTypeCode.cs" />
     <Compile Include="TypeSystem\DataTypeInfo.cs" />
     <Compile Include="TypeSystem\DataTypeUtility.cs" />

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

@@ -0,0 +1,142 @@
+using BExIS.Dlm.Entities.Data;
+using BExIS.Dlm.Entities.SpeciesMatching;
+using System;
+using System.Collections.Generic;
+using System.Diagnostics.Contracts;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+using Vaiona.Persistence.Api;
+
+namespace BExIS.Dlm.Services.SpeciesMatching
+{
+    public class SpeciesMatchingResultManager : IDisposable
+    {
+
+        private IUnitOfWork guow = null;
+
+        public SpeciesMatchingResultManager()
+        {
+            guow = this.GetIsolatedUnitOfWork();
+            this.Repo = guow.GetReadOnlyRepository<SpeciesMatchingResult>();
+        }
+
+        private bool isDisposed = false;
+
+        ~SpeciesMatchingResultManager()
+        {
+            Dispose(true);
+        }
+
+        public void Dispose()
+        {
+            Dispose(true);
+        }
+
+        protected virtual void Dispose(bool disposing)
+        {
+            if (!isDisposed)
+            {
+                if (disposing)
+                {
+                    if (guow != null)
+                        guow.Dispose();
+                    isDisposed = true;
+                }
+            }
+        }
+
+        public IReadOnlyRepository<SpeciesMatchingResult> Repo { get; private set; }
+
+        public SpeciesMatchingResult Create(SpeciesMatchingResult matchingResult)
+        {
+            if (matchingResult == null) throw new ArgumentNullException("Species matching result must not be null.");
+            if (matchingResult.Dataset == null) throw new ArgumentNullException("Dataset must not be null.");
+            if (matchingResult.OriginalName == null) throw new ArgumentNullException("Dataset must not be null.");
+
+            using (IUnitOfWork uow = this.GetUnitOfWork())
+            {
+                try
+                {
+                    IRepository<SpeciesMatchingResult> repo = uow.GetRepository<SpeciesMatchingResult>();
+                    repo.Put(matchingResult);
+                    uow.Commit();
+
+                    return (matchingResult);
+                }
+                catch (Exception ex)
+                {
+                    throw new Exception("SpeciesMatchingResult creation failed.", ex);
+                }
+            }
+        }
+
+        public SpeciesMatchingResult Update(SpeciesMatchingResult matchingResult)
+        {
+            if (matchingResult == null) throw new ArgumentNullException("Species matching result must not be null.");
+
+            Contract.Ensures(Contract.Result<SpeciesMatchingResult>() != null && Contract.Result<SpeciesMatchingResult>().Id >= 0);
+
+            using (IUnitOfWork uow = this.GetUnitOfWork())
+            {
+                try
+                {
+                    IRepository<SpeciesMatchingResult> repo = uow.GetRepository<SpeciesMatchingResult>();
+                    repo.Merge(matchingResult);
+                    var merged = repo.Get(matchingResult.Id);
+                    repo.Put(merged);
+                    uow.Commit();
+
+                    return (merged);
+                }
+                catch (Exception ex)
+                {
+                    throw new Exception("SpeciesMatchingResult creation failed.", ex);
+                }
+            }
+        }
+        public bool Delete(long id)
+        {
+            if (id == 0) throw new ArgumentException("Species matching result must not be null.");
+
+            Contract.Ensures(Contract.Result<SpeciesMatchingResult>() != null && Contract.Result<SpeciesMatchingResult>().Id >= 0);
+
+            using (IUnitOfWork uow = this.GetUnitOfWork())
+            {
+                IRepository<SpeciesMatchingResult> repo = uow.GetRepository<SpeciesMatchingResult>();
+
+                var e = repo.Get(id);
+
+                if (e != null)
+                {
+                    repo.Delete(e);
+                    uow.Commit();
+
+                    return true;
+                }
+                else
+                {
+                    throw new ArgumentException(string.Format("the species matching result with the id {0} does not exist", id));
+                }
+            }
+        }
+
+        public bool Delete(SpeciesMatchingResult matchingResult)
+        {
+            if (matchingResult == null) throw new ArgumentNullException("Entity template must not be null.");
+
+            Contract.Ensures(Contract.Result<SpeciesMatchingResult>() != null && Contract.Result<SpeciesMatchingResult>().Id >= 0);
+
+            using (IUnitOfWork uow = this.GetUnitOfWork())
+            {
+                IRepository<SpeciesMatchingResult> repo = uow.GetRepository<SpeciesMatchingResult>();
+
+                repo.Delete(matchingResult);
+                uow.Commit();
+
+                return true;
+            }
+        }
+
+    }
+}

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

@@ -231,6 +231,7 @@
     <Compile Include="Services\Party\PartyManagerTests.cs" />
     <Compile Include="Services\Party\PartyRelationshipTypeManagerTest.cs" />
     <Compile Include="Services\Party\PartyTypeManagerTests.cs" />
+    <Compile Include="Services\SpeciesMatching\SpeciesMatchingResultManagerTest.cs" />
   </ItemGroup>
   <ItemGroup>
     <None Include="app.config">