Merge pull request #1825 from HicServices/task/RDMP-182-use-synthehr

update to use synthehr

CHANGELOG.md

@@ -14,6 +14,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Add prompt to reanem container when adding a cohort filter
 - Fix to remove stack trace button from non error popups
 - Add ability to set Extraction Categort as "Not Extractable"
+- Replace BadMedicine v1.2.1 with SynthEHR v2.0.0
 
 ## [8.1.5] - 2024-04-03
 

Directory.Packages.props

@@ -4,7 +4,7 @@
 		<PackageVersion Include="Equ" Version="2.3.0"/>
 		<PackageVersion Include="ExcelNumberFormat" Version="1.1.0"/>
 		<PackageVersion Include="FluentFTP" Version="50.0.1"/>
-		<PackageVersion Include="HIC.BadMedicine" Version="1.2.1"/>
+		<PackageVersion Include="HIC.SynthEHR" Version="2.0.0"/>
 		<PackageVersion Include="HIC.FAnsiSql" Version="3.2.2"/>
 		<PackageVersion Include="LibArchive.Net" Version="0.1.5"/>
 		<PackageVersion Include="Microsoft.SourceLink.GitHub" Version="8.0.0">

Documentation/CodeTutorials/Packages.md

@@ -25,7 +25,7 @@
 | LibArchive.Net | [GitHub](https://github.com/jas88/libarchive.net) | [BSD](https://opensource.org/license/bsd-2-clause/) | Access archive formats without the LZMA bugs of SharpCompress | |
 | [NLog](https://nlog-project.org/) | [GitHub](https://github.com/NLog/NLog) | [BSD 3-Clause](https://github.com/NLog/NLog/blob/dev/LICENSE.txt) | Flexible user configurable logging | |
 | HIC.FAnsiSql |[GitHub](https://github.com/HicServices/FAnsiSql) | [GPL 3.0](https://www.gnu.org/licenses/gpl-3.0.html) | [DBMS] abstraction layer |
-| HIC.BadMedicine | [GitHub](https://github.com/HicServices/BadMedicine) | [GPL 3.0](https://www.gnu.org/licenses/gpl-3.0.html) | Generate Test Datasets for tests/exericses |
+| HIC.SynthEHR | [GitHub](https://github.com/HicServices/SynthEHR) | [GPL 3.0](https://www.gnu.org/licenses/gpl-3.0.html) | Generate Test Datasets for tests/exericses |
 | SSH.NET  | [GitHub](https://github.com/sshnet/SSH.NET)  | [MIT](https://github.com/sshnet/SSH.NET/blob/develop/LICENSE) | Enables fetching files from SFTP servers |
 | Moq 4 | [GitHub](https://github.com/moq/moq4) |[BSD 3](https://github.com/moq/moq4/blob/master/License.txt)  | Mock objects during unit testing |
 | [Newtonsoft.Json](https://www.newtonsoft.com/json) | [GitHub](https://github.com/JamesNK/Newtonsoft.Json) | [MIT](https://opensource.org/licenses/MIT) | Serialization of objects for sharing/transmission |

Documentation/CodeTutorials/PluginWriting.md

@@ -1436,7 +1436,7 @@ When packaging `dotnet publish` results you can exclude dlls that already come w
 ```
 <files>
     <file src="Plugin\windows\bin\$configuration$\net6.0-windows\win-x64\publish\*"
-          exclude="**\BadMedicine.Core.dll;**\FAnsi.*;**\MapsDirectlyToDatabaseTable.dll;**\MySql.Data.dll;**\Oracle.ManagedDataAccess.dll;**\Rdmp.Core.dll;**\NPOI.*;**\Renci.*;**\MathNet.Numerics.dll*;**\Rdmp.UI.dll;**\ScintillaNET.dll;**\ReusableUIComponents.dll;**\ObjectListView.dll;**\WeifenLuo.WinFormsUI.Docking*"
+          exclude="**\SynthEHR.Core.dll;**\FAnsi.*;**\MapsDirectlyToDatabaseTable.dll;**\MySql.Data.dll;**\Oracle.ManagedDataAccess.dll;**\Rdmp.Core.dll;**\NPOI.*;**\Renci.*;**\MathNet.Numerics.dll*;**\Rdmp.UI.dll;**\ScintillaNET.dll;**\ReusableUIComponents.dll;**\ObjectListView.dll;**\WeifenLuo.WinFormsUI.Docking*"
           target="lib\windows" />
 </files>
 ```

Documentation/CodeTutorials/UserManual.md

@@ -129,7 +129,7 @@ _\* Unless using [file system backend](./YamlRepository.md)_
 ## Example Data
 Example data can be setup on install by ticking the 'Example Datasets' checkbox during platform database setup.
 
-New example data can be generated through the `Diagnostics=>Generate Test  Data` menu. Or with the [BadMedicine](https://github.com/HicServices/BadMedicine) command line tool. 
+New example data can be generated through the `Diagnostics=>Generate Test  Data` menu. Or with the [SynthEHR](https://github.com/HicServices/SynthEHR) command line tool. 
 
 ## Importing a flat file as a new dataset
 If you have some CSV files (or Excel/Fixed Width) that you want to load into your database, you can do so with the RDMP bulk import tool.
@@ -384,7 +384,7 @@ drop trigger Prescribing_OnUpdate;
 
 Each data load in RDMP has a single [LoadMetadata] object which acts as the root for the configuration.  A given configuration will load one or more tables (which must have primary keys).  The tables loaded includes all the tables that underly the [Catalogues] which are ­associated with the [LoadMetadata].  For example if a Catalogue 'Biochemistry' includes a join on two tables 'Header' and 'Results' then a [LoadMetadata] which includes 'Biochemistry' would include both the 'Header' and 'Results' tables.
 
-Create a new Biochemistry CSV file with [BadMedicine] and add a primary key to the 'Biochemistry' table in your example data.  The key should be a composite primary key of:
+Create a new Biochemistry CSV file with [SynthEHR] and add a primary key to the 'Biochemistry' table in your example data.  The key should be a composite primary key of:
 
 - chi
 - SampleDate
@@ -458,7 +458,7 @@ Set the following properties:
 
 ### Running the load
 
-Place the Biochemistry.csv file generated by [BadMedicine] into the ForLoading directory of your load (e.g. `C:\temp\biochem\Data\ForLoading`).
+Place the Biochemistry.csv file generated by [SynthEHR] into the ForLoading directory of your load (e.g. `C:\temp\biochem\Data\ForLoading`).
 
 Right click the [LoadMetadata] and select 'Check and Execute'
 
@@ -838,7 +838,7 @@ _The question mark after ExtractionConfiguration means match all where the Proje
 
 
 [AggregateConfiguration]: ./Glossary.md#AggregateConfiguration
-[BadMedicine]: https://github.com/HicServices/BadMedicine
+[SynthEHR]: https://github.com/HicServices/SynthEHR
 [Catalogue]: ./Glossary.md#Catalogue
 [Catalogues]: ./Glossary.md#Catalogue
 [CohortIdentificationConfiguration]: ./Glossary.md#CohortIdentificationConfiguration

Rdmp.Core.Tests/Curation/Unit/ExerciseData/TestBiochemistryCreation.cs

@@ -6,8 +6,8 @@
 
 using System;
 using System.IO;
-using BadMedicine;
-using BadMedicine.Datasets;
+using SynthEHR;
+using SynthEHR.Datasets;
 using NUnit.Framework;
 
 namespace Rdmp.Core.Tests.Curation.Unit.ExerciseData;

Rdmp.Core.Tests/Curation/Unit/ExerciseData/TestDemographyCreation.cs

@@ -6,8 +6,8 @@
 
 using System;
 using System.IO;
-using BadMedicine;
-using BadMedicine.Datasets;
+using SynthEHR;
+using SynthEHR.Datasets;
 using NUnit.Framework;
 
 namespace Rdmp.Core.Tests.Curation.Unit.ExerciseData;

Rdmp.Core.Tests/Curation/Unit/ExerciseData/TestPrescribingCreation.cs

@@ -7,8 +7,8 @@
 using System;
 using System.IO;
 using System.Linq;
-using BadMedicine;
-using BadMedicine.Datasets;
+using SynthEHR;
+using SynthEHR.Datasets;
 using NUnit.Framework;
 
 namespace Rdmp.Core.Tests.Curation.Unit.ExerciseData;

Rdmp.Core.Tests/DataExport/DataExtraction/ExecuteFullExtractionToDatabaseMSSqlDestinationTest.cs

@@ -8,7 +8,7 @@
 using System.Data;
 using System.IO;
 using System.Linq;
-using BadMedicine.Datasets;
+using SynthEHR.Datasets;
 using FAnsi.Discovery;
 using NUnit.Framework;
 using Rdmp.Core.Curation.Data;

Rdmp.Core.Tests/QueryCaching/QueryCachingCrossServerTests.cs

@@ -7,8 +7,8 @@
 using System;
 using System.Linq;
 using System.Threading;
-using BadMedicine;
-using BadMedicine.Datasets;
+using SynthEHR;
+using SynthEHR.Datasets;
 using FAnsi;
 using FAnsi.Discovery;
 using NUnit.Framework;

Rdmp.Core/CohortCreation/Execution/ExamplePluginCohortCompiler.cs

@@ -9,7 +9,7 @@
 using System.Data;
 using System.Linq;
 using System.Threading;
-using BadMedicine;
+using SynthEHR;
 using Rdmp.Core.Curation.Data;
 using Rdmp.Core.Curation.Data.Aggregation;
 using Rdmp.Core.QueryCaching.Aggregation;

Rdmp.Core/CommandExecution/AtomicCommands/ExecuteCommandGenerateTestData.cs

@@ -7,13 +7,13 @@
 using System;
 using System.IO;
 using System.Linq;
-using BadMedicine;
-using BadMedicine.Datasets;
+using SynthEHR;
+using SynthEHR.Datasets;
 
 namespace Rdmp.Core.CommandExecution.AtomicCommands;
 
 /// <summary>
-/// Generates CSV files on disk for RDMP example datasets (based on BadMedicine library)
+/// Generates CSV files on disk for RDMP example datasets (based on SynthEHR library)
 /// </summary>
 public class ExecuteCommandGenerateTestData : BasicCommandExecution
 {

Rdmp.Core/CommandLine/DatabaseCreation/ExampleDatasetsCreation.cs

@@ -9,8 +9,8 @@
 using System.IO;
 using System.Linq;
 using System.Text.RegularExpressions;
-using BadMedicine;
-using BadMedicine.Datasets;
+using SynthEHR;
+using SynthEHR.Datasets;
 using FAnsi;
 using FAnsi.Discovery;
 using FAnsi.Discovery.ConnectionStringDefaults;
@@ -641,7 +641,7 @@ private ICatalogue ImportCatalogue(ITableInfo ti)
         var forwardEngineer = new ForwardEngineerCatalogue(ti, ti.ColumnInfos);
         forwardEngineer.ExecuteForwardEngineering(out var cata, out _, out var eis);
 
-        //get descriptions of the columns from BadMedicine
+        //get descriptions of the columns from SynthEHR
         cata.Description = Trim(Descriptions.Get(cata.Name));
         if (cata.Description != null)
         {

Rdmp.Core/CommandLine/DatabaseCreation/NightmareDatasets.cs

@@ -7,8 +7,8 @@
 using System;
 using System.Collections.Generic;
 using System.IO;
-using BadMedicine;
-using BadMedicine.Datasets;
+using SynthEHR;
+using SynthEHR.Datasets;
 using FAnsi.Discovery;
 using Rdmp.Core.CohortCommitting.Pipeline;
 using Rdmp.Core.Curation.Data;

Rdmp.Core/Curation/Data/SafeDirectoryCatalog.cs

@@ -71,7 +71,7 @@ public static class SafeDirectoryCatalog
         "autoupdater.net.resources.dll",
         "azure.core.dll",
         "azure.identity.dll",
-        "badmedicine.core.dll",
+        "syntehr.core.dll",
         "bouncycastle.crypto.dll",
         "clretwrc.dll",
         "clrjit.dll",

Rdmp.Core/Logging/TableLoadInfo.cs

@@ -8,7 +8,7 @@
 using System.Data;
 using System.Threading;
 using Amazon.Auth.AccessControlPolicy;
-using BadMedicine;
+using SynthEHR;
 using FAnsi.Connections;
 using FAnsi.Discovery;
 using Rdmp.Core.ReusableLibraryCode.Settings;

Rdmp.Core/Rdmp.Core.csproj

@@ -303,7 +303,7 @@
 		<PackageReference Include="Equ" />
 		<PackageReference Include="ExcelNumberFormat" />
 		<PackageReference Include="FluentFTP" />
-		<PackageReference Include="HIC.BadMedicine" />
+		<PackageReference Include="HIC.SynthEHR" />
 		<PackageReference Include="HIC.FAnsiSql" />
 		<PackageReference Include="LibArchive.Net" />
 		<PackageReference Include="Microsoft.SourceLink.GitHub">

Rdmp.UI/SimpleDialogs/Reports/DataGeneratorUI.cs

@@ -8,8 +8,8 @@
 using System.IO;
 using System.Threading;
 using System.Windows.Forms;
-using BadMedicine;
-using BadMedicine.Datasets;
+using SynthEHR;
+using SynthEHR.Datasets;
 
 namespace Rdmp.UI.SimpleDialogs.Reports;
 

Rdmp.UI/SimpleDialogs/Reports/GenerateTestDataUI.cs

@@ -10,8 +10,8 @@
 using System.IO;
 using System.Linq;
 using System.Windows.Forms;
-using BadMedicine;
-using BadMedicine.Datasets;
+using SynthEHR;
+using SynthEHR.Datasets;
 using Rdmp.Core.CommandExecution;
 using Rdmp.UI.ItemActivation;
 using Rdmp.UI.TestsAndSetup.ServicePropogation;

Tests.Common/Scenarios/BulkTestsData.cs

@@ -7,8 +7,8 @@
 using System;
 using System.Data;
 using System.Linq;
-using BadMedicine;
-using BadMedicine.Datasets;
+using SynthEHR;
+using SynthEHR.Datasets;
 using FAnsi.Discovery;
 using Rdmp.Core.Curation;
 using Rdmp.Core.Curation.Data;

Tests.Common/Scenarios/TestsRequiringA.cs

@@ -7,8 +7,8 @@
 using System;
 using System.Collections.Generic;
 using System.Linq;
-using BadMedicine;
-using BadMedicine.Datasets;
+using SynthEHR;
+using SynthEHR.Datasets;
 using FAnsi.Discovery;
 using FAnsi.Discovery.TableCreation;
 using Rdmp.Core.Curation.Data;

Tests.Common/Scenarios/TestsRequiringADle.cs

@@ -4,8 +4,8 @@
 // RDMP is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
 // You should have received a copy of the GNU General Public License along with RDMP. If not, see <https://www.gnu.org/licenses/>.
 
-using BadMedicine;
-using BadMedicine.Datasets;
+using SynthEHR;
+using SynthEHR.Datasets;
 using FAnsi.Discovery;
 using NUnit.Framework;
 using Rdmp.Core.CommandLine.Options;

directory.build.props

@@ -4,4 +4,4 @@
     <Version>8.1.6</Version>
 		<ManagePackageVersionsCentrally>true</ManagePackageVersionsCentrally>
   </PropertyGroup>
-</Project>
+</Project>