Merge pull request #314 from HicServices/develop

Release v6.0.2

.github/workflows/dotnet-core.yml

@@ -12,7 +12,7 @@ jobs:
     runs-on: windows-latest
     steps:
       - uses: actions/checkout@v3
-      - uses: actions/setup-dotnet@v2
+      - uses: actions/setup-dotnet@v3
         with:
           dotnet-version: 6.0.x
       - name: Get version

CHANGELOG.md

@@ -6,6 +6,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+## [6.0.2] 2022-11-04
+
+- Documentation updates
+- Updated to target RDMP version 8.0.5
+- Update for changed CsvHelper API from RDMP
+
 ## [6.0.1] 2022-09-27
 
 - Fixed issue running `ExecuteCommandCreateNewImagingDatasetSuite` when using a YamlRepository
@@ -382,7 +388,8 @@ Updated to be compatible with RDMP 4.2
 
 - Initial commit from private repo
 
-[Unreleased]: https://github.com/HicServices/RdmpDicom/compare/v6.0.1...develop
+[Unreleased]: https://github.com/HicServices/RdmpDicom/compare/v6.0.2...develop
+[6.0.2]: https://github.com/HicServices/RdmpDicom/compare/v6.0.1...v6.0.2
 [6.0.1]: https://github.com/HicServices/RdmpDicom/compare/v6.0.0...v6.0.1
 [6.0.0]: https://github.com/HicServices/RdmpDicom/compare/v5.0.12...v6.0.0
 [5.0.12]: https://github.com/HicServices/RdmpDicom/compare/v5.0.11...v5.0.12

Documentation/NlpPlugin.md

@@ -0,0 +1,61 @@
+# NLP Cohort Building
+
+1. [Background](#Background)
+1. [Loading Data](#loading-data)
+1. [Starting the REST API](#starting-the-rest-api)
+1. [Adding the API endpoint in RDMP](#adding-the-api-endpoint-in-rdmp)
+
+## Background
+Imaging studies are often accompanied by a clinical report of findings.  This is typically
+stored in a 'Structured Report' (SR).  The text stored in these reports can be very helpful
+for cohort building.  The free text and tree structure of SRs make them difficult to process
+into a relational database.  A better approach is to use a dedicated NLP framework and query
+it from the Cohort Builder.  One such NLP tool is [SemEHR]
+
+RDMP supports [cohort building plugins](https://github.com/HicServices/RDMP/blob/develop/Documentation/CodeTutorials/CohortBuildingApiPlugins.md#cohort-building-api-plugins).
+A plugin has been created to interface with SR data held in a [SemEHR] instance.
+
+## Loading Data
+Before you can use the plugin you must first load your data into a SemEHR instance.
+
+https://github.com/SMI/SmiServices/tree/master/src/applications/SRAnonTool
+
+## Starting the REST API
+The REST API must be configured and accessible over HTTPS.  Test that you are able
+to get a response from the API with your web browser
+
+## Adding the API endpoint in RDMP
+
+In RDMP API endpoints are modelled as [Catalogue] objects in the same way as regular relational database datasets.  Create a new one by right clicking any existing [Catalogue] and selecting 'Create New Sem EHR Catalogue':
+
+![Adding SemEHR Catalogue](Images/AddSemEHRCatalogue.png)
+
+Alternatively from the command line you can run:
+
+```
+./rdmp CreateNewSemEHRCatalogue
+```
+
+## Using the API endpoint in Cohort Builder
+Create a new [CohortIdentificationConfiguration].  Ensure you have [enabled query caching](https://github.com/HicServices/RDMP/blob/develop/Rdmp.Core/CohortCreation/Readme.md#creating-a-cache).  
+
+Add your new 'Sem EHR Catalogue' to the root container of the configuration
+
+![Adding SemEHR Catalogue to Cohort Identification Configuration](Images/AddSemEHRCatalogueToCic.png)
+
+Double click the added cohort set to launch the configuration screen.
+
+![Configure SemEHR Query](Images/SemEhrConfigUI.png)
+
+Enter a search term, negation (optional), date range (optional) and Modality.
+
+Ensure the Settings are correct and run the query.  If the 'Working' column changes to 'Crashed' then you can double click the row to view the error:
+
+![SemEHR Run Error](Images/SemEHRError.png)
+
+To get back to the settings/query screen after error right click the cohort set and choose 'Edit'
+
+
+[SemEHR]: https://github.com/CogStack/CogStack-SemEHR
+[Catalogue]: https://github.com/HicServices/RDMP/blob/develop/Documentation/CodeTutorials/Glossary.md#catalogue
+[CohortIdentificationConfiguration]: https://github.com/HicServices/RDMP/blob/develop/Documentation/CodeTutorials/Glossary.md#cohortidentificationconfiguration

Packages.md

@@ -10,6 +10,6 @@
 | Package | Source Code | Version | License | Purpose | Additional Risk Assessment |
 | ------- | ------------| --------| ------- | ------- | -------------------------- |
 | HIC.DicomTypeTranslation | [GitHub](https://github.com/HicServices/DicomTypeTranslation) | [4.0.1](https://www.nuget.org/packages/HIC.DicomTypeTranslation/4.0.1) | [GPL 3.0](https://www.gnu.org/licenses/gpl-3.0.html) | Translate dicom types into C# / database types | |
-| HIC.RDMP.Plugin | [GitHub](https://github.com/HicServices/RDMP) | [8.0.0](https://www.nuget.org/packages/HIC.RDMP.Plugin/8.0.0) | [GPL 3.0](https://www.gnu.org/licenses/gpl-3.0.html) | Interact with RDMP objects, base classes for plugin components etc | |
+| HIC.RDMP.Plugin | [GitHub](https://github.com/HicServices/RDMP) | [8.0.5](https://www.nuget.org/packages/HIC.RDMP.Plugin/8.0.5) | [GPL 3.0](https://www.gnu.org/licenses/gpl-3.0.html) | Interact with RDMP objects, base classes for plugin components etc | |
 | SharpCompress | [GitHub](https://github.com/adamhathcock/sharpcompress) | [0.32.2](https://www.nuget.org/packages/SharpCompress/0.32.2) | [MIT] | Access diverse archive formats including RAR, 7zip | |
 | Terminal.Gui | [GitHub](https://github.com/migueldeicaza/gui.cs) | [1.8.2](https://www.nuget.org/packages/Terminal.Gui/1.8.2) | [MIT] | UIs compatible with RDMP gui command line | |

README.md

@@ -18,6 +18,7 @@ Once installed the following functionality is available:
 - [Data Load](./Documentation/DataLoad.md)
 - [Data Extraction](./Documentation/DataExtraction.md)
 - [Caching (Fetching images from a DicomServer)](./Documentation/Caching.md)
+- [NLP Cohort Building Plugin](./Documentation/NlpPlugin.md)
 
 # Building
 
@@ -37,6 +38,31 @@ nuget pack ./Rdmp.Dicom.nuspec -Properties Configuration=Release -IncludeReferen
 
 This will produce a nupkg file (e.g. Rdmp.Dicom.0.0.1.nupkg) which can be consumed by both the RDMP client and dot net core RDMP CLI.
 
+# Debugging
+Since it is annoying to have to upload a new version of the plugin to test changes you can instead publish directly to the RDMP bin directory.
+
+For example imagine that you have RDMP checked out and building in the following directory:
+```
+D:\Repos\RDMP\Application\ResearchDataManagementPlatform\bin\Debug\net6.0-windows
+```
+
+Build the RdmpDicom project to this directory:
+
+```
+cd D:\Repos\RdmpDicom
+dotnet publish -o D:\Repos\RDMP\Application\ResearchDataManagementPlatform\bin\Debug\net6.0-windows -r win-x64
+cd D:\Repos\RdmpDicom\Rdmp.Dicom.UI
+dotnet publish -o D:\Repos\RDMP\Application\ResearchDataManagementPlatform\bin\Debug\net6.0-windows -r win-x64
+```
+
+Now run RDMP:
+```
+D:\Repos\RDMP\Application\ResearchDataManagementPlatform\bin\Debug\net6.0-windows\ResearchDataManagementPlatform.exe
+```
+
+Attach the visual studio debugger with `Debug=>Attach To Process...`
+
+
 
 # New CLI Commands
 
@@ -53,3 +79,15 @@ _Connects to the given PACS and writes CFind response for date range into output
 ```
 _Connects to the given PACS and fetches all images between the date ranges (requires firewall allows incomming connections from destination server)_
 
+# Troubleshooting
+Ensure that you have the Rdmp.Dicom plugin installed and that it has loaded correctly.  Search for it with `Ctrl+F` and enter "Plugin".  If it is not appearing at all then it is not installed.  If it appears under 'Old Plugins' then your Rdmp.Dicom version is out of date and you will need to get the latest version from GitHub Releases.
+
+Check the messages that appear when starting RDMP from the command line, e.g.:
+
+`./rdmp.exe listsupportedcommands --logstartup > out.txt`
+
+If using the RDMP Windows Client you can check that Rdmp.Dicom has loaded correctly by looking at the Types loaded.  Use the menu  `Diagnostics=>Plugins=>List All Types`.  This will generate a file with all the Types RDMP sees (~33,000) you should see all plugin Types here too, for example:
+
+- Rdmp.Dicom.ExternalApis.SemEHRApiCaller
+- Rdmp.Dicom.ExternalApis.SemEHRConfiguration
+- Rdmp.Dicom.ExternalApis.SemEHRResponse

Rdmp.Dicom.Library.nuspec

@@ -14,7 +14,7 @@
         <copyright>Copyright 2018-2019</copyright>
         <dependencies>
           <dependency id="HIC.DicomTypeTranslation" version="4.0.1" />
-          <dependency id="HIC.RDMP.Plugin" version="8.0.0" />
+          <dependency id="HIC.RDMP.Plugin" version="8.0.5" />
           <dependency id="SharpCompress" version="0.32.2" />
 		  <dependency id="Terminal.Gui" version="1.8.2" />
         </dependencies>

Rdmp.Dicom.Tests/Rdmp.Dicom.Tests.csproj

@@ -40,11 +40,11 @@
     <ProjectReference Include="..\Rdmp.Dicom\Rdmp.Dicom.csproj" />
   </ItemGroup>
   <ItemGroup>
-    <PackageReference Include="HIC.BadMedicine.Dicom" Version="0.0.14" />
-    <PackageReference Include="HIC.RDMP.Plugin.Test" Version="8.0.0" />
+    <PackageReference Include="HIC.BadMedicine.Dicom" Version="0.0.15" />
+    <PackageReference Include="HIC.RDMP.Plugin.Test" Version="8.0.5" />
     <PackageReference Include="Microsoft.NET.Test.Sdk" Version="17.3.2" />
     <PackageReference Include="NUnit" Version="3.13.3" />
-    <PackageReference Include="NUnit3TestAdapter" Version="4.2.1" />
+    <PackageReference Include="NUnit3TestAdapter" Version="4.3.0" />
     <PackageReference Include="NunitXml.TestLogger" Version="3.0.127" />
   </ItemGroup>
   <ItemGroup>

Rdmp.Dicom.UI/Rdmp.Dicom.UI.csproj

@@ -13,7 +13,7 @@
     <ProjectReference Include="..\Rdmp.Dicom\Rdmp.Dicom.csproj" />
   </ItemGroup>
   <ItemGroup>
-    <PackageReference Include="HIC.RDMP.Plugin.UI" Version="8.0.0" />
+    <PackageReference Include="HIC.RDMP.Plugin.UI" Version="8.0.5" />
     <PackageReference Include="Newtonsoft.Json" Version="13.0.1" />
   </ItemGroup>
   <ItemGroup>

Rdmp.Dicom.sln

@@ -9,8 +9,6 @@ Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "Solution Items", "Solution
 		Databases.Integration.yaml = Databases.Integration.yaml
 		.github\workflows\dotnet-core.yml = .github\workflows\dotnet-core.yml
 		Packages.md = Packages.md
-		rakeconfig.rb = rakeconfig.rb
-		rakefile.rb = rakefile.rb
 		Rdmp.Dicom.Library.nuspec = Rdmp.Dicom.Library.nuspec
 		Rdmp.Dicom.nuspec = Rdmp.Dicom.nuspec
 		README.md = README.md
@@ -33,6 +31,7 @@ Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "Documentation", "Documentat
 		Documentation\Caching.md = Documentation\Caching.md
 		Documentation\DataExtraction.md = Documentation\DataExtraction.md
 		Documentation\DataLoad.md = Documentation\DataLoad.md
+		Documentation\NlpPlugin.md = Documentation\NlpPlugin.md
 	EndProjectSection
 EndProject
 Global

Rdmp.Dicom/Cache/Pipeline/CFindSource.cs

@@ -67,7 +67,7 @@ public override SMIDataChunk DoGetChunk(ICacheFetchRequest cacheRequest, IDataLo
             var filepath = Path.Combine(workingDirectory.FullName, filename);
 
             var sw = new StreamWriter(filepath);
-            var writer = new CsvWriter(sw,new(CultureInfo.CurrentCulture));
+            var writer = new CsvWriter(sw,CultureInfo.CurrentCulture);
 
             WriteHeaders(writer);
 

Rdmp.Dicom/Rdmp.Dicom.csproj

@@ -26,7 +26,7 @@
   </ItemGroup>
   <ItemGroup>
     <PackageReference Include="HIC.DicomTypeTranslation" Version="4.0.1" />
-    <PackageReference Include="HIC.RDMP.Plugin" Version="8.0.0" />
+    <PackageReference Include="HIC.RDMP.Plugin" Version="8.0.5" />
     <PackageReference Include="SharpCompress" Version="0.32.2" />
     <PackageReference Include="Terminal.Gui" Version="1.8.2" />
   </ItemGroup>

SharedAssemblyInfo.cs

@@ -8,7 +8,7 @@
 [assembly: AssemblyCulture("")]
 
 // These should be replaced with correct values by the release process
-[assembly: AssemblyVersion("6.0.1")]
-[assembly: AssemblyFileVersion("6.0.1")]
-[assembly: AssemblyInformationalVersion("6.0.1")]
+[assembly: AssemblyVersion("6.0.2")]
+[assembly: AssemblyFileVersion("6.0.2")]
+[assembly: AssemblyInformationalVersion("6.0.2")]
 [assembly: InternalsVisibleTo("Rdmp.Dicom.Tests")]