Merge pull request #421 from SMI/feature/docsfix

Feature/docsfix

.linkspector.yml

@@ -0,0 +1,10 @@
+files:
+- ./Documentation/DataExtraction.md
+- ./Documentation/Caching.md
+- ./Documentation/NlpPlugin.md
+- ./Documentation/DataLoad.md
+- ./CHANGELOG.md
+- ./Rdmp.Dicom/PipelineComponents/PrimaryKeyCollisionIsolationMutilation.md
+- ./README.md
+- ./.github/ISSUE_TEMPLATE/bug_report.md
+- ./Packages.md

CHANGELOG.md

@@ -472,4 +472,4 @@ Updated to be compatible with RDMP 4.2
 [1.3.0]: https://github.com/SMI/RdmpDicom/compare/v1.1.0...v1.3.0
 [1.1.0]: https://github.com/SMI/RdmpDicom/compare/v1.0.2...v1.1.0
 [1.0.2]: https://github.com/SMI/RdmpDicom/compare/1581c5ae3a12db1873f4cf1a930215750ad2ae14...v1.0.2
-[Tag Elevation]:https://github.com/SMI/DicomTypeTranslation/tree/develop/DicomTypeTranslation/Elevation
+[Tag Elevation]:https://github.com/SMI/DicomTypeTranslation/tree/main/DicomTypeTranslation/Elevation

Documentation/DataLoad.md

@@ -1,9 +1,9 @@
 # Data Load
 
-1. [Background](#Background)
-3. [Image Tables]
-1. [Implementation](#Implementation)
-1. [Study Series Image Level](#Study-Series-Image-Level)
+1. [Background](#background)
+3. [Image Tables](#image-tables)
+1. [Implementation](#implementation)
+1. [Study Series Image Level](#study-series-image-level)
 
 ## Background
 The Rdmp.Dicom plugin allows you to create and load Dicom [Image Tables].  These tables contain the location (on disk) of the image and relevant metadata (e.g. dicom tags) about each image.
@@ -20,7 +20,7 @@ You can create image tables (and an accompanying data load configuration) with t
 
 ![Create Imaging Table](./Images/CreateImagingTables.png)
 
-You can find some [sample templates](https://github.com/SMI/DicomTypeTranslation/tree/develop/Templates) in the DicomTypeTranslation repository].
+You can find some [sample templates](https://github.com/SMI/DicomTypeTranslation/tree/main/Templates) in the DicomTypeTranslation repository].
 
 All tables should have a unique primary key e.g. SOPInstanceUID.  Identical duplication is automatically handled when migrating from RAW to STAGING (prior to MERGE with LIVE) so you can use high level fields as primary keys (e.g. StudyInstanceUID) provided all values in all images are the same for that value (e.g. PatientID, PatientBirthDate etc - these are unlikely to change during a study!).
 
@@ -50,4 +50,4 @@ Sometimes there are differences in study/series level tags between images when y
 |[PrimaryKeyCollisionIsolationMutilation](./../Rdmp.Dicom/PipelineComponents/PrimaryKeyCollisionIsolationMutilation.md) | If all the above components failed then you can use this one to isolate the colliding records into a store (and drop them from the data load) |
 
 
-[Image Tables]: #Image-Tables
+[Image Tables]: #image-tables

Documentation/NlpPlugin.md

@@ -1,6 +1,6 @@
 # NLP Cohort Building
 
-1. [Background](#Background)
+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)
@@ -18,7 +18,7 @@ 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
+https://github.com/SMI/StructuredReports/tree/main/src/applications/SRAnonTool
 
 ## Starting the REST API
 The REST API must be configured and accessible over HTTPS.  Test that you are able
@@ -37,7 +37,7 @@ Alternatively from the command line you can run:
 ```
 
 ## 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).  
+Create a new [CohortIdentificationConfiguration].  Ensure you have [enabled query caching](https://github.com/HicServices/RDMP/blob/develop/Rdmp.Core/CohortCreation/CohortCreation.md#creating-a-cache).  
 
 Add your new 'Sem EHR Catalogue' to the root container of the configuration
 

README.md

@@ -1,4 +1,5 @@
-[![Build status](https://github.com/SMI/RdmpDicom/actions/workflows/dotnet-core.yml/badge.svg)](https://github.com/SMI/RdmpDicom/actions/workflows/dotnet-core.yml) [![Total alerts](https://img.shields.io/lgtm/alerts/g/SMI/RdmpDicom.svg?logo=lgtm&logoWidth=18)](https://lgtm.com/projects/g/SMI/RdmpDicom/alerts/) [![NuGet Badge](https://buildstats.info/nuget/HIC.RDMP.Dicom)](https://buildstats.info/nuget/HIC.RDMP.Dicom)
+[![Build status](https://github.com/SMI/RdmpDicom/actions/workflows/dotnet-core.yml/badge.svg)](https://github.com/SMI/RdmpDicom/actions/workflows/dotnet-core.yml)
+[![NuGet Badge](https://buildstats.info/nuget/HIC.RDMP.Dicom)](https://buildstats.info/nuget/HIC.RDMP.Dicom)
 
 # RdmpDicom
 Plugin for [RDMP](https://github.com/HicServices/RDMP) that adds support for load, linking (with EHR data in relational databases) and extracting anonymous DICOM images for researchers.