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Marge v8.1.6 into main (#1842)
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* bump to net8

* add sqlcli

* Bump Autoupdater.NET.Official from 1.8.4 to 1.8.5

Bumps [Autoupdater.NET.Official](https://github.com/ravibpatel/AutoUpdater.NET) from 1.8.4 to 1.8.5.
- [Release notes](https://github.com/ravibpatel/AutoUpdater.NET/releases)
- [Commits](ravibpatel/AutoUpdater.NET@v1.8.4...v1.8.5)

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* Delete .nuget/packages.config (#1758)

* Delete .nuget/packages.config

Remove  hopefully obsolete package list confusing dependency tracking

* Remove .nuget folder

---------

Co-authored-by: James A Sutherland <>

* Bump svenstaro/upload-release-action from 2.7.0 to 2.9.0 (#1759)

* Bump shogo82148/actions-setup-perl from 1.28.0 to 1.29.0 (#1751)

Bumps [shogo82148/actions-setup-perl](https://github.com/shogo82148/actions-setup-perl) from 1.28.0 to 1.29.0.
- [Release notes](https://github.com/shogo82148/actions-setup-perl/releases)
- [Commits](shogo82148/actions-setup-perl@v1.28.0...v1.29.0)

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* Bump CsvHelper from 30.0.3 to 30.1.0 (#1737)

Bumps [CsvHelper](https://github.com/JoshClose/CsvHelper) from 30.0.3 to 30.1.0.
- [Commits](JoshClose/CsvHelper@30.0.3...30.1.0)

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* Bump SSH.NET from 2023.0.1 to 2024.0.0

Bumps [SSH.NET](https://github.com/sshnet/SSH.NET) from 2023.0.1 to 2024.0.0.
- [Release notes](https://github.com/sshnet/SSH.NET/releases)
- [Commits](sshnet/SSH.NET@2023.0.1...2024.0.0)

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* Bump SixLabors.ImageSharp.Drawing from 2.1.0 to 2.1.1

Bumps [SixLabors.ImageSharp.Drawing](https://github.com/SixLabors/ImageSharp.Drawing) from 2.1.0 to 2.1.1.
- [Release notes](https://github.com/SixLabors/ImageSharp.Drawing/releases)
- [Commits](SixLabors/ImageSharp.Drawing@v2.1.0...v2.1.1)

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* Bump MongoDB.Driver from 2.23.1 to 2.24.0

Bumps [MongoDB.Driver](https://github.com/mongodb/mongo-csharp-driver) from 2.23.1 to 2.24.0.
- [Release notes](https://github.com/mongodb/mongo-csharp-driver/releases)
- [Commits](mongodb/mongo-csharp-driver@v2.23.1...v2.24.0)

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* Bump NUnit from 4.0.1 to 4.1.0

Bumps [NUnit](https://github.com/nunit/nunit) from 4.0.1 to 4.1.0.
- [Release notes](https://github.com/nunit/nunit/releases)
- [Changelog](https://github.com/nunit/nunit/blob/master/CHANGES.md)
- [Commits](nunit/nunit@v4.0.1...4.1.0)

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* Bump FluentFTP from 49.0.1 to 49.0.2

Bumps [FluentFTP](https://github.com/robinrodricks/FluentFTP) from 49.0.1 to 49.0.2.
- [Release notes](https://github.com/robinrodricks/FluentFTP/releases)
- [Changelog](https://github.com/robinrodricks/FluentFTP/blob/master/RELEASES.md)
- [Commits](https://github.com/robinrodricks/FluentFTP/commits)

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* Task/rdmp-140 Update Dependabot yml file (#1756)

* centrally managed dependacies

* add directory.project.props file

* fix typo

* fix build

* fix up test

* Whitespace cleanup

* Avoid searching for and reading all csproj files twice

* remove console log

* update dependabot actions

* remove dependabot lower bounds

---------

Co-authored-by: James A Sutherland <>

* fix merge

* run net8

* Bump YamlDotNet from 15.1.1 to 15.1.2 (#1767)

Bumps [YamlDotNet](https://github.com/aaubry/YamlDotNet) from 15.1.1 to 15.1.2.
- [Release notes](https://github.com/aaubry/YamlDotNet/releases)
- [Commits](aaubry/YamlDotNet@v15.1.1...v15.1.2)

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* update sqlclient

* add version

* remove obsolete properties from tests

* workaround depricated formatter

* add text fix

* add package listing

* Bump coverlet.collector from 6.0.0 to 6.0.1 (#1757)

Bumps [coverlet.collector](https://github.com/coverlet-coverage/coverlet) from 6.0.0 to 6.0.1.
- [Release notes](https://github.com/coverlet-coverage/coverlet/releases)
- [Commits](coverlet-coverage/coverlet@v6.0.0...v6.0.1)

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* RDMP-143 Reorder Excel Attacher Processes (#1752)

* update excel attacher processing ordering

* Bump CsvHelper from 30.0.1 to 31.0.0 (#1761)

* Bump SixLabors.ImageSharp from 3.1.2 to 3.1.3 (#1770)

Bumps [SixLabors.ImageSharp](https://github.com/SixLabors/ImageSharp) from 3.1.2 to 3.1.3.
- [Release notes](https://github.com/SixLabors/ImageSharp/releases)
- [Commits](SixLabors/ImageSharp@v3.1.2...v3.1.3)

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* Bump SixLabors.ImageSharp.Drawing from 2.1.1 to 2.1.2

Bumps [SixLabors.ImageSharp.Drawing](https://github.com/SixLabors/ImageSharp.Drawing) from 2.1.1 to 2.1.2.
- [Release notes](https://github.com/SixLabors/ImageSharp.Drawing/releases)
- [Commits](SixLabors/ImageSharp.Drawing@v2.1.1...v2.1.2)

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* Resetting Dependabot for central versioning

* Reinstate Dependabot to reset state

* Move ManagePackageVersionsCentrally flag to Directory.Build.props

* Fix casing on Directory.Build.props file

* Task/tidy up net 8 migration (#1775)

* fix packages.md

* Bump coverlet.collector from 6.0.1 to 6.0.2

Bumps [coverlet.collector](https://github.com/coverlet-coverage/coverlet) from 6.0.1 to 6.0.2.
- [Release notes](https://github.com/coverlet-coverage/coverlet/releases)
- [Commits](coverlet-coverage/coverlet@v6.0.1...v6.0.2)

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* Bump HIC.BadMedicine from 1.1.2 to 1.2.0 (#1776)

* Bump HIC.BadMedicine from 1.1.2 to 1.2.0

Bumps [HIC.BadMedicine](https://github.com/HicServices/BadMedicine) from 1.1.2 to 1.2.0.
- [Release notes](https://github.com/HicServices/BadMedicine/releases)
- [Changelog](https://github.com/HicServices/BadMedicine/blob/develop/CHANGELOG.md)
- [Commits](HicServices/SynthEHR@v1.1.2...v1.2.0)

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* BadMedicine API update

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* bump fansisql (#1778)

* Bump Terminal.Gui from 1.15.1 to 1.16.0 (#1781)

Bumps [Terminal.Gui](https://github.com/gui-cs/Terminal.Gui) from 1.15.1 to 1.16.0.
- [Release notes](https://github.com/gui-cs/Terminal.Gui/releases)
- [Commits](gui-cs/Terminal.Gui@v1.15.1...v1.16.0)

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* Bump NUnit.Analyzers from 4.0.1 to 4.1.0 (#1780)

Bumps [NUnit.Analyzers](https://github.com/nunit/nunit.analyzers) from 4.0.1 to 4.1.0.
- [Release notes](https://github.com/nunit/nunit.analyzers/releases)
- [Changelog](https://github.com/nunit/nunit.analyzers/blob/master/CHANGES.txt)
- [Commits](nunit/nunit.analyzers@4.0.1...4.1.0)

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* Bump HIC.BadMedicine from 1.2.0 to 1.2.1

Bumps [HIC.BadMedicine](https://github.com/HicServices/BadMedicine) from 1.2.0 to 1.2.1.
- [Release notes](https://github.com/HicServices/BadMedicine/releases)
- [Changelog](https://github.com/HicServices/BadMedicine/blob/develop/CHANGELOG.md)
- [Commits](HicServices/SynthEHR@v1.2.0...v1.2.1)

---
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  update-type: version-update:semver-patch
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* external database commands saved

* Bigfix: Bring Notification Boxes To Front (#1785)

* bring notification to front

* add top most

* Bump NPOI from 2.6.2 to 2.7.0 (#1787)

Bumps [NPOI](https://github.com/nissl-lab/npoi) from 2.6.2 to 2.7.0.
- [Release notes](https://github.com/nissl-lab/npoi/releases)
- [Commits](https://github.com/nissl-lab/npoi/commits)

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* fix value to string conversion (#1788)

* fix value to string conversion

* Update ExcelDataFlowSource.cs

* Task/RDMP-65 remember last used extraction pipeline (#1768)

* extractions remember pipeline

* update changelog

* reorder testing

* fix test

* revert test

* add order to test

* updates from codeql

* tidy up code

* Update ExecuteExtractionUI.cs

* Task/allow extended timeouts (#1773)

* add 50min timeout

* interim

* add optional timeout

* add changelog

* tidy up from codeql

* update

* Task/rdmp 145 improve bak experience (#1772)

* improve bak file usage

* add documentation stub

* add docs

* tidy up code

* bump sixLabors

* update to ui

* restore files

* improve documentation

* add using statement

* specify server when importing existing cohorts

* Task/RDMP-129 Remove wix toolset (#1789)

* start of msi upgrade

* remove wix

* update build steps

* tidy up

* restore file

* update sln

* Feature/rdmp 117 multiple loads per catalogue (#1754)

* basic db objects

* fix typo

* working db linkage

* working build

* add sql update

* update sql

* update tests

* update sql

* update create sql

* update sql

* update sql

* update class

* fix extra space

* attempt to fix tests

* remove linkage

* fix typo

* add test case

* attempt image fix

* fix up image

* add missing file

* add changelog

* interim

* interim

* tidy up code

* fix build

* icons

* rename icon file (#1755)

* working icon

* update create sql

* update patch

* add patch

* working patches

* add basic tests

* tidy up code

* add go

* attempt to fix patch

* tidy up code

* remove true equal true check

* tidy up from review

* update migration

* remove dupe file (#1774)

* fix build

* interim sql

* update patch

* fix sql patch

* update patch id

* update patch id

* fix bad merge

* tidy up code

* tidy up code

---------

Co-authored-by: James A Sutherland <j.a.sutherland@dundee.ac.uk>

* allow for multiple identifiers in an project catalogue (#1791)

* fix logic issue

* update changelog

* only convert core categories

* add release date

* update changelog

* Task/rdmp-156 prep 8.1.5 release (#1793)

* add release date

* update changelog

* attempt to fix nuge tpackaging

* Update build.yml

* Task/rdmp 156 prep 8.1.5 release (#1795)

* disable tag check

* add sgen

* revert bad fix

* nudge deps

* fix duplicate deps

* drop dep

* fix build

* Bump SixLabors.ImageSharp from 3.1.3 to 3.1.4

Bumps [SixLabors.ImageSharp](https://github.com/SixLabors/ImageSharp) from 3.1.3 to 3.1.4.
- [Release notes](https://github.com/SixLabors/ImageSharp/releases)
- [Commits](SixLabors/ImageSharp@v3.1.3...v3.1.4)

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* Task/RDMP-164 Fix Plugin Dependency Issue (#1800)

* add asyncinterfaces dep

* add package info

* Bump FluentFTP from 49.0.2 to 50.0.0

Bumps [FluentFTP](https://github.com/robinrodricks/FluentFTP) from 49.0.2 to 50.0.0.
- [Release notes](https://github.com/robinrodricks/FluentFTP/releases)
- [Changelog](https://github.com/robinrodricks/FluentFTP/blob/master/RELEASES.md)
- [Commits](https://github.com/robinrodricks/FluentFTP/commits)

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* Bump MongoDB.Driver from 2.24.0 to 2.25.0

Bumps [MongoDB.Driver](https://github.com/mongodb/mongo-csharp-driver) from 2.24.0 to 2.25.0.
- [Release notes](https://github.com/mongodb/mongo-csharp-driver/releases)
- [Commits](mongodb/mongo-csharp-driver@v2.24.0...v2.25.0)

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* Bump SixLabors.ImageSharp.Drawing from 2.1.2 to 2.1.3 (#1804)

Bumps [SixLabors.ImageSharp.Drawing](https://github.com/SixLabors/ImageSharp.Drawing) from 2.1.2 to 2.1.3.
- [Release notes](https://github.com/SixLabors/ImageSharp.Drawing/releases)
- [Commits](SixLabors/ImageSharp.Drawing@v2.1.2...v2.1.3)

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* Bump FluentFTP from 50.0.0 to 50.0.1

Bumps [FluentFTP](https://github.com/robinrodricks/FluentFTP) from 50.0.0 to 50.0.1.
- [Release notes](https://github.com/robinrodricks/FluentFTP/releases)
- [Changelog](https://github.com/robinrodricks/FluentFTP/blob/master/RELEASES.md)
- [Commits](https://github.com/robinrodricks/FluentFTP/commits)

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- dependency-name: FluentFTP
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* update readme and changelog

* tidy up

* add default value

* tidy up

* add variable usage

* add some documentation

* multi-instance replace

* add button

* working yaml read

* tidy up code

* re-add selectdialog

* consistant casing

* fix codeql

* Bump Spectre.Console from 0.48.0 to 0.49.0

Bumps [Spectre.Console](https://github.com/spectreconsole/spectre.console) from 0.48.0 to 0.49.0.
- [Release notes](https://github.com/spectreconsole/spectre.console/releases)
- [Commits](spectreconsole/spectre.console@0.48.0...0.49.0)

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* Bump NUnit.Analyzers from 4.1.0 to 4.2.0

Bumps [NUnit.Analyzers](https://github.com/nunit/nunit.analyzers) from 4.1.0 to 4.2.0.
- [Release notes](https://github.com/nunit/nunit.analyzers/releases)
- [Changelog](https://github.com/nunit/nunit.analyzers/blob/master/CHANGES.md)
- [Commits](nunit/nunit.analyzers@4.1.0...4.2.0)

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* Bump LibArchive.Net from 0.1.4 to 0.1.5

Bumps [LibArchive.Net](https://github.com/jas88/libarchive.net) from 0.1.4 to 0.1.5.
- [Release notes](https://github.com/jas88/libarchive.net/releases)
- [Changelog](https://github.com/jas88/libarchive.net/blob/main/CHANGELOG.md)
- [Commits](jas88/libarchive.net@v0.1.4...v0.1.5)

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* Bump Spectre.Console from 0.49.0 to 0.49.1

Bumps [Spectre.Console](https://github.com/spectreconsole/spectre.console) from 0.49.0 to 0.49.1.
- [Release notes](https://github.com/spectreconsole/spectre.console/releases)
- [Commits](spectreconsole/spectre.console@0.49.0...0.49.1)

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* Bump NLog from 5.2.8 to 5.3.1

Bumps [NLog](https://github.com/NLog/NLog) from 5.2.8 to 5.3.1.
- [Release notes](https://github.com/NLog/NLog/releases)
- [Changelog](https://github.com/NLog/NLog/blob/dev/CHANGELOG.md)
- [Commits](NLog/NLog@v5.2.8...v5.3.1)

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* prompt for rename of filter change

* Bump NLog from 5.3.1 to 5.3.2

Bumps [NLog](https://github.com/NLog/NLog) from 5.3.1 to 5.3.2.
- [Release notes](https://github.com/NLog/NLog/releases)
- [Changelog](https://github.com/NLog/NLog/blob/dev/CHANGELOG.md)
- [Commits](NLog/NLog@v5.3.1...v5.3.2)

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* Update CodeQL Config (#1817)

* add codeql config

* dont double init

* tidy up config file

* Task/rdmp 19 fix codescanning (#1818)

* add codeql config

* dont double init

* tidy up config file

* ignore .designer in codeql

* remove number identifier

* Bump coverallsapp/github-action from 2.2.3 to 2.3.0 (#1819)

Bumps [coverallsapp/github-action](https://github.com/coverallsapp/github-action) from 2.2.3 to 2.3.0.
- [Release notes](https://github.com/coverallsapp/github-action/releases)
- [Commits](coverallsapp/github-action@v2.2.3...v2.3.0)

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* Task/RDMP-161 Add ability to mark as not extractable (#1796)

* add ability to mark as not extractable

* add code comments

* update changelog

* Bump YamlDotNet from 15.1.2 to 15.1.4 (#1822)

Bumps [YamlDotNet](https://github.com/aaubry/YamlDotNet) from 15.1.2 to 15.1.4.
- [Release notes](https://github.com/aaubry/YamlDotNet/releases)
- [Commits](aaubry/YamlDotNet@v15.1.2...v15.1.4)

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Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Bump Autoupdater.NET.Official from 1.8.5 to 1.8.6 (#1821)

Bumps [Autoupdater.NET.Official](https://github.com/ravibpatel/AutoUpdater.NET) from 1.8.5 to 1.8.6.
- [Release notes](https://github.com/ravibpatel/AutoUpdater.NET/releases)
- [Commits](ravibpatel/AutoUpdater.NET@v1.8.5...v1.8.6)

---
updated-dependencies:
- dependency-name: Autoupdater.NET.Official
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: James Friel <jfriel001@dundee.ac.uk>

* Bugfix/rdmp 162 Fix Error Msg Being Swallowed (#1798)

* update dll imports

* tidy up code

* update ddl import to libraryimport

* use getScrolPos

* Update directory.build.props

* RDMP-70 Change made to cause view stack trace to appear only when popup is an exception (#1810)

* Change made to cause view stack trace to appear only when popup is an exception

* Update CHANGELOG.md

Added change to changelog under 8.1.5

* Update CHANGELOG.md

Second update into correct release

---------

Co-authored-by: James Friel <jfriel001@dundee.ac.uk>

* update to use synthehr

* tidy up

* Task/document test plan (#1823)

* add pull request template and test plan

* add to test plan

* use real link

* update test plan

* Task/RDMP-184 Fix RDMP Slow start Issue (#1827)

* attempt fix

* add null checking

* tidy up

* fix typos

* Update LoggingDatabasePatcher.cs (#1833)

* Update LoggingDatabasePatcher.cs

Wrap identifiers correctly according to target DB platform

* Note pgsql logging creation fix, fix changelog typos

---------

Co-authored-by: James A Sutherland <>

* Fix bcl.AsyncInterfaces issue in plugins (#1835)

* Fix bcl.AsyncInterfaces issue in plugins

* Remove AsyncInterfaces ref

* tidy up docs

---------

Co-authored-by: James A Sutherland <>
Co-authored-by: James Friel <jfriel001@dundee.ac.uk>

* Update SharedAssemblyInfo.cs

* Bump Microsoft.NET.Test.Sdk from 17.9.0 to 17.10.0

Bumps [Microsoft.NET.Test.Sdk](https://github.com/microsoft/vstest) from 17.9.0 to 17.10.0.
- [Release notes](https://github.com/microsoft/vstest/releases)
- [Changelog](https://github.com/microsoft/vstest/blob/main/docs/releases.md)
- [Commits](microsoft/vstest@v17.9.0...v17.10.0)

---
updated-dependencies:
- dependency-name: Microsoft.NET.Test.Sdk
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>

* Bump HIC.FAnsiSql from 3.2.2 to 3.2.3

Bumps [HIC.FAnsiSql](https://github.com/HicServices/FAnsiSql) from 3.2.2 to 3.2.3.
- [Release notes](https://github.com/HicServices/FAnsiSql/releases)
- [Changelog](https://github.com/HicServices/FAnsiSql/blob/main/CHANGELOG.md)
- [Commits](HicServices/FAnsiSql@v3.2.2...v3.2.3)

---
updated-dependencies:
- dependency-name: HIC.FAnsiSql
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>

* Update ServerDatabaseTableSelector.cs

Fix async enumeration since it's actually async now

* Update DataTableUploadDestinationTests.cs

Fix bit vs tinyint boolean

* add release date

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: James A Sutherland <j.a.sutherland@dundee.ac.uk>
Co-authored-by: Brian <76164974+bpeacock001@users.noreply.github.com>
Co-authored-by: James A Sutherland <>
Co-authored-by: James A Sutherland <j@sutherland.pw>
Co-authored-by: rdteviotdale <r.d.teviotdale@dundee.ac.uk>
Co-authored-by: JBaird00183 <109660435+JBaird00183@users.noreply.github.com>
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7 people authored May 27, 2024
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12 changes: 12 additions & 0 deletions .github/configs/codeql.yml
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name: CodeQL Configuration

paths-ignore:
- "**/*.md"
- "**/*.txt"
- "**/obj/**"
- "**/bin/**"
- "**/*.Designer.cs"

query-filters:
- exclude:
id: cs/catch-of-all-exceptions
24 changes: 24 additions & 0 deletions .github/pull_request_template.md
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## Proposed Change

Summarise your proposed changes here, including any notes for reviewers.

## Type of change

What types of changes does your code introduce? Tick all that apply.

- [ ] Bugfix (non-breaking change which fixes an issue)
- [ ] New Feature (non-breaking change which adds functionality)
- [ ] Breaking Change (fix or feature that would cause existing functionality to not work as expected)
- [ ] Documentation-Only Update
- [ ] Other (if none of the other choices apply)

## Checklist

By opening this PR, I confirm that I have:

- [ ] Ensured that the PR branch is in sync with the target branch (i.e. it is automatically merge-able)
- [ ] Created or updated any tests if relevant
- [ ] Have validated this change against the [Test Plan](https://github.com/HicServices/RDMP/blob/develop/Documentation/CodeTutorials/TestPlan.md)
- [ ] Requested a review by one of the repository maintainers
- [ ] Have written new documentation or updated existing documentation to detail any new or updated functionality and how to use it
- [ ] Have added an entry into the changelog
4 changes: 2 additions & 2 deletions .github/workflows/build.yml
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Expand Up @@ -66,7 +66,7 @@ jobs:
mv `find coverage -type f` db-ui.lcov
dotnet test Rdmp.Core.Tests/Rdmp.Core.Tests.csproj --nologo --collect:"XPlat Code Coverage" --no-build --verbosity minimal -c Release --results-directory coverage -- DataCollectionRunSettings.DataCollectors.DataCollector.Configuration.Format=lcov
mv `find coverage -type f` db-core.lcov
- uses: coverallsapp/github-action@v2.2.3
- uses: coverallsapp/github-action@v2.3.0
with:
github-token: ${{ secrets.github_token }}
files: ./db-ui.lcov ./db-core.lcov
Expand Down Expand Up @@ -128,7 +128,7 @@ jobs:
mv `find coverage -type f` fs-ui.lcov
dotnet test Rdmp.Core.Tests/Rdmp.Core.Tests.csproj --nologo --collect:"XPlat Code Coverage" --no-build --verbosity minimal -c Release --results-directory coverage -- DataCollectionRunSettings.DataCollectors.DataCollector.Configuration.Format=lcov
mv `find coverage -type f` fs-core.lcov
- uses: coverallsapp/github-action@v2.2.3
- uses: coverallsapp/github-action@v2.3.0
with:
github-token: ${{ secrets.github_token }}
files: ./fs-ui.lcov ./fs-core.lcov
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1 change: 1 addition & 0 deletions .github/workflows/codeql.yml
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Expand Up @@ -31,6 +31,7 @@ jobs:
with:
languages: ${{ matrix.language }}
queries: +security-and-quality
config-file: ./.github/configs/codeql.yml

- name: Build
run: dotnet build
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16 changes: 16 additions & 0 deletions CHANGELOG.md
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@@ -1,9 +1,25 @@



# Changelog
All notable changes to this project will be documented in this file.

The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

## [8.1.6] - 2024-05-27

## Changed

- Improve error messages for Multi-ExtractionIdentifier extractions
- Add prompt to rename container when adding a cohort filter
- Allow for column selection when using the RemoteTableAttacher
- Fix to remove stack trace button from non error popups
- Add ability to set Extraction Category as "Not Extractable"
- Replace BadMedicine v1.2.1 with SynthEHR v2.0.0
- Fix issue with RDMP being slow to load when having numerous Load Metadatas
- Fix issue creating logging databases on PostgreSQL servers

## [8.1.5] - 2024-04-03

## Changed
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26 changes: 13 additions & 13 deletions Directory.Packages.props
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Expand Up @@ -3,26 +3,26 @@
<PackageVersion Include="CommandLineParser" Version="2.9.1"/>
<PackageVersion Include="Equ" Version="2.3.0"/>
<PackageVersion Include="ExcelNumberFormat" Version="1.1.0"/>
<PackageVersion Include="FluentFTP" Version="49.0.2"/>
<PackageVersion Include="HIC.BadMedicine" Version="1.2.1"/>
<PackageVersion Include="HIC.FAnsiSql" Version="3.2.2"/>
<PackageVersion Include="LibArchive.Net" Version="0.1.4"/>
<PackageVersion Include="FluentFTP" Version="50.0.1"/>
<PackageVersion Include="HIC.SynthEHR" Version="2.0.0"/>
<PackageVersion Include="HIC.FAnsiSql" Version="3.2.3"/>
<PackageVersion Include="LibArchive.Net" Version="0.1.5"/>
<PackageVersion Include="Microsoft.SourceLink.GitHub" Version="8.0.0">
<PrivateAssets>all</PrivateAssets>
<IncludeAssets>runtime; build; native; contentfiles; analyzers; buildtransitive</IncludeAssets>
</PackageVersion>
<PackageVersion Include="MongoDB.Driver" Version="2.24.0"/>
<PackageVersion Include="MongoDB.Driver" Version="2.25.0"/>
<PackageVersion Include="Newtonsoft.Json" Version="13.0.3"/>
<PackageVersion Include="NPOI" Version="2.7.0"/>
<PackageVersion Include="NLog" Version="5.2.8"/>
<PackageVersion Include="SixLabors.ImageSharp" Version="3.1.3"/>
<PackageVersion Include="SixLabors.ImageSharp.Drawing" Version="2.1.2"/>
<PackageVersion Include="Spectre.Console" Version="0.48.0"/>
<PackageVersion Include="NLog" Version="5.3.2"/>
<PackageVersion Include="SixLabors.ImageSharp" Version="3.1.4"/>
<PackageVersion Include="SixLabors.ImageSharp.Drawing" Version="2.1.3"/>
<PackageVersion Include="Spectre.Console" Version="0.49.1"/>
<PackageVersion Include="SSH.NET" Version="2024.0.0"/>
<PackageVersion Include="Terminal.Gui" Version="1.16.0"/>
<PackageVersion Include="YamlDotNet" Version="15.1.2"/>
<PackageVersion Include="YamlDotNet" Version="15.1.4"/>
<PackageVersion Include="ConsoleControl" Version="1.3.0"/>
<PackageVersion Include="Autoupdater.NET.Official" Version="1.8.5"/>
<PackageVersion Include="Autoupdater.NET.Official" Version="1.8.6"/>
<PackageVersion Include="DockPanelSuite.ThemeVS2015" Version="3.1.0"/>
<PackageVersion Include="System.Threading.ThreadPool" Version="4.3.0"/>
<PackageVersion Include="WeCantSpell.Hunspell" Version="5.0.0"/>
Expand All @@ -34,9 +34,9 @@
<PackageVersion Include="HIC.System.Windows.Forms.DataVisualization" Version="1.0.1"/>
<PackageVersion Include="NunitXml.TestLogger" Version="3.1.20"/>
<PackageVersion Include="NUnit3TestAdapter" Version="4.5.0"/>
<PackageVersion Include="NUnit.Analyzers" Version="4.1.0"/>
<PackageVersion Include="NUnit.Analyzers" Version="4.2.0"/>
<PackageVersion Include="NSubstitute" Version="5.1.0"/>
<PackageVersion Include="Microsoft.NET.Test.Sdk" Version="17.9.0"/>
<PackageVersion Include="Microsoft.NET.Test.Sdk" Version="17.10.0"/>
<PackageVersion Include="coverlet.collector" Version="6.0.2"/>
</ItemGroup>
</Project>
2 changes: 1 addition & 1 deletion Documentation/CodeTutorials/Packages.md
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Expand Up @@ -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 |
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2 changes: 1 addition & 1 deletion Documentation/CodeTutorials/PluginWriting.md
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Expand Up @@ -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>
```
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56 changes: 56 additions & 0 deletions Documentation/CodeTutorials/TestPlan.md
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# RDMP Test Plan
The RDMP test plan outlines the questions that should be asked of new changes to help ensure the correct changes are being made at the correct time.
These questions are designed to help highlight any steps in the testing process that may have been missed.

If you are looking to release a new version with this change, please look at the [Release Testing](#release_testing) section below.

## Generating Test Data
There is functionality to generate example data built into RDMP. This functionality has a 'nightmare' mode, which can generate large amounts of data for testing purposes.
This mode can be enabled when creating platform databases by adding the 'Nightmare' flag to the example data settings during platform creation.
Additional data can be used by using the 'Factor' flag to increase the amount of data, this will multiply the number of objects created by your specified Factor.

## Questions To Ask
### Does this change add a database migration?
If the change adds a database migration, ask yourself the following questions:
* Is the change backwards compatable?
* Have I tested the change with a fresh install of RDMP?
* Have I tested the change through the upgrade path with populated data that my change affects?
* Should this change be included in a patch release? or be part of the next minor release? Or even a major release?
* Patch releases contain small improvements and should be usable interchangably with other versions within the same minor version e.g v8.1.4 and v8.1.5
* Minor released contain new functionality and should be backwards compatable with other versions in the same major version e.g. v8.1.0 and v8.2.0
* Major releases contain changes that are not backwards compatable

### Does this change add new functionality?
If the change adds new functionality, ask yourself the following questions:
* Is the functionality usable via the GUI? If no ,why not?
* Is the functionality usable via the CLI? If no, why not?
* Has the functionalty been covered via unit tests?
* Has the functionalty been manually tested?
* Has the happy path been tested?
* This is the expected path, where users are paying attention and are on their best behaviour
* Has the sad path been tested?
* This is where the user tries to be as obtuse as possible
* Does this change do any data processing? If so, check the performance questions below

### Does this change have any impact on performance?
If the change adds or amends functionality that processes data
* Is the functionality performant?
* Can the space/time complexity of the functions be reduced?
* Does the functionality handle large datasets (>1GB) efficiently?


### What assumptions have been made?
* Have any assumptions about how this functionality will be used been made?
* Have any assumptions about the input data been made? Can these assumptions be extracted out into configuration?

## <a name="release_testing"></a>Release Testing
The release testing process should be completed once the release is feature complete and no more code changes are due to take place.
This testing is to ensure that all code changes made during this release play nicely together and have no unintended side effcts.
It may be useful at this point to revisit each piece of functionality and ensure they work as expected and perform some user acceptance testing on them, in light with the questions above.
### What's changed?
* Does the changelog accuratly reflect the pull request changes made?
* If there are database migrations, are they all correctly sequenced and not overlapping?
* Does the release work as epxected with a fresh install and via the upgrade path?
* Is all functionality documented?
* Are all version numbers bumped correctly?
* Do all of the managed plugins work with the new release without issues or warnings?
8 changes: 4 additions & 4 deletions Documentation/CodeTutorials/UserManual.md
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Expand Up @@ -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.
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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'
Expand Down Expand Up @@ -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
Expand Down
12 changes: 10 additions & 2 deletions Documentation/DataLoadEngine/RemoteAttachers.md
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Expand Up @@ -48,7 +48,8 @@ The full configuration options are
| Delta Reading Look Forward Days | If using the Delta Reading fetch duration, this is how many days forward in time you wish to look each time |
| Set Delta Reading To Last Seen Date Post Load | Optional overwrite to the Delta Reading fetch option. Will use the most recently seen date in the fetched data rather than the adding the forward look days amount onto the stored minimum date |
| Culture | Optionally specify a custom date format |
| Explicit Date Time Format | Optionally specify a specific datetime format
| Explicit Date Time Format | Optionally specify a specific datetime format
| Selected Columns | Optionally select which columns you wish to pull from the remote server (defaults to "*" )

## Configuring the Remote Database Attacher
The Remote Database Attacher has a number of configuration options the required fields are:
Expand All @@ -68,4 +69,11 @@ The Remote Database Attacher has a number of configuration options the required
| Delta Reading Look Forward Days | If using the Delta Reading fetch duration, this is how many days forward in time you wish to look each time |
| Set Delta Reading To Last Seen Date Post Load | Optional overwrite to the Delta Reading fetch option. Will use the most recently seen date in the fetched data rather than the adding the forward look days amount onto the stored minimum date |
| Culture | Optionally specify a custom date format |
| Explicit Date Time Format | Optionally specify a specific datetime format
| Explicit Date Time Format | Optionally specify a specific datetime format
| Selected Columns | Optionally select which columns you wish to pull from the remote server (defaults to "*" )


## Using Historical Loading with custom SQL
By default, historical fetch configuration will be ignored in custome select SQL.
To enable the use of hostorical fetching, include the string "$RDMPDefinedWhereClause" in the where clause of your query
e.e. "Select * from Biochemistry Where $RDMPDefinedWhereClause"
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