Merge branch 'dependabot/nuget/RabbitMQ.Client-7.0.0' of https://gith…

…ub.com/SMI/SmiServices into dependabot/nuget/RabbitMQ.Client-7.0.0
SMI · Dec 4, 2024 · abb74ad · abb74ad
2 parents aa37099 + 70bd684
commit abb74ad
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Showing 134 changed files with 862 additions and 839 deletions.
diff --git a/.github/workflows/codeql.yml b/.github/workflows/codeql.yml
@@ -10,6 +10,9 @@ on:
   schedule:
     - cron: "0 5 * * *"
 
+env:
+  python-version: "3.10"
+
 jobs:
   analyze:
     name: Analyze
@@ -23,6 +26,9 @@ jobs:
       matrix:
         language: ["csharp", "java", "python"]
     steps:
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ env.python-version }}
       - name: Checkout repository
         uses: actions/checkout@v4
       - name: Initialize CodeQL
@@ -32,13 +38,17 @@ jobs:
       - name: Build Python
         if: ${{ matrix.language == 'python' }}
         uses: github/codeql-action/autobuild@v3
+      - name: setup .NET
+        if: ${{ matrix.language == 'csharp' }}
+        # NOTE(rkm 2022-02-20) Uses global.json
+        uses: actions/[email protected]
       - name: Build .Net
         if: ${{ matrix.language == 'csharp' }}
-        run: ./bin/smi/build.py -c Release
+        run: ./bin/smi/smi_build.py -c Release
       - name: Build java
         if: ${{ matrix.language == 'java' }}
         # NOTE(rkm 2023-03-21) Ensure test code is detected but don't actually run anything
-        run: ./bin/ctp/test.py --install-libs -DskipTests
+        run: ./bin/ctp/ctp_test.py --install-libs -DskipTests
       - name: SecurityCodescan
         if: ${{ matrix.language == 'csharp' }}
         run: |

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -22,15 +22,18 @@ env:
   java-version: 11
   java-distribution: temurin
   # python
-  python-version: 3.6
+  python-version: "3.10"
 
 jobs:
   init:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
     outputs:
       matrix: ${{ steps.matrix.outputs.matrix }}
       build_ref: ${{ steps.build_ref.outputs.build_ref }}
     steps:
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ env.python-version }}
       - name: checkout
         uses: actions/checkout@v4
       - name: set matrix
@@ -59,16 +62,19 @@ jobs:
       - name: "[linux] enable disk caching"
         if: ${{ matrix.os == 'linux' }}
         run: sudo apt-get install -y libeatmydata1
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ env.python-version }}
       - name: checkout
         uses: actions/checkout@v4
       - name: setup .NET
         # NOTE(rkm 2022-02-20) Uses global.json
         uses: actions/[email protected]
       - name: download tessdata
-        run: ./bin/smi/downloadTessdata.py
+        run: ./bin/smi/download_tessdata.py
       - name: "[linux] start services"
         if: ${{ matrix.os == 'linux' }}
-        run: ./bin/smi/startDockerLinux.py ${{ env.db-password }}
+        run: ./bin/smi/smi_start_docker_linux.py ${{ env.db-password }}
       - name: "[linux] re-write database strings"
         if: ${{ matrix.os == 'linux' }}
         run: |
@@ -96,12 +102,12 @@ jobs:
           set -euxo pipefail
           cov=""
           [ "${{ matrix.os }}" == "windows" ] && cov="--no-coverage"
-          ./bin/smi/buildTestPackage.py \
+          ./bin/smi/smi_build_test_package.py \
               ${{ needs.init.outputs.build_ref }} \
               "$cov"
       - name: upload coverage to codecov
         if: ${{ matrix.os == 'linux' }}
-        uses: codecov/[email protected].4
+        uses: codecov/[email protected].7
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           directory: coverage/
@@ -126,6 +132,9 @@ jobs:
       matrix: ${{ fromJson(needs.init.outputs.matrix) }}
     runs-on: ${{ matrix.image }}
     steps:
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ env.python-version }}
       - name: "[linux] enable disk caching"
         if: ${{ matrix.os == 'linux' }}
         run: sudo apt-get install -y libeatmydata1
@@ -139,12 +148,12 @@ jobs:
           cache: maven
       - name: "[linux] start services"
         if: ${{ matrix.os == 'linux' }}
-        run: ./bin/ctp/startDockerLinux.py
+        run: ./bin/ctp/ctp_start_docker_linux.py
       - name: "[windows] skip integration tests"
         if: ${{ matrix.os == 'windows' }}
         run: echo "JAVA_TESTS=--skip-integration-tests" >> $GITHUB_ENV
       - name: build, test, and package ctp
-        run: ./bin/ctp/buildTestPackage.py --install-libs ${{ needs.init.outputs.build_ref }} ${{ env.JAVA_TESTS }}
+        run: ./bin/ctp/ctp_build_test_package.py --install-libs ${{ needs.init.outputs.build_ref }} ${{ env.JAVA_TESTS }}
       - name: "[linux] upload packages"
         if: ${{ matrix.os == 'linux' }}
         uses: actions/upload-artifact@v4
@@ -155,7 +164,7 @@ jobs:
   upload-to-release:
     if: contains(github.ref, 'refs/tags/v')
     needs: [init, smi, ctp]
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
     steps:
       - name: "[linux] enable disk caching"
         run: sudo apt-get install -y libeatmydata1

diff --git a/.meta/flake8.conf b/.meta/flake8.conf
@@ -0,0 +1,8 @@
+[flake8]
+
+# https://github.com/psf/black
+max-line-length = 120
+
+# Ignoring:
+# E203 - Whitespace before ':'
+extend-ignore = E203
diff --git a/.meta/isort.cfg b/.meta/isort.cfg
@@ -0,0 +1,3 @@
+[isort]
+profile = black
+force_single_line = True
diff --git a/.meta/mypy.ini b/.meta/mypy.ini
@@ -0,0 +1,9 @@
+[mypy]
+check_untyped_defs = true
+disallow_any_generics = true
+disallow_incomplete_defs = true
+disallow_untyped_defs = true
+no_implicit_optional = true
+warn_redundant_casts = true
+warn_unused_ignores = true
+mypy_path = ./bin
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,4 +1,6 @@
 ---
+default_language_version:
+  python: python3.10
 exclude: |
     (?x)^(
         .*/packages.lock.json|
@@ -60,7 +62,7 @@ repos:
           )$
   # Markdown
   - repo: https://github.com/executablebooks/mdformat
-    rev: 0.7.18
+    rev: 0.7.19
     hooks:
     - id: mdformat
       additional_dependencies:
@@ -74,3 +76,50 @@ repos:
     hooks:
       - id: markdown-link-check
         args: [--quiet, --config, .meta/markdown-link-check.json]
+  # Python
+  - repo: https://github.com/pre-commit/pygrep-hooks
+    rev: "v1.10.0"
+    hooks:
+      - id: python-check-blanket-noqa
+      - id: python-check-mock-methods
+      - id: python-use-type-annotations
+      - id: python-no-log-warn
+  - repo: https://github.com/asottile/add-trailing-comma
+    rev: "v3.1.0"
+    hooks:
+      - id: add-trailing-comma
+  - repo: https://github.com/asottile/pyupgrade
+    rev: "v3.19.0"
+    hooks:
+      - id: pyupgrade
+        args: [--py310-plus]
+  - repo: https://github.com/asottile/yesqa
+    rev: "v1.5.0"
+    hooks:
+      - id: yesqa
+        additional_dependencies:
+        - pep8-naming==0.14.1
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: "v1.13.0"
+    hooks:
+      - id: mypy
+        args: [--config-file, .meta/mypy.ini]
+  - repo: https://github.com/psf/black-pre-commit-mirror
+    rev: "24.10.0"
+    hooks:
+      - id: black
+  - repo: https://github.com/pycqa/isort
+    rev: 5.13.2
+    hooks:
+      - id: isort
+        name: isort (python)
+        args: [--settings=.meta/isort.cfg]
+  - repo: https://github.com/pycqa/flake8
+    rev: "7.1.1"
+    hooks:
+      - id: flake8
+        additional_dependencies:
+        - flake8-bugbear==24.10.31
+        - flake8-assert-msg==1.1.1
+        - pep8-naming==0.14.1
+        args: [--config, .meta/flake8.conf]
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -253,7 +253,7 @@ A raw git diff can be seen [here][unreleased].
 - [#1450](https://github.com/SMI/SmiServices/pull/1450) by darshad-github. Update contributing.md with feature branch workflow guidelines
 - [#1451](https://github.com/SMI/SmiServices/pull/1451) by rkm. adopt dotnet central package management (CPM)
 - [#1468](https://github.com/SMI/SmiServices/pull/1468) by rkm. switch rabbitmq docker-compose images to include management plugin
-- [#1494](https://github.com/SMI/SmiServices/pull/1494) by rkm. \[actions\] replace deprecated set-output with GITHUB_OUTPUT
+- [#1494](https://github.com/SMI/SmiServices/pull/1494) by rkm. [actions] replace deprecated set-output with GITHUB_OUTPUT
 - [#1496](https://github.com/SMI/SmiServices/pull/1496) by rkm. add CodeQL scan
 
 ## [5.3.0] 2022-11-08
@@ -353,7 +353,7 @@ A raw git diff can be seen [here][unreleased].
 
 ### Bugfix
 
-- [#1087](https://github.com/SMI/SmiServices/pull/1087) by rkm. \[CI\] Misc. CI
+- [#1087](https://github.com/SMI/SmiServices/pull/1087) by rkm. [CI] Misc. CI
   fixes
   - Fixes the build scripts to respect any intermediate non-zero return
     codes
@@ -927,7 +927,7 @@ A raw git diff can be seen [here][unreleased].
 
 ### Added
 
-- \[breaking\] Add identifiable extraction support
+- [breaking] Add identifiable extraction support
   - New service "FileCopier" which sits in place of CTP for identifiable
     extractions and copies source files to their output dirs
   - Changes to MongoDB extraction schema, but backwards compatibility has
@@ -948,7 +948,7 @@ A raw git diff can be seen [here][unreleased].
 
 ### Changed
 
-- \[breaking\] Environment variables are no longer required. Previous settings
+- [breaking] Environment variables are no longer required. Previous settings
   now appear in configuration file
   - Environment variable `SMI_LOGS_ROOT` is now `GlobalOptions.LogsRoot`
   - Environment variable `MONGO_SERVICE_PASSWORD` is now
@@ -1050,7 +1050,7 @@ A raw git diff can be seen [here][unreleased].
   - Records in the referenced table will blacklist where any UID is found
     (StudyInstanceUID, SeriesInstanceUID or SOPInstanceUID). This allows
     blacklisting an entire study or only specific images.
-  - \[breaking\] Config on live system may need updated
+  - [breaking] Config on live system may need updated
 - Change the extraction directory generation to be
   `<projname>/image-requests/<extractname>`. Fixes
   [MVP Service #159](https://dev.azure.com/smiops/MVP%20Service/_workitems/edit/159/)
@@ -1103,8 +1103,8 @@ A raw git diff can be seen [here][unreleased].
 
 ### Changed
 
-- \[Breaking\] Promote the PT modality to its own collection in MongoDB
-- \[Breaking\] Renamed `RedisHost` to `RedisConnectionString` in the config
+- [Breaking] Promote the PT modality to its own collection in MongoDB
+- [Breaking] Renamed `RedisHost` to `RedisConnectionString` in the config
   options for clarity
 - Update to .Net Core 3.1 (supported until Dec 2022) since 2.2 support ended
   last year
@@ -1190,12 +1190,12 @@ A raw git diff can be seen [here][unreleased].
 
 ## [1.5.0] - 2020-03-05
 
-- \[Breaking\] Updated RabbitMQ extraction config to match extraction plan v2
+- [Breaking] Updated RabbitMQ extraction config to match extraction plan v2
 - Refactor Java exception handling and use of threads
-- `TessDirectory` option in \[IsIdentifiable\] now expects tesseract models file
+- `TessDirectory` option in [IsIdentifiable] now expects tesseract models file
   to exist (no longer downloads it on demand)
 - Added support for outsourcing classification (e.g. NLP) to other processes
-  via TCP (entered in \[SocketRules\] in `Rules.yaml`)
+  via TCP (entered in [SocketRules] in `Rules.yaml`)
 - IsIdentifiable NLP text classification now outsourced via TCP to any
   services configured in
   - StanfordNER implementation written in Java

diff --git a/Directory.Build.props b/Directory.Build.props
@@ -4,10 +4,11 @@
     <AppendRuntimeIdentifierToOutputPath>false</AppendRuntimeIdentifierToOutputPath>
     <DebugSymbols>true</DebugSymbols>
     <DebugType>full</DebugType>
+    <DisableImplicitNuGetFallbackFolder>true</DisableImplicitNuGetFallbackFolder>
     <GenerateAssemblyInfo>false</GenerateAssemblyInfo>
     <IsPackable>false</IsPackable>
     <IsPublishable>false</IsPublishable>
-    <LangVersion>12.0</LangVersion>
+    <LangVersion>13.0</LangVersion>
     <MSBuildTreatWarningsAsErrors>true</MSBuildTreatWarningsAsErrors>
     <Nullable>enable</Nullable>
     <RestoreLockedMode Condition="'$(CI)' == 'true'">true</RestoreLockedMode>
@@ -18,7 +19,7 @@
     <RuntimeIdentifier Condition="$([MSBuild]::IsOSPlatform('Windows'))">win-x64</RuntimeIdentifier>
     <SatelliteResourceLanguages>none</SatelliteResourceLanguages>
     <SelfContained>true</SelfContained>
-    <TargetFramework>net8.0</TargetFramework>
+    <TargetFramework>net9.0</TargetFramework>
     <TargetLatestRuntimePatch>true</TargetLatestRuntimePatch>
     <TreatWarningsAsErrors>true</TreatWarningsAsErrors>
     <!-- Many build warnings for missing docstrings when enabling this - we may want to fix and enable per-project where needed instead? -->

diff --git a/Directory.Packages.props b/Directory.Packages.props
@@ -25,17 +25,17 @@
     <PackageVersion Include="NLog" Version="5.3.4" />
     <PackageVersion Include="RabbitMQ.Client" Version="7.0.0" />
     <PackageVersion Include="Spectre.Console" Version="0.49.1" />
-    <PackageVersion Include="StackExchange.Redis" Version="2.8.16" />
+    <PackageVersion Include="StackExchange.Redis" Version="2.8.22" />
     <PackageVersion Include="System.IO.Abstractions" Version="21.1.3" />
     <PackageVersion Include="System.IO.FileSystem" Version="4.3.0" />
     <PackageVersion Include="System.Private.Uri" Version="4.3.2" />
     <PackageVersion Include="Terminal.Gui" Version="1.17.1" />
-    <PackageVersion Include="YamlDotNet" Version="16.2.0" />
+    <PackageVersion Include="YamlDotNet" Version="16.2.1" />
     <!-- Test Packages -->
     <PackageVersion Include="HIC.BadMedicine.Dicom" Version="0.1.1" />
     <PackageVersion Include="HIC.RDMP.Plugin.Test" Version="8.3.0" />
     <PackageVersion Include="Microsoft.CodeCoverage" Version="17.12.0" />
-    <PackageVersion Include="Microsoft.NET.Test.Sdk" Version="17.11.1" />
+    <PackageVersion Include="Microsoft.NET.Test.Sdk" Version="17.12.0" />
     <PackageVersion Include="Moq" Version="4.20.72" />
     <PackageVersion Include="NUnit" Version="4.2.2" />
     <PackageVersion Include="NUnit.Analyzers" Version="4.4.0" />

diff --git a/bin/checkDocs.py b/bin/checkDocs.py
@@ -1,15 +1,11 @@
 #!/usr/bin/env python3
-
 import collections
-import glob
 import os
 import re
-import sys
-
-import common as C
 
+import common as c
 
-_VERB_CS_PATH = f"{C.PROJ_ROOT}/src/SmiServices/ServiceVerbs.cs"
+_VERB_CS_PATH = f"{c.PROJ_ROOT}/src/SmiServices/ServiceVerbs.cs"
 _VERB_RE = re.compile(r'\[Verb\(("\S*?")')
 
 
@@ -63,7 +59,7 @@ def main() -> int:
 
     for tool_type in ("application", "service"):
         for tool in tools[tool_type]:
-            doc_path = f"{C.PROJ_ROOT}/docs/{tool_type}s/{tool}.md"
+            doc_path = f"{c.PROJ_ROOT}/docs/{tool_type}s/{tool}.md"
             if not os.path.isfile(doc_path):
                 print(f"Missing {doc_path}")
                 rc |= 1