SQ adding comments for all code, not just changed code

Stu_Sklinar · August 6, 2025, 10:07am

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ALM used Azure DevOps
CI system used Azure DevOps,
Languages of the repository dotnet

We have a quality gate set to process Pull/Merge Requests, and analyse new code.

Our issue is, we have an MR/PR with one line change, but it’s commented on the whole file with issues - not just the diff for what has changed.

Only the code in green/red has changed.

This is causing a huge problem - as we want our baseline to be as is, and anything new be stopped, but anything existing, fixed later.

This is how we’re calling our prepare

      - task: SonarCloudPrepare@3
        displayName: '.NET Code Analysis - Begin (PR)'
        inputs:
          SonarCloud: 'SonarQubeCloud'
          organization: '....'
          scannerMode: dotnet
          projectKey: '.....'
          projectVersion: '$(Build.BuildId)'
          extraProperties: |
            sonar.cs.opencover.reportsPaths="$(CoveragePath)/*.xml"
            sonar.cs.vstest.reportsPaths="$(UnitTestResultsPath)/*.trx"
            sonar.test.exclusions="$(UnitTestExclusionsPattern)"
            sonar.analysis.buildNumber=$(Build.BuildId)
            sonar.analysis.pipeline=$(Build.BuildId)
            sonar.analysis.sha1=$(System.PullRequest.SourceCommitId)
            sonar.analysis.prNumber=$(System.PullRequest.PullRequestNumber)
            sonar.analysis.repository=$(Build.Repository.ID)
            sonar.cpd.exclusions=$(CpdExclusionsPattern)
            sonar.cs.analyzeRazorCode=false
            sonar.dotnet.excludeTestProjects=true

ganncamp · August 7, 2025, 12:52pm

Hi,

This sounds like a problem with the SCM metadata available to analysis. Please make sure you are not doing a shallow clone and make sure that the prerequisites are in place.

Thx,
Ann

Stu_Sklinar · August 7, 2025, 1:01pm

Thanks, I think I’ve started to narrow it.

What values are expected in:

        sonar.pullrequest.branch
        sonar.pullrequest.base

is it just the branch name (my-feature) or refs/heads/my-feature?

For context my SQ logs show:

- sonar.pullrequest.base=refs/heads/develop

- sonar.pullrequest.branch=refs/heads/features/Reduce-session-push-exceptions

Thanks

ganncamp · August 7, 2025, 1:10pm

Hi,

Those values should be read automatically from the SCM metadata in your environment.

HTH,
Ann

Stu_Sklinar · August 7, 2025, 1:11pm

Thanks, I’ve removed them - but I’m still gettting “402 lines changed” for a single line change.

I have this at the top of my file

```

      - checkout: self
        fetchDepth: 0
        persistCredentials: true
        clean: true

ganncamp · August 7, 2025, 1:11pm

Hi,

Are the prerequisites in place?

Ann

Stu_Sklinar · August 7, 2025, 1:15pm

Yes they are

I have this setting checked.

ganncamp · August 7, 2025, 1:16pm

Hi,

I provided a link in an earlier post to a list of prerequisites.

Ann

Stu_Sklinar · August 7, 2025, 1:17pm

Thank you - yes I’ve checked them now. They should all be set

Stu_Sklinar · August 7, 2025, 2:30pm

Thanks - it looks to have been a “Skill issue” (Or lack thereof) AZDO doesn’t check fetch the develop branch on a shallow clone - and a message “400 files changes of xxx” was misleading.

Once I let the whole thing run out - it was fine

Stu_Sklinar · August 11, 2025, 3:33pm

Hello - turns out I was mistaken.

This is still commenting on files that haven’t changed.

I can run this whole process and locally and get the same results

When only change a single file on my PR I get the below

Incremental PR analysis: 49 files out of 2295 are unchanged

dotnet sonarscanner begin   /k:"key"   /o:"oeg"   /d:sonar.token="token"   /d:sonar.pullrequest.key="11463"   /d:sonar.pullrequest.branch="feature/dt-2066-Automatically-reload-bookings-page-2"   /d:sonar.pullrequest.base="develop"

SonarScanner for MSBuild 10.3
Using the .NET Core version of the Scanner for MSBuild
Pre-processing started.
Preparing working directories...
16:31:09.487  Updating build integration targets...
16:31:10.172  Using SonarCloud.
16:31:10.498  Fetching analysis configuration settings...
16:31:11.369  Provisioning analyzer assemblies for cs...
16:31:11.369  Installing required Roslyn analyzers...
16:31:11.369  Processing plugin: securitycsharpfrontend version 11.7.0.39363
16:31:11.374  Processing plugin: csharpenterprise version 10.15.0.120848
16:31:11.877  Provisioning analyzer assemblies for vbnet...
16:31:11.877  Installing required Roslyn analyzers...
16:31:11.877  Processing plugin: securityvbnetfrontend version 11.7.0.39363
16:31:11.877  Processing plugin: vbnetenterprise version 10.15.0.120848
16:31:11.995  Downloading cache. Project key: KEY, branch: develop.
16:31:21.703  Incremental PR analysis: 49 files out of 2295 are unchanged.
16:31:21.767  Pre-processing succeeded.

I have done a git fetch develop and this is local, so shouldn’t be shallow

Then my build runs.

Then on my PR a string of comments for code that hasn’t changed. So I’m not quite sure what happening - I’d expect to see 1 file has changed.

ganncamp · August 11, 2025, 3:40pm

Hi,

Is develop the PR source branch? Its target branch?

And and you provide a full debug log?

Share the Scanner for .NET verbose logs

Add /d:"sonar.verbose=true" to the Scanner BEGIN step. Examples:

dotnet sonarscanner begin /k:"MyProject" /d:"sonar.verbose=true"

SonarScanner.MSBuild.exe begin /k:"MyProject" /d:"sonar.verbose=true"

- task: SonarCloudPrepare@3 # or SonarQubePrepare@3
    inputs:
      SonarCloud: 'sonarcloud'
      organization: 'foo'
      scannerMode: 'dotnet'
      projectKey: 'foo_sonar-scanning-someconsoleapp'
      projectName: 'sonar-scanning-someconsoleapp'
      extraProperties: |
        sonar.verbose=true

Please note that most of the relevant logging will happen during the END step, i.e. in SonarCloudAnalyze, SonarQubeAnalyze or Run Code Analysis.

Share the msbuild detailed logs

MsBuild.exe /t:Rebuild /v:d

or

dotnet build -v:d

Share the binlog

When investigating a performance issue, it is helpful to also have access to the binlog:

MsBuild.exe /p:reportanalyzer=true /bl:build.binlog

or

dotnet build /p:reportanalyzer=true /bl:build.binlog

The parameters for detailed logs and binlogs can be combined.

Thx,
Ann

Stu_Sklinar · August 11, 2025, 4:16pm

Hello - Develop is the target branch, the source branch is feature/dt-2066-Automatically-reload-bookings-page-2So I want to merge changes made in feature/dt-2066-Automatically-reload-bookings-page-2 to Develop

Begin Output.

 dotnet sonarscanner begin   /k:"ProjectKey"   /o:"myOrg"  /d:sonar.token="MYTOKEN"   /d:sonar.pullrequest.key="11463"   /d:sonar.pullrequest.branch="feature/dt-2066-Automatically-reload-bookings-page-2"   /d:sonar.pullrequest.base="develop" /d:"sonar.verbose=true"
SonarScanner for MSBuild 10.3
Using the .NET Core version of the Scanner for MSBuild
Default properties file was found at /home/stu/.dotnet/tools/.store/dotnet-sonarscanner/10.3.0/dotnet-sonarscanner/10.3.0/tools/netcoreapp3.1/any/SonarQube.Analysis.xml
Loading analysis properties from /home/stu/.dotnet/tools/.store/dotnet-sonarscanner/10.3.0/dotnet-sonarscanner/10.3.0/tools/netcoreapp3.1/any/SonarQube.Analysis.xml
sonar.verbose=true was specified - setting the log verbosity to 'Debug'
Pre-processing started.
Preparing working directories...
Using environment variables to determine the download directory...
16:44:32.033  Loading analysis properties from /home/stu/.dotnet/tools/.store/dotnet-sonarscanner/10.3.0/dotnet-sonarscanner/10.3.0/tools/netcoreapp3.1/any/SonarQube.Analysis.xml
16:44:32.057  Server Url: https://sonarcloud.io
16:44:32.057  Api Url: https://api.sonarcloud.io
16:44:32.057  Is SonarCloud: True
16:44:32.059  No truststore provided; attempting to use the default location.
16:44:32.06  No truststore found at the default location; proceeding without a truststore.
16:44:32.061  sonar.verbose=true was specified - setting the log verbosity to 'Debug'
16:44:32.062  Updating build integration targets...
16:44:32.064  The file SonarQube.Integration.ImportBefore.targets is up to date at /home/stu/.local/share/Microsoft/MSBuild/4.0/Microsoft.Common.targets/ImportBefore
16:44:32.064  The file SonarQube.Integration.ImportBefore.targets is up to date at /home/stu/.local/share/Microsoft/MSBuild/10.0/Microsoft.Common.targets/ImportBefore
16:44:32.064  The file SonarQube.Integration.ImportBefore.targets is up to date at /home/stu/.local/share/Microsoft/MSBuild/11.0/Microsoft.Common.targets/ImportBefore
16:44:32.064  The file SonarQube.Integration.ImportBefore.targets is up to date at /home/stu/.local/share/Microsoft/MSBuild/12.0/Microsoft.Common.targets/ImportBefore
16:44:32.064  The file SonarQube.Integration.ImportBefore.targets is up to date at /home/stu/.local/share/Microsoft/MSBuild/14.0/Microsoft.Common.targets/ImportBefore
16:44:32.064  The file SonarQube.Integration.ImportBefore.targets is up to date at /home/stu/.local/share/Microsoft/MSBuild/15.0/Microsoft.Common.targets/ImportBefore
16:44:32.064  The file SonarQube.Integration.ImportBefore.targets is up to date at /home/stu/.local/share/Microsoft/MSBuild/Current/Microsoft.Common.targets/ImportBefore
16:44:32.064  The file SonarQube.Integration.ImportBefore.targets is up to date at /home/stu/Microsoft/MSBuild/15.0/Microsoft.Common.targets/ImportBefore
16:44:32.064  The file SonarQube.Integration.ImportBefore.targets is up to date at /home/stu/Microsoft/MSBuild/Current/Microsoft.Common.targets/ImportBefore
16:44:32.088  Installed SonarQube.Integration.targets to /mnt/c/users/Stu Sklinar.FA-0425/code.sonarqube/bin/targets
16:44:32.088  Creating config and output folders...
16:44:32.089  Creating directory: /mnt/c/users/Stu Sklinar.FA-0425/code.sonarqube/conf
16:44:32.09  Creating directory: /mnt/c/users/Stu Sklinar.FA-0425/code.sonarqube/out
16:44:32.099  Downloading from https://sonarcloud.io/api/settings/values?component=unknown...
16:44:32.548  Response received from https://sonarcloud.io/api/settings/values?component=unknown...
16:44:32.549  Fetching server version...
16:44:32.55  Downloading from https://api.sonarcloud.io/analysis/version...
16:44:32.652  Response received from https://api.sonarcloud.io/analysis/version...
16:44:32.653  Downloading from https://api.sonarcloud.io/analysis/version failed. Http status code is Forbidden.
16:44:32.654  Downloading from https://sonarcloud.io/api/server/version...
16:44:32.692  Response received from https://sonarcloud.io/api/server/version...
16:44:32.693  Using SonarCloud.
16:44:32.693  SonarCloud detected, skipping server version check.
16:44:32.694  SonarCloud detected, skipping license check.
16:44:32.695  JreResolver: Resolving JRE path.
16:44:32.697  Downloading from https://api.sonarcloud.io/analysis/jres?os=linux&arch=x64...
16:44:32.874  Response received from https://api.sonarcloud.io/analysis/jres?os=linux&arch=x64...
16:44:32.957  JreResolver: Cache hit '/home/stu/.sonar/cache/bcb1b7b8ad68c93093f09b591b7cb17161d39891f7d29d33a586f5a328603707/OpenJDK17U-jre_x64_linux_hotspot_17.0.11_9.tar.gz_extracted/jdk-17.0.11+9-jre/bin/java'.
16:44:32.959  Fetching analysis configuration settings...
16:44:32.961  Fetching properties for project 'ProjectKey'...
16:44:32.961  Downloading from https://sonarcloud.io/api/settings/values?component=ProjectKey...
16:44:33.147  Response received from https://sonarcloud.io/api/settings/values?component=ProjectKey...
16:44:33.159  Downloading from https://sonarcloud.io/api/languages/list...
16:44:33.194  Response received from https://sonarcloud.io/api/languages/list...
16:44:33.197  Fetching quality profile for project 'ProjectKey'...
16:44:33.197  Downloading from https://sonarcloud.io/api/qualityprofiles/search?project=ProjectKey&organization=myOrg...
16:44:33.511  Response received from https://sonarcloud.io/api/qualityprofiles/search?project=ProjectKey&organization=myOrg...
16:44:33.516  Fetching rules for quality profile 'AZZh3_8nezy56TkBb94X'...
16:44:33.516  Downloading from https://sonarcloud.io/api/rules/search?f=repo,name,severity,lang,internalKey,templateKey,params,actives&ps=500&qprofile=AZZh3_8nezy56TkBb94X&p=1...
16:44:33.666  Response received from https://sonarcloud.io/api/rules/search?f=repo,name,severity,lang,internalKey,templateKey,params,actives&ps=500&qprofile=AZZh3_8nezy56TkBb94X&p=1...
16:44:33.686  Local analyzer cache: /tmp/.sonarqube/resources
16:44:33.688  Writing Roslyn generated ruleset to /mnt/c/users/Stu Sklinar.FA-0425/code.sonarqube/conf/Sonar-cs.ruleset...
16:44:33.729  Writing Roslyn generated ruleset to /mnt/c/users/Stu Sklinar.FA-0425/code.sonarqube/conf/Sonar-cs-none.ruleset...
16:44:33.762  Provisioning analyzer assemblies for cs...
16:44:33.762  Installing required Roslyn analyzers...
16:44:33.763  Processing plugin: securitycsharpfrontend version 11.7.0.39363
16:44:33.767  Cache hit: using plugin files from /tmp/.sonarqube/resources/0
16:44:33.768  Processing plugin: csharpenterprise version 10.15.0.120848
16:44:33.768  Cache hit: using plugin files from /tmp/.sonarqube/resources/1
16:44:33.79  Writing Roslyn analyzer additional file to /mnt/c/users/Stu Sklinar.FA-0425/code.sonarqube/conf/cs/SonarLint.xml...
16:44:33.821  Fetching quality profile for project 'ProjectKey'...
16:44:33.821  Downloading from https://sonarcloud.io/api/qualityprofiles/search?project=ProjectKey&organization=myOrg...
16:44:34.097  Response received from https://sonarcloud.io/api/qualityprofiles/search?project=ProjectKey&organization=myOrg...
16:44:34.099  Fetching rules for quality profile 'AZZh3_8nezy56TkBb94O'...
16:44:34.099  Downloading from https://sonarcloud.io/api/rules/search?f=repo,name,severity,lang,internalKey,templateKey,params,actives&ps=500&qprofile=AZZh3_8nezy56TkBb94O&p=1...
16:44:34.199  Response received from https://sonarcloud.io/api/rules/search?f=repo,name,severity,lang,internalKey,templateKey,params,actives&ps=500&qprofile=AZZh3_8nezy56TkBb94O&p=1...
16:44:34.209  Local analyzer cache: /tmp/.sonarqube/resources
16:44:34.21  Writing Roslyn generated ruleset to /mnt/c/users/Stu Sklinar.FA-0425/code.sonarqube/conf/Sonar-vbnet.ruleset...
16:44:34.241  Writing Roslyn generated ruleset to /mnt/c/users/Stu Sklinar.FA-0425/code.sonarqube/conf/Sonar-vbnet-none.ruleset...
16:44:34.27  Provisioning analyzer assemblies for vbnet...
16:44:34.27  Installing required Roslyn analyzers...
16:44:34.27  Processing plugin: securityvbnetfrontend version 11.7.0.39363
16:44:34.271  Cache hit: using plugin files from /tmp/.sonarqube/resources/2
16:44:34.271  Processing plugin: vbnetenterprise version 10.15.0.120848
16:44:34.271  Cache hit: using plugin files from /tmp/.sonarqube/resources/3
16:44:34.287  Writing Roslyn analyzer additional file to /mnt/c/users/Stu Sklinar.FA-0425/code.sonarqube/conf/vbnet/SonarLint.xml...
16:44:34.315  Processing analysis cache
16:44:34.317  Fetching properties for project 'ProjectKey:develop'...
16:44:34.317  Downloading from https://sonarcloud.io/api/settings/values?component=ProjectKey%3Adevelop...
16:44:34.355  Response received from https://sonarcloud.io/api/settings/values?component=ProjectKey%3Adevelop...
16:44:34.355  No settings for project ProjectKey:develop. Getting global settings...
16:44:34.355  Downloading from https://sonarcloud.io/api/settings/values...
16:44:34.413  Response received from https://sonarcloud.io/api/settings/values...
16:44:34.415  Downloading cache. Project key: ProjectKey, branch: develop.
16:44:34.417  Incremental PR Analysis: Requesting 'prepare_read' from https://api.sonarcloud.io/analysis/sensor-cache/prepare-read?organization=myOrg&project=ProjectKey&branch=develop
16:44:35.148  Using cache base path: /mnt/c/users/Stu Sklinar.FA-0425/code/
16:44:49.426  Incremental PR analysis: 49 files out of 2295 are unchanged.
16:44:49.431  JAVA_HOME environment variable not set. Try to infer Java home from Java executable.
16:44:49.437  Executing file /usr/bin/sh
  Args: -c command -v java
  Working directory:
  Timeout (ms):-1
  Process id: 6085
16:44:49.438  Process returned exit code 0
16:44:49.441  Java executable located at: '/usr/bin/java
'.
16:44:49.442  Executing file /usr/bin/sh
  Args: -c readlink -f /usr/bin/java

  Working directory:
  Timeout (ms):-1
  Process id: 6086
16:44:49.445  Process returned exit code 0
16:44:49.445  Java executable symbolic link resolved to: '/usr/lib/jvm/java-11-openjdk-amd64/bin/java
'.
16:44:49.446  Java Keystore file found: '/usr/lib/jvm/java-11-openjdk-amd64/lib/security/cacerts'.
16:44:49.482  Pre-processing succeeded.

I can’t share the build log here - its just too large.

Same for the Analysis end - its massive.

But here is the scanner context.


SonarScanner Context:   [Project Analysis]
SonarCloud plugins:
  - Text Code Quality and Security 2.26.0.7517 (textenterprise)
  - JaCoCo 1.3.0.1538 (jacoco)
  - IaC Code Quality and Security 1.48.0.15768 (iacenterprise)
  - IaC Code Quality and Security 1.48.0.15768 (iac)
Project server settings:
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Close

I am noticing in the .sonarqube folder there are a lot of files included that again, haven’‘t changed, with a lot of /out/n/Issues.json files appearing with changes.

Is there a way to share the large outputs?

Thanks,

ganncamp · August 11, 2025, 4:28pm

Hi,

You should be able to post a zip.

Ann

Stu_Sklinar · August 12, 2025, 9:14am

sonarqube.zip (9.4 MB)Hi @ganncamp - please find attached our bin logs, and our SQ End Step logs.

Thanks

ganncamp · August 12, 2025, 11:59am

Hi,

Is this the log for that

?

Because what I see in this (non-DEBUG) log is

Can you share how you’re doing your checkout? And can you share a sonar.verbose=true log?

Thx,
Ann

Stu_Sklinar · August 12, 2025, 12:38pm

I think this was a different branch - but that 12 files analyzed looks correct. In this branch, 12 files have changed, but we’re getting comments across the entire file, not the changes.

I still see:

Incremental PR analysis: 49 files out of 2295 are unchanged

My local checkout is:
git checkout xyz

In Azure Devops we’re doing:

      - checkout: self
        fetchDepth: 0
        persistCredentials: true
        clean: true

      - script: |
          TARGET_BRANCH_NAME=$(echo "$(System.PullRequest.TargetBranch)" | sed 's|refs/heads/||')
          echo "Fetching target branch $TARGET_BRANCH_NAME"
          git fetch origin $TARGET_BRANCH_NAME:refs/remotes/origin/$TARGET_BRANCH_NAME
        displayName: 'Fetch target branch'

The extra bit was an extra step to ensure we have develop fetched (That didn’t work).

I have found that running this locally generates no PR comments, where as running it Azure Pipelines, we get comments on the entire file, not the diff.

ganncamp · August 12, 2025, 2:16pm

Hi,

If the changed files are correctly identified, but not the changed lines within them, then I have to wonder if you have some automated process touching your files to e.g. change tabs to spaces or vice versa.

When you click in the margin in SonarQube Cloud to see the blame information on an “untouched” line, what do you see?

Ann

Stu_Sklinar · August 12, 2025, 2:21pm

Hello,

To my knowledge there are no automated processes to change the code after checkout.

In SQ we have a blame as so:

ganncamp · August 12, 2025, 2:44pm

Hi,

Thanks for the screenshot.

When you fetch the target branch, can you try not giving it a local name with slashes in it?

Thx
Ann

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New Code always 0 for PRs – Issues detected only after PR is merged in Azure DevOps SonarQube Server / Community Build sonarqube , pull-request , coverage	28	319	July 3, 2025
Sonarqube pull request analysis not showing any measures SonarQube Server / Community Build pull-request , sonarqube-team	7	3183	December 20, 2022
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The report is generated but is not reflected in the project overview SonarQube Cloud csharp , dotnet , sonarqube-cloud	13	1341	February 16, 2023
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SQ adding comments for all code, not just changed code

Share the Scanner for .NET verbose logs

Share the msbuild detailed logs

Share the binlog

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