8000 download workflows and test clam by denis-yuen · Pull Request #514 · dockstore/dockstore-support · GitHub
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download workflows and test clam #514

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Merged
merged 10 commits into from
Jun 6, 2025
Merged

download workflows and test clam #514

merged 10 commits into from
Jun 6, 2025

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denis-yuen
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@denis-yuen denis-yuen commented May 9, 2025

Description
Killing a couple birds with one stone, this module is becoming less relevant since it doesn't seem we're going to be backing up docker containers ourselves. So rigging this up to download descriptors so that we can run clamav on them ourselves. More details on JIRA

Review Instructions
Could replicate process in JIRA if desired

Issue
https://ucsc-cgl.atlassian.net/browse/SEAB-6983

Security
Not exactly, but could cause annoying WAF noise

  • Check that you pass the basic style checks and unit tests by running mvn clean install in the project that you have modified (until https://ucsc-cgl.atlassian.net/browse/SEAB-5300 adds multi-module support properly)
  • Ensure that the PR targets the correct branch. Check the milestone or fix version of the ticket.
  • If you are changing dependencies, check with dependabot to ensure you are not introducing new high/critical vulnerabilities
  • If this PR is for a user-facing feature, create and link a documentation ticket for this feature (usually in the same milestone as the linked issue). Style points if you create a documentation PR directly and link that instead.

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codecov bot commented May 9, 2025

Codecov Report

Attention: Patch coverage is 0% with 59 lines in your changes missing coverage. Please review.

Project coverage is 10.34%. Comparing base (dce6673) to head (5f900ec).
Report is 1 commits behind head on develop.

Files with missing lines Patch % Lines
...ava/io/dockstore/toolbackup/client/cli/Client.java 0.00% 59 Missing ⚠️
Additional details and impacted files
@@              Coverage Diff              @@
##             develop     #514      +/-   ##
=============================================
+ Coverage       9.90%   10.34%   +0.44%     
  Complexity        75       75              
=============================================
  Files             44       43       -1     
  Lines           2372     2271     -101     
  Branches         203      194       -9     
=============================================
  Hits             235      235              
+ Misses          2121     2020     -101     
  Partials          16       16              
Flag Coverage Δ
tooltester 10.34% <0.00%> (+0.44%) ⬆️

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@denis-yuen
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  • Can ignore hotspot (we create the zip ourselves)

8000

@denis-yuen denis-yuen changed the title Feature/test clam download and test clam May 12, 2025
ZipEntry entry = entries.nextElement();
File entryDestination = new File(dirVersionPath, entry.getName());
if (entry.isDirectory()) {
entryDestination.mkdirs();

Check failure

Code scanning / SonarCloud

Extracting archives should not lead to zip slip vulnerabilities High

Change this code to not construct the path from file name entry of an archive. See more on SonarQube Cloud
@denis-yuen denis-yuen changed the title download and test clam download workflows and test clam May 20, 2025
@denis-yuen denis-yuen marked this pull request as ready for review May 26, 2025 20:24
@denis-yuen denis-yuen self-assigned this May 26, 2025
@denis-yuen denis-yuen requested review from a team, kathy-t and svonworl and removed request for a team May 26, 2025 20:25
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Do any READMEs have to updated due to these changes? Maybe https://github.com/dockstore/dockstore-support?tab=readme-ov-file#client?

if no dockstore-support cache is available
but other changes seemed to have worked
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sonarqubecloud bot commented Jun 6, 2025

Quality Gate Failed Quality Gate failed

Failed conditions
1 Security Hotspot
0.0% Coverage on New Code (required ≥ 80%)
E Security Rating on New Code (required ≥ A)
C Reliability Rating on New Code (required ≥ A)

See analysis details on SonarQube Cloud

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@denis-yuen denis-yuen merged commit d6342d0 into develop Jun 6, 2025
10 of 14 checks passed
@denis-yuen denis-yuen deleted the feature/test_clam branch June 6, 2025 18:42
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