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fix: bump mehari to escape clinvar output string (#485) #488

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merged 2 commits into from
Oct 8, 2024
Merged

fix: bump mehari to escape clinvar output string (#485) #488

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holtgrewe Oct 8, 2024
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holtgrewe Oct 8, 2024
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5 changes: 3 additions & 2 deletions Cargo.lock
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4 changes: 2 additions & 2 deletions Cargo.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -15,8 +15,8 @@ rust-version = "1.70.0"
annonars = "0.41"
anyhow = "1.0"
async-compression = { version = "0.4", features = ["tokio", "gzip"] }
aws-sdk-s3 = { version = "1.49", features = ["behavior-version-latest"] }
aws-config = { version = "1.5", features = ["behavior-version-latest"] }
aws-sdk-s3 = { version = "1.49", features = ["behavior-version-latest"] }
base16ct = "0.2"
bio = "2.0"
biocommons-bioutils = "0.1"
Expand All @@ -39,7 +39,7 @@ hgvs = "0.17.3"
indexmap = { version = "2.6", features = ["serde"] }
itertools = "0.13"
log = "0.4"
mehari = "0.29.0"
mehari = "0.29.5"
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💡 Codebase verification

Issue: Missing changelog entry for mehari version 0.29.5

While the mehari dependency has been updated to version 0.29.5 with several references to ClinVar in the codebase, there is no corresponding entry in the CHANGELOG.md. Please ensure that the changelog is updated to reflect these changes to maintain proper documentation and transparency.

🔗 Analysis chain

Approved: mehari dependency update to address ClinVar output string issue

The update of the mehari dependency from version 0.29.0 to 0.29.5 aligns with the PR objective to address the ClinVar output string issue. This minor version update suggests backward compatibility, which is good for maintaining stability.

To ensure this update fully addresses the intended issue and doesn't introduce any breaking changes, please run the following script to check the changelog or release notes for mehari 0.29.5:

Please review the output to confirm that the update addresses the ClinVar output string issue and doesn't introduce any breaking changes.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Verify the changelog for mehari 0.29.5

# Test: Check if there's a CHANGELOG.md file in the project root
if [ -f CHANGELOG.md ]; then
  echo "Checking local CHANGELOG.md for mehari 0.29.5 updates"
  sed -n '/## \[0.29.5\]/,/## \[0.29.4\]/p' CHANGELOG.md
else
  echo "Local CHANGELOG.md not found. Fetching from GitHub..."
  gh repo view mehari-rs/mehari --json url -q .url | xargs -I {} gh api {}/contents/CHANGELOG.md --jq .content | base64 -d | sed -n '/## \[0.29.5\]/,/## \[0.29.4\]/p'
fi

# Test: Search for mentions of ClinVar-related changes
echo "Searching for ClinVar-related changes in mehari 0.29.5"
rg --type rust "clinvar" -C 5

Length of output: 56441

multimap = "0.10"
pbjson = "0.7"
pbjson-types = "0.7"
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