feat: Update of datavzrd Version for boolean spell and use of clin_sig spell #342
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… of the clin_sig spell instead of function
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🧹 Outside diff range and nitpick comments (1)
workflow/resources/datavzrd/variant-calls-template.datavzrd.yaml (1)
480-483: Consider DRY optimization for repeated boolean configurationsThe boolean spell configurations are identical across coding and noncoding sections. Consider extracting these common configurations into a reusable YAML anchor to reduce duplication.
Example optimization:
# At the top of the file __definitions__: boolean_spell: &boolean_spell url: v1.2.1/logic/boolean with: true_value: "True" false_value: "False" # In the configuration canonical: spell: *boolean_spell mane_plus_clinical: spell: *boolean_spellAlso applies to: 488-491
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workflow/resources/datavzrd/variant-calls-template.datavzrd.yaml(3 hunks)
🔇 Additional comments (3)
workflow/resources/datavzrd/variant-calls-template.datavzrd.yaml (3)
309-312: LGTM: Boolean spell configuration is now more explicit
The update properly defines true/false values for the boolean spell, improving clarity and consistency.
317-320: LGTM: Consistent boolean configuration
The boolean spell configuration matches the canonical flag, maintaining consistency across the configuration.
205-206: Verify the new clinical significance spell functionality
The update to use the specialized clin_sig spell (v1.2.1) aligns with the PR objectives. This change should provide better visualization of clinical significance data.
Let's verify the spell's existence and compatibility:
✅ Verification successful
The clinical significance spell update is appropriate and consistent with the codebase
The verification shows that:
- The clinical significance functionality is properly implemented in
clinical_significance.jswith color mappings for different significance levels - The spell update to
v1.2.1/med/clin_sigis consistent with other v1.2.1 spells used in the same file (e.g., for boolean values) - The clinical significance column is properly integrated in the datavzrd configuration and is marked as optional
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Verify the existence and compatibility of the new clin_sig spell
# Check if the new spell version exists in the repository
rg -l "v1.2.1/med/clin_sig" .
# Look for any existing usage patterns of clinical significance
rg "'clinical significance':" -A 5 -B 5
Length of output: 77
Script:
#!/bin/bash
# Let's try different search patterns to understand the clinical significance configuration
# Search for clin_sig in any context
rg "clin_sig" -A 3 -B 3
# Search for clinical significance without quotes
rg "clinical.?significance" -A 3 -B 3
# Look for spell configurations in the datavzrd yaml
fd ".*\.datavzrd\.yaml$" --exec grep -A 5 -B 5 "spell:"
# Check if there are any other version references
rg "v1\.2\.1" -A 3 -B 3
Length of output: 2134
Script:
#!/bin/bash
# Let's examine the clinical_significance.js file and check the datavzrd yaml file content
# Check the content of clinical_significance.js
cat workflow/resources/datavzrd/clinical_significance.js
# Examine the full variant-calls-template.datavzrd.yaml
cat workflow/resources/datavzrd/variant-calls-template.datavzrd.yaml
# Look for any documentation about spells
fd "README|CHANGELOG" --exec grep -A 5 -B 5 -i "spell"
Length of output: 17871
workflow/resources/datavzrd/variant-calls-template.datavzrd.yaml
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (1)
workflow/resources/datavzrd/variant-calls-template.datavzrd.yaml (1)
309-312: LGTM: Boolean spell configurations consistently updatedThe boolean spell configurations have been consistently updated across all instances with:
- Version upgrade to v1.2.1
- Explicit false_value setting
Consider extracting the common boolean spell configuration into a YAML anchor to reduce duplication. Example:
# At the top of the file __definitions__: boolean_spell: &boolean_spell url: v1.2.1/logic/boolean with: true_value: "True" false_value: "False" # Then in the configurations canonical: spell: *boolean_spellAlso applies to: 317-320, 480-483, 488-491
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📒 Files selected for processing (1)
workflow/resources/datavzrd/variant-calls-template.datavzrd.yaml(3 hunks)
🔇 Additional comments (2)
workflow/resources/datavzrd/variant-calls-template.datavzrd.yaml (2)
205-206: LGTM: Clinical significance spell version updated as suggested
The update to v1.2.1 for the clinical significance spell has been implemented as previously suggested.
Line range hint 341-371: LGTM: Well-defined visualization configurations
The visualization configurations for SpliceAI and AlphaMissense scores are well-structured with:
- Clear domain boundaries for score ranges
- Appropriate color schemes for representing different ranges
- Consistent configuration between coding and noncoding sections
Also applies to: 531-561
An updated version of datavzrd is used for the boolean spell, which now visualizes via badges. The clinical significance function is replaced by the clin_sig spell.
Summary by CodeRabbit
New Features
Bug Fixes
Documentation
Chores
clinical_significance.jsfile and associated functions to streamline the codebase.