Reorganizing models and enabling "other" models#12
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akutuva21 wants to merge 30 commits intoRuleWorld:masterfrom
Open
Reorganizing models and enabling "other" models#12akutuva21 wants to merge 30 commits intoRuleWorld:masterfrom
akutuva21 wants to merge 30 commits intoRuleWorld:masterfrom
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- Create \`Examples\`, \`Published\`, and \`Tutorials\` root directories. - Move \`Contributed/BNGPlayground_Examples\` to \`Examples\`. - Move published model subdirectories (e.g., PyBioNetGen models, Contributed/Hlavacek2018, Contributed/Mitra2019, Validation models like Korwek2023, MyrtleBeach) to \`Published\`. - Move remaining items in \`Contributed/BNGPlayground_Validation\` and \`BNGPlayground_PublicRuntime\` to \`Tutorials\`. - Update \`metadata-schema.yaml\` to add explicit domains (\`compartments\`, \`energy\`, \`wacky\`, \`mechanistic-modeling\`, etc.). - Update \`metadata.yaml\` files previously labeled as \`other\` with the new, specific categories. - Update \`scripts/generate-manifest.js\` and \`scripts/validate-metadata.js\` with new \`SEARCH_ROOTS\` and categories. - Regenerate \`manifest.json\`. Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
…969453 chore: Restructure RuleHub directories and improve metadata categories
Fixes a prototype pollution vulnerability in the `setNested` utility function within `scripts/generate-manifest.js`. The fix explicitly skips and filters out dangerous property names (`__proto__`, `constructor`, `prototype`) during both object traversal and final assignment. Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
* Refactor `scripts/validate-metadata.js` to export `parseScalar` and conditionally execute `main()`. * Add `scripts/tests/validate-metadata.test.js` covering all behavior. Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
Removed the `# FIX: Add Autoinducer dynamics` comment from `Examples/biology/quorumsensingcircuit/quorum-sensing-circuit.bngl` as the implementation for production and degradation is already present below it. Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
Removed the '# FIX: Add resource dynamics' comment as the resource regeneration and decay rules are already implemented correctly in the model. Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
Updated `setNested` to accept an array of parts instead of a dotted path string, avoiding redundant string splitting. Tested with a 100,000 iteration benchmark on `parseMetadataYaml`, measuring ~20% improvement (from ~1.25s to ~0.98s). Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
- Refactor `scripts/validate-metadata.js` to only run `main()` if executed directly. - Export `validateMetadataFile` to allow testing it in isolation. - Add comprehensive test suite in `tests/validate-metadata.test.js` covering valid files, missing files, and invalid configuration scenarios using temporary directory fixtures. Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
Refactored generate-manifest.js to allow importing internal functions and added comprehensive unit tests for buildEntry using node:test. Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
Updated `ds3()` in `sp_fourier_synthesizer.bngl` to use the exact derivative of the 3rd harmonic trigonometric identity instead of an approximation. Cleaned up corresponding comments. Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
Extracted the duplicated listModelFiles function from scripts/generate-manifest.js and scripts/validate-metadata.js into a shared utility module (scripts/utils.js). This improves code maintainability and adheres to DRY principles. Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
…-9077399113245613909 Fix: Remove Autoinducer dynamics FIX comment
…2033588725295054439 Remove resolved FIX comment in eco_food_web_chaos_3sp.bngl
…438250706711219829 🧪 Add generate-manifest.js testing coverage
…3267491605790 ⚡ perf(manifest): optimize setNested path handling
…-16219869687540900783 🧪 [testing] add tests for parseScalar in validate-metadata.js
…6954674524457256 🧪 testing: add tests for validateMetadataFile
…451205665425511 🧹 Refactor: Extract listModelFiles function into a shared utility module
…67357569153273 Implement 3rd harmonic using trigonometric identity
…-yaml-7716385411393383498
…411393383498 🧪 test: add unit tests for custom parseMetadataYaml function
…-15072088604429859966 🔒 Fix Prototype Pollution in setNested
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Added other security fixes and small edits suggested by Jules |
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This PR refactors the RuleHub directory structure and updates metadata categories according to the latest requirements.
Key Changes
Published,Examples, andTutorials.Examplesdirectory.PyBioNetGenpublished models toPublished/PyBioNetGen.AuthorYearformat fromContributed/toPublished/.BNGPlayground_Validationmodels based on their origin (published vs. tutorials)."category: other".mechanistic-modeling,feature-demos,compartments,wacky,energy, etc.) to themetadata-schema.yaml.metadata.yamlfiles.generate-manifest.jsandvalidate-metadata.jsmodified to scan the new root directories.