Directory structure validation

directory-structure-validation

License: restricted — no clear open-source license detected for the underlying tool; verify licensing before commercial use or redistribution. <!-- asb-license-banner -->

Summary

Validates that edited script files (Modular.r, genEIC.r, MS1Spectragen.r, Stats.R) are placed into the correct target directories within LipidMatch-4.2 distribution to ensure developer changes integrate properly into both Flow and Modular analysis versions.

When to use

Apply this skill after editing core R scripts in the Core-Match repository and before running LipidMatch-4.2 analysis, to verify that developer modifications have been correctly distributed across the Flow version (LipidMatch_Distribution) and Modular version (FluoroMatch_Modular) directory trees.

When NOT to use

• When using pre-compiled binary distributions where script files cannot be edited or replaced
• When script files are being downloaded directly from innovativeomics.com/software (use official binary distribution instead)
• When working with a cloned Core-Match repository alone without an installed LipidMatch-4.2 distribution

Inputs

• edited R script files (Modular.r, genEIC.r, MS1Spectragen.r, Stats.R)
• LipidMatch-4.2 distribution directory structure (downloaded from InnovativeOmics)
• README or methods specification file documenting target paths

Outputs

• manifest file mapping source files to target paths (CSV or JSON format)
• validated directory tree or layout document
• confirmation that all script files are placed in correct locations

How to apply

First, identify the four edited script files (Modular.r, genEIC.r, MS1Spectragen.r, Stats.R) from your source submission package. Next, create a manifest file (CSV or JSON) that maps each source file to its required target path(s): Modular.r must be placed in both LipidMatch-4.2\Flow\LipidMatch_Distribution and LipidMatch-4.2\FluoroMatch_Modular to replace existing code; genEIC.r, MS1Spectragen.r, and Stats.R must all be placed into LipidMatch-4.2\Flow\LipidMatch_Distribution\LipidMatch_Libraries\Scripts. Then, verify that each target directory exists within your downloaded LipidMatch-4.2 distribution (typically downloaded from innovativeomics.com/software). Finally, generate a directory tree or layout document showing the final file placement structure to confirm all files are in their specified locations before executing analysis workflows.

Related tools

• LipidMatch (target software distribution into which edited scripts must be integrated) — https://github.com/InnovativeOmics/Core-Match
• FluoroMatch (alternative analysis version of LipidMatch requiring Modular.r placement for integration) — https://github.com/InnovativeOmics/Core-Match
• R (runtime environment for executing edited script files (Modular.r, genEIC.r, MS1Spectragen.r, Stats.R))

Evaluation signals

• All four script files (Modular.r, genEIC.r, MS1Spectragen.r, Stats.R) are present in their specified target directories
• Modular.r exists in both LipidMatch-4.2\Flow\LipidMatch_Distribution AND LipidMatch-4.2\FluoroMatch_Modular directories
• genEIC.r, MS1Spectragen.r, and Stats.R all exist in LipidMatch-4.2\Flow\LipidMatch_Distribution\LipidMatch_Libraries\Scripts
• Manifest file entries match actual file locations verified via directory listing or tree output
• No orphaned script files remain in intermediate or incorrect directories

Limitations

• Validation assumes target directories already exist within the LipidMatch-4.2 distribution; missing parent directories will prevent proper file placement
• Windows and Unix path separators differ (backslash vs. forward slash); cross-platform deployment requires path normalization
• No changelog is available to document which versions of scripts are compatible with which LipidMatch-4.2 releases; version mismatches may cause runtime errors
• The skill validates structural placement only; it does not verify script syntax, dependencies, or functional correctness

Evidence

• [readme] Modular.r must replace existing code in both directories: "put Modular.r into two directories (replace existing code): LipidMatch-4.2\Flow\LipidMatch_Distribution LipidMatch-4.2\FluoroMatch_Modular"
• [readme] Other edited scripts go into the Scripts subdirectory: "Place any edited script files (genEIC.r, MS1Spectragen.r, Stats.R) into: LipidMatch-4.2\Flow\LipidMatch_Distribution\LipidMatch_Libraries\Scripts"
• [readme] Developers edit scripts on GitHub and must integrate into downloaded distributions: "Developers can edit the main algorithms here on github as a team. Then the code needs to be integrated by placing the edited code in the correct directory from the downloaded distribution"
• [readme] Users download the distribution from the official website: "For LipidMatch, FluoroMatch, and PolyMatch users should directly download from innovativeomics.com/software for the latest stable release."
• [readme] Installation is prerequisite to integration: "Install FluoroMatch or LipidMatch from InnovativeOmics.com"