[WIP] Improve input validation and help descriptions for genome utility functions

[Copilot]

Coding agent has begun work on Improve MATLAB Help Descriptions and Input Validation for Genome Utility Functions and will update this pull request as work progresses.

Original prompt

improve this function by adding if validators of inputs like this for example nargin<1 || isempty(fileName) [fileName, pathName] = uigetfile({'.xml;.sbml'}, 'Please select the model file'); if fileName == 0 error('You should select a model file') else fileName = fullfile(pathName,fileName); end end fileName=char(fileName); if nargin<2 || isempty(removeExcMets) removeExcMets=true; end if nargin<3 || isempty(removePrefix) removePrefix=true; end if nargin<4 supressWarnings=false; end

The user has attached the following files from their workspace:

• curation/downloadGenomeData.m

TITLE: Improve MATLAB Help Descriptions and Input Validation for Genome Utility Functions

---

USER INTENT: Summarize the full conversation, which covers two sequential tasks: (1) rewriting help blocks for three MATLAB functions, and (2) adding nargin-style input validators to those same functions following an established RAVEN pattern.

---

TASK DESCRIPTION:

• Rewrite the MATLAB help documentation for downloadGenomeData, getGeneData, and renameModelGenes following the structured style used in importModel and curateModelFromTables (Parameters / Returns / Examples / Notes / See also sections).
• Add defensive input validators to each function using the nargin < N || isempty(...) pattern already used in RAVEN, including uigetfile prompts where appropriate, char() casts, default values, and descriptive error() messages.

---

EXISTING:
Completed:

• downloadGenomeData.m — full structured help block written; input validation block added, including:
  • nargin < 1 || isempty(accession) guard with descriptive error
  • char() cast on accession
  • strncmpi format check for GCF_/GCA_ prefix
  • varargin parsed via a for loop with switch/case for 'outputDir' and 'verbose'
  • logMsg wrapper for conditional fprintf
  • Output variables gffFile and faaFile explicitly assigned at end of function
• getGeneData.m — full structured help block written (input validation not yet added)
• renameModelGenes.m — full structured help block written (input validation not yet added)

---

PENDING:

• getGeneData.m — add nargin-style input validators for:
  • accession (required, char cast, GCF_/GCA_ prefix check)
  • outputFile (optional, default '')
  • gffFile (optional, default triggers downloadGenomeData)
  • faaFile (optional, default triggers downloadGenomeData)
• renameModelGenes.m — add nargin-style input validators for:
  • model (required, must be a struct with .genes and .grRules fields)
  • geneTable (required, accept table or char path; if char, load with readtable)
  • fromCol (required, must be a valid column name in geneTable)
  • toCol (required, must be a valid column name in geneTable)

---

CODE STATE:

downloadGenomeData.m — validation block (completed):

function [gffFile, faaFile] = downloadGenomeData(accession, varargin)
% ... (structured help block) ...

% -------------------------------------------------------------------------
% Input validation
% -------------------------------------------------------------------------
if nargin < 1 || isempty(accession)
    error('downloadGenomeData:missingInput', ...
        ['accession is required. ', ...
         'Provide an NCBI assembly accession, e.g. ''GCF_000002595.2''.']);
end
accession = char(accession);

if ~any(strncmpi(accession, {'GCF_', 'GCA_'}, 4))
    error('downloadGenomeData:invalidAccession', ...
        ['Accession must start with ''GCF_'' (RefSeq) or ''GCA_'' (GenBank). ', ...
         'Received: ''%s''.'], accession);
end

% -------------------------------------------------------------------------
% Parse optional name-value arguments
% -------------------------------------------------------------------------
downloadDir = pwd;   % default: current working directory
verbose     = true;  % default: print progress

for i = 1:2:numel(varargin)
    if ~ischar(varargin{i}) && ~isstring(varargin{i})
        error('downloadGenomeData:invalidParam', ...
            'Parameter names must be character vectors or strings.');
    end
    switch lower(char(varargin{i}))
        case 'outputdir'
            if i+1 > numel(varargin) || isempty(varargin{i+1})
                error('downloadGenomeData:missingValue', ...
                    '''outputDir'' requires a non-empty directory path.');
            end
            downloadDir = char(varargin{i+1});
        case 'verbose'
            if i+1 > numel(varargin)
                error('downloadGenomeData:missingValue', ...
                    '''verbose'' requires a logical value.');
            end
            verbose = logical(varargin{i+1});
        otherwise
            error('downloadGenomeData:unknownParam', ...
                'Unknown parameter: ''%s''.', varargin{i});
    end
end

logMsg = @(varargin) verbose && fprintf(varargin{:});

% ......

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