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Start EASY debugging

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This commit is contained in:
Bryan Roessler
2024-07-27 12:15:17 -04:00
parent 78d5e26d71
commit 5a4bb8c90a
1 changed files with 8 additions and 8 deletions
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16
workflow/templates/easy/EASYconsole.m
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@@ -35,11 +35,11 @@ function varargout = EASYconsole(varargin)
% Set scansDir intelligently (project scans directory) % Set scansDir intelligently (project scans directory)
% Allow users to specify a PROJECT=/mnt/data/ExpJobs/Job directory to analyze with EASY % Allow users to specify a PROJECT=/mnt/data/ExpJobs/Job directory to analyze with EASY
% This better enables running the new EASY in standalone mode % This better enables running the new EASY in standalone mode
if exist('PROJECT', 'env') && ~isempty(getenv('PROJECT')) if exist('PROJECT', 'var') && ~isempty(getenv('PROJECT'))
scansDir=get_env('PROJECT'); scansDir=get_env('PROJECT');
disp(strcat('Using project path: ', scansDir, ' from environment variable PROJECT')); disp(strcat('Using project path: ', scansDir, ' from environment variable PROJECT'));
disp('This usually indicates that we are in standalone mode'); disp('This usually indicates that we are in standalone mode');
elseif exist('SCANS_DIR', 'env') && ~isempty(getenv('SCANS_DIR')) elseif exist('SCANS_DIR', 'var') && ~isempty(getenv('SCANS_DIR'))
scansDir=get_env('SCANS_DIR'); scansDir=get_env('SCANS_DIR');
disp(strcat('Using scans directory: ', scansDir, ' from environment variable SCANS_DIR')); disp(strcat('Using scans directory: ', scansDir, ' from environment variable SCANS_DIR'));
disp('This usually indicates that we are in module mode'); disp('This usually indicates that we are in module mode');
@@ -55,7 +55,7 @@ function varargout = EASYconsole(varargin)
end end
% If we don't have the EASY_SUFFIX from the module, generate it from scansDir % If we don't have the EASY_SUFFIX from the module, generate it from scansDir
if exist('EASY_SUFFIX', 'env') && ~isempty(getenv('EASY_SUFFIX')) if exist('EASY_SUFFIX', 'var') && ~isempty(getenv('EASY_SUFFIX'))
easySuffix=get_env('EASY_SUFFIX'); easySuffix=get_env('EASY_SUFFIX');
else else
[dirName, ~]=fileparts(scansDir); [dirName, ~]=fileparts(scansDir);
@@ -82,7 +82,7 @@ function varargout = EASYconsole(varargin)
end end
% Helpful variables for running in workflow mode that I'll probably have to reimplement in matlab anyways for standalone mode % Helpful variables for running in workflow mode that I'll probably have to reimplement in matlab anyways for standalone mode
if exist('EASY_DIR','env') && ~isempty(getenv('EASY_DIR')) if exist('EASY_DIR','var') && ~isempty(getenv('EASY_DIR'))
EASY_DIR=fullfile(get_env('EASY_DIR')); EASY_DIR=fullfile(get_env('EASY_DIR'));
if easyDir ~= EASY_DIR % sanity check if easyDir ~= EASY_DIR % sanity check
disp("WARNING: EASY_DIR does not match this script's hardcoded EASY location"); disp("WARNING: EASY_DIR does not match this script's hardcoded EASY location");
@@ -94,13 +94,13 @@ function varargout = EASYconsole(varargin)
disp(strcat('Using EASY script directory: ', easyDir, ' from hardcoded default')); disp(strcat('Using EASY script directory: ', easyDir, ' from hardcoded default'));
end end
if exist('PROJECT_USER', 'env') && ~isempty(getenv('PROJECT_USER')) if exist('PROJECT_USER', 'var') && ~isempty(getenv('PROJECT_USER'))
if get_env('PROJECT_USER') ~= userName % sanity check if get_env('PROJECT_USER') ~= userName % sanity check
disp("WARNING: PROJECT_USER does not match the current namespace"); disp("WARNING: PROJECT_USER does not match the current namespace");
end end
end end
if exist('EASY_RESULTS_DIR', 'env') && ~isempty(getenv('EASY_RESULTS_DIR')) if exist('EASY_RESULTS_DIR', 'var') && ~isempty(getenv('EASY_RESULTS_DIR'))
easyResultsDir=fullfile(get_env('EASY_RESULTS_DIR')); easyResultsDir=fullfile(get_env('EASY_RESULTS_DIR'));
disp(strcat('Using output directory: ', easyResultsDir, ' from environment variable EASY_RESULTS_DIR')) disp(strcat('Using output directory: ', easyResultsDir, ' from environment variable EASY_RESULTS_DIR'))
else else
@@ -110,7 +110,7 @@ function varargout = EASYconsole(varargin)
disp(strcat('Using output directory: ', PROJECT_PREFIX, ' from environment variable PROJECT_PREFIX')) disp(strcat('Using output directory: ', PROJECT_PREFIX, ' from environment variable PROJECT_PREFIX'))
end end
if exist('MASTER_PLATE_FILE', 'env') && ~isempty(getenv('MASTER_PLATE_FILE')) if exist('MASTER_PLATE_FILE', 'var') && ~isempty(getenv('MASTER_PLATE_FILE'))
masterPlateFile=fullfile(get_env('MASTER_PLATE_FILE')); masterPlateFile=fullfile(get_env('MASTER_PLATE_FILE'));
disp(strcat('Using drug media file: ', masterPlateFile, ' from environment variable MASTER_PLATE_FILE')) disp(strcat('Using drug media file: ', masterPlateFile, ' from environment variable MASTER_PLATE_FILE'))
else else
@@ -124,7 +124,7 @@ function varargout = EASYconsole(varargin)
end end
end end
if exist('DRUG_MEDIA_FILE', 'env') && ~isempty(getenv('DRUG_MEDIA_FILE')) if exist('DRUG_MEDIA_FILE', 'var') && ~isempty(getenv('DRUG_MEDIA_FILE'))
drugMediaFile=fullfile(get_env('DRUG_MEDIA_FILE')); drugMediaFile=fullfile(get_env('DRUG_MEDIA_FILE'));
disp(strcat('Using drug media file: ', drugMediaFile, ' from environment variable DRUG_MEDIA_FILE')) disp(strcat('Using drug media file: ', drugMediaFile, ' from environment variable DRUG_MEDIA_FILE'))
else else