master: -m

test_everything.m → test_all_eight_major_configurations.m

@@ -1,8 +1,8 @@
-function test_everything()
+function test_all_eight_major_configurations()
     for freezing_or_thawing = { 'freezing', 'thawing' } ,
         for raw_tiles_or_octree = { 'raw-tiles', 'octree' } ,
             for local_or_cluster = { 'local', 'cluster' } ,
-                test_something(freezing_or_thawing{1}, raw_tiles_or_octree{1}, local_or_cluster{1})
+                test_single_major_configuration(freezing_or_thawing{1}, raw_tiles_or_octree{1}, local_or_cluster{1}) ;
             end
         end
     end    

test_all_verification_conditions.m

@@ -0,0 +1,17 @@
+function test_all_verification_conditions()
+    %for freezing_or_thawing = { 'freezing', 'thawing' } ,
+    for freezing_or_thawing = { 'thawing' } ,
+        %for raw_tiles_or_octree = { 'raw-tiles', 'octree' } ,
+        for raw_tiles_or_octree = { 'octree' } ,
+            %for local_or_cluster = { 'local', 'cluster' } ,
+            for local_or_cluster = { 'local' } ,
+                for stack_or_non_stack = { 'stack', 'non-stack' } ,
+                    for exact_problem = { 'deleted', 'zero-length', 'corrupt' } ,
+                        test_verification_condition( ...
+                            freezing_or_thawing{1}, raw_tiles_or_octree{1}, local_or_cluster{1}, stack_or_non_stack{1}, exact_problem{1}) ;
+                    end
+                end
+            end
+        end
+    end    
+end

test_single_major_configuration.m

@@ -0,0 +1,54 @@
+function test_single_major_configuration(freezing_or_thawing, raw_tiles_or_octree, local_or_cluster)
+    % Test, in one of 2^3==8 possible configurations.
+
+    % Deal with the arguments
+    if ~strcmp(freezing_or_thawing, 'freezing') && ~strcmp(freezing_or_thawing, 'thawing') ,
+        error('freezing_or_thawing must be ''freezing'' or ''thawing''') ;
+    end
+    if ~strcmp(raw_tiles_or_octree, 'raw-tiles') && ~strcmp(raw_tiles_or_octree, 'octree') ,
+        error('raw_tiles_or_octree must be ''raw-tiles'' or ''octree''') ;
+    end
+    if ~strcmp(local_or_cluster, 'local') && ~strcmp(local_or_cluster, 'cluster') ,
+        error('local_or_cluster must be ''local'' or ''cluster''') ;
+    end
+
+    % Define all the needed inputs
+    path_to_this_folder = fileparts(mfilename('fullpath')) ;
+    output_folder_name = sprintf('%s-%s-test-output-folder', raw_tiles_or_octree, freezing_or_thawing) ;
+    output_folder_path = fullfile(path_to_this_folder, output_folder_name) ;
+    input_folder_name = sprintf('%s-%s-test-input-folder', raw_tiles_or_octree, freezing_or_thawing) ;
+    input_folder_path = fullfile(path_to_this_folder, input_folder_name) ;
+    compression_ratio = 10 ;  % only used for freezing
+    do_run_on_cluster = strcmp(local_or_cluster, 'cluster') ;
+    do_try = false ;  % if running locally, don't wrap in try so easier to debug
+    maximum_running_slot_count = 40 ;
+    submit_host_name = if_not_a_submit_host('login2.int.janelia.org') ;
+
+    % Delete the test output folder
+    reset_for_test(output_folder_path) ;
+
+    % Make sure the input folder exists
+    if ~logical(exist(input_folder_path, 'dir')) ,
+        error('Input folder %s is missing, or is not a folder', input_folder_path) ;
+    end
+
+    % Call the script
+    if strcmp(freezing_or_thawing, 'freezing') ,
+        freeze_mouselight_folder(...
+            output_folder_path, ...
+            input_folder_path, ...
+            compression_ratio, ...
+            do_run_on_cluster, ...
+            do_try, ...
+            maximum_running_slot_count, ...
+            submit_host_name) ;
+    else
+        thaw_mouselight_folder(...
+            output_folder_path, ...
+            input_folder_path, ...
+            do_run_on_cluster, ...
+            do_try, ...
+            maximum_running_slot_count, ...
+            submit_host_name) ;        
+    end
+end

test_verification_condition.m

@@ -0,0 +1,146 @@
+function test_verification_condition(freezing_or_thawing, raw_tiles_or_octree, local_or_cluster, stack_or_non_stack, exact_problem)    
+    % Deal with the arguments
+    if ~strcmp(freezing_or_thawing, 'freezing') && ~strcmp(freezing_or_thawing, 'thawing') ,
+        error('freezing_or_thawing must be ''freezing'' or ''thawing''') ;
+    end
+    if ~strcmp(raw_tiles_or_octree, 'raw-tiles') && ~strcmp(raw_tiles_or_octree, 'octree') ,
+        error('raw_tiles_or_octree must be ''raw-tiles'' or ''octree''') ;
+    end
+    if ~strcmp(local_or_cluster, 'local') && ~strcmp(local_or_cluster, 'cluster') ,
+        error('local_or_cluster must be ''local'' or ''cluster''') ;
+    end
+    if ~strcmp(stack_or_non_stack, 'stack') && ~strcmp(stack_or_non_stack, 'non-stack') ,
+        error('stack_or_non_stack must be ''stack'' or ''non-stack''') ;
+    end
+    if ~any(strcmp(exact_problem, {'deleted', 'zero-length', 'corrupt'})) ,
+        error('exact_problem must be one of ''deleted'', ''zero-length'', or ''corrupt''') ;
+    end
+
+    % Declare what test we're doing
+    fprintf('Testing %s %s %s %s %s...\n', ...
+            freezing_or_thawing, raw_tiles_or_octree, local_or_cluster, stack_or_non_stack, exact_problem) ;
+
+    % Define all the needed inputs
+    path_to_this_folder = fileparts(mfilename('fullpath')) ;
+    output_folder_name = sprintf('%s-%s-test-output-folder', raw_tiles_or_octree, freezing_or_thawing) ;
+    output_folder_path = fullfile(path_to_this_folder, output_folder_name) ;
+    input_folder_name = sprintf('%s-%s-test-input-folder', raw_tiles_or_octree, freezing_or_thawing) ;
+    input_folder_path = fullfile(path_to_this_folder, input_folder_name) ;
+    compression_ratio = 10 ;  % only used for freezing
+    do_run_on_cluster = false ;
+    do_try = true ;  % if running locally, don't wrap in try so easier to debug
+    maximum_running_slot_count = 40 ;
+    submit_host_name = if_not_a_submit_host('login2.int.janelia.org') ;
+
+    % Delete the test output folder
+    reset_for_test(output_folder_path) ;
+
+    % Make sure the input folder exists
+    if ~logical(exist(input_folder_path, 'dir')) ,
+        error('Input folder %s is missing, or is not a folder', input_folder_path) ;
+    end
+
+    % Call the script, but don't do verification
+    if strcmp(freezing_or_thawing, 'freezing') ,
+        freeze_mouselight_folder(...
+            output_folder_path, ...
+            input_folder_path, ...
+            compression_ratio, ...
+            do_run_on_cluster, ...
+            do_try, ...
+            maximum_running_slot_count, ...
+            submit_host_name, ...
+            'do_freezing', true, ...
+            'do_verification', false) ;
+    else
+        thaw_mouselight_folder(...
+            output_folder_path, ...
+            input_folder_path, ...
+            do_run_on_cluster, ...
+            do_try, ...
+            maximum_running_slot_count, ...
+            submit_host_name, ...
+            'do_thawing', true, ...
+            'do_verification', false) ;
+    end
+
+    % Figure out what file we will mess with
+    if strcmp(stack_or_non_stack, 'stack') ,
+        if strcmp(freezing_or_thawing, 'freezing') ,
+            if strcmp(raw_tiles_or_octree, 'octree') ,
+                perverted_output_file_relative_path = '1/default.1.mj2' ;
+            else
+                perverted_output_file_relative_path = '2018-12-12/00/00241/00241-ngc.0.mj2' ;
+            end
+        else
+            % thawing
+            if strcmp(raw_tiles_or_octree, 'octree') ,
+                perverted_output_file_relative_path = '1/default.1.tif' ;
+            else
+                perverted_output_file_relative_path = 'Tiling/2017-11-03/02/02013-ngc.0_comp-10.tif' ;
+            end
+        end
+    else
+        % non-stack file
+        if strcmp(freezing_or_thawing, 'freezing') ,
+            if strcmp(raw_tiles_or_octree, 'octree') ,
+                perverted_output_file_relative_path = 'set_parameters.jl' ;
+            else
+                perverted_output_file_relative_path = '2018-12-09/02/02017/02017-ngc.microscope' ;
+            end
+        else
+            % thawing 
+            if strcmp(raw_tiles_or_octree, 'octree') ,
+                perverted_output_file_relative_path = 'tilebase.cache.yml' ;
+            else
+                perverted_output_file_relative_path = 'Tiling/2017-11-03/02/02013-ngc.acquisition' ;
+            end
+        end
+    end
+
+    % Fake a failure by messing with one of the destination files
+    perverted_output_file_path = fullfile(output_folder_path, perverted_output_file_relative_path) ;    
+    if strcmp(exact_problem, 'deleted') ,
+        delete(perverted_output_file_path) ;
+    elseif strcmp(exact_problem, 'zero-length') ,
+        delete(perverted_output_file_path) ;
+        touch(perverted_output_file_path) ;        
+    else         
+        set_all_file_bytes_to_zero(perverted_output_file_path) ;
+    end
+
+    % Now do verification, which should fail
+    try 
+        if strcmp(freezing_or_thawing, 'freezing') ,
+            freeze_mouselight_folder(...
+                output_folder_path, ...
+                input_folder_path, ...
+                compression_ratio, ...
+                do_run_on_cluster, ...
+                do_try, ...
+                maximum_running_slot_count, ...
+                submit_host_name, ...
+                'do_freezing', false, ...
+                'do_verification', true) ;
+        else
+            thaw_mouselight_folder(...
+                output_folder_path, ...
+                input_folder_path, ...
+                do_run_on_cluster, ...
+                do_try, ...
+                maximum_running_slot_count, ...
+                submit_host_name, ...
+                'do_thawing', false, ...
+                'do_verification', true) ;            
+        end
+        error('Verification succeeded, even though a destination file was corrupted') ;
+    catch me
+        if strcmp(me.identifier, 'mouselight_toolbox:verification_failed') ,
+            % All is well, nothing to do
+            fprintf('Test %s %s %s %s %s passed.\n', ...
+                    freezing_or_thawing, raw_tiles_or_octree, local_or_cluster, stack_or_non_stack, exact_problem) ;
+        else
+            rethrow(me) ;
+        end           
+    end    
+end