Merge pull request #29 from thomas-vincent/fix_installation

Fix installation
Nirstorm · May 22, 2018 · 8ae8298 · 8ae8298
2 parents 7d8005f + da7db38
commit 8ae8298
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Showing 8 changed files with 71 additions and 57 deletions.
diff --git a/bst_plugin/nst_request_files.m b/bst_plugin/nst_request_files.m
@@ -93,7 +93,7 @@
 bst_progress('start', download_title, 'Checking data on server...', 1, length(relative_fns));
 for ifn=1:length(relative_fns)
     local_fns{ifn} = fullfile(local_repository, strjoin(relative_fns{ifn}, filesep));
-    output_dir = dirname(local_fns{ifn});
+    [output_dir, ignore_bfn, ignore_ext] = fileparts(local_fns{ifn});
     if ~exist(output_dir, 'dir')
         mkdir(output_dir)
     end
@@ -220,3 +220,8 @@
     ssize = sprintf('%1.2f Tb', size / 1e12);
 end
 end
+
+
+function dn = dirname(fn)
+[dn, tmpf, tmpe] = fileparts(fn);
+end
diff --git a/dist_tools/get_installable_extras.m b/dist_tools/get_installable_extras.m
@@ -37,7 +37,7 @@
             if  compare_matlab_versions(matlab_version, manifest_mat_version) >= 0
                 suffixes = [suffixes ['_only_from.' manifest_mat_rdate]];
             else
-                new_funcs = readlines(fullfile(item.folder, item.name));
+                new_funcs = readlines(fullfile(manifest_dir, item.name));
                 funcs_not_installed = [funcs_not_installed new_funcs];
                 funcs_not_installed_requirements = [funcs_not_installed_requirements ...
                                                     repmat({manifest_mat_rdate}, ...

diff --git a/dist_tools/get_older_matlab_extras.m b/dist_tools/get_older_matlab_extras.m
@@ -44,9 +44,9 @@
 if ~isempty(suffixes)
     s_extras = suffixes{1};
     for iextra=2:length(suffixes)
-        s_extras = [s_extras ', ' suffixes{iextra}];
+        s_extras = ['MANIFEST' s_extras ', ' suffixes{iextra}];
     end
-    fprintf('Adding functions for matlab versions %s to support current version %s.\n', ...
+    fprintf('Adding functions from %s to support matlab version %s.\n', ...
             s_extras, matlab_version);
 end
 

diff --git a/dist_tools/install_package.m b/dist_tools/install_package.m
@@ -184,13 +184,13 @@ function make_file_operations_script(operations, script_fn, header, dry)
     for ifn=1:length(source_rfns)
         source_fn = fullfile(source_dir, source_rfns{ifn});
         if ~exist(source_fn, 'file')
-            throw(MException('DistPackage:FileNotFound', [source_fn ' does not exist in source dir']));
+            throw(MException('DistPackage:FileNotFound', [protect_path(source_fn) ' does not exist in source dir']));
         end
         target_fn = fullfile(target_dir, source_rfns{ifn});
         if exist(target_fn, 'file')
             backup_rfn = add_fn_prefix(source_rfns{ifn}, backup_prefix);
             warning('DistPackage:ExistingTarget', ...
-                    ['"' source_rfns{ifn} '" already exists in target directory. ' ...
+                    ['"' protect_path(source_rfns{ifn}) '" already exists in target directory. ' ...
                      'It will be backuped to "' backup_rfn '"']);
             install_operations(iop).file1 = target_fn;
             install_operations(iop).action = 'move';
@@ -227,11 +227,13 @@ function make_file_operations_script(operations, script_fn, header, dry)
 function fns = read_manifest(manifest_fn)
 fns = cellfun(@(fn) strtrim(fn), strsplit_(fileread(manifest_fn), '\n'), 'UniformOutput', false);
 fns = fns(~cellfun(@isempty, fns));
-files_not_found = cellfun(@(fn) ~exist(fullfile(fileparts(manifest_fn), fn), 'file'), fns);
+[root, ignore_bfn, ignore_ext] = fileparts(manifest_fn);
+files_not_found = cellfun(@(fn) ~exist(fullfile(root, fn), 'file'), fns);
 if any(files_not_found)
+    fns_not_found = cellfun(@(fn) protect_path(fn), fns(files_not_found), 'UniformOutput', false);
     throw(MException('DistPackage:FileNotFound', ...
                      sprintf('Non-existing files from %s:\n%s', ...
-                             manifest_fn, strjoin_(fns(files_not_found), '\n'))));
+                             protect_path(manifest_fn), strjoin_(fns_not_found, '\n'))));
 end
 end
 
@@ -245,12 +247,12 @@ function execute_file_operations(operations, dry)
     operation = operations(iop);
     if isdir(operation.file2) && exist(operation.file2, 'dir') || exist(operation.file2, 'file')
         throw(MException('DistPackage:TargetExists', ... 
-                         ['Target ' operation.file2 ' already exists. ' ...
+                         ['Target ' protect_path(operation.file2) ' already exists. ' ...
                           'Installation aborted, consider manually cleaning target directory.']));
     end
     if ~isfield(operation, 'dont_check_file1') && (isdir(operation.file1) && ~exist(operation.file1, 'dir') || ~exist(operation.file1, 'file'))
         throw(MException('DistPackage:FileNotFound', ...
-                         [operation.file1 ' does not exist. ' ...
+                         [protect_path(operation.file1) ' does not exist. ' ...
                           'Installation aborted, consider manually cleaning target directory.']));
     end
     if ~dry
@@ -290,13 +292,13 @@ function execute_file_operations(operations, dry)
     else
         switch operation.action
             case 'copy'
-                disp(['copy ' operation.file1 ' to ' operation.file2]);
+                disp(['copy ' protect_path(operation.file1) ' to ' protect_path(operation.file2)]);
             case 'link'
-                disp(['link ' operation.file1 ' to ' operation.file2]);
+                disp(['link ' protect_path(operation.file1) ' to ' protect_path(operation.file2)]);
             case 'remove'
-                disp(['remove ' operation.file1]);
+                disp(['remove ' protect_path(operation.file1)]);
             case 'move'
-                disp(['move ' operation.file1 ' to ' operation.file2]);
+                disp(['move ' protect_path(operation.file1) ' to ' protect_path(operation.file2)]);
         end
     end
 end
@@ -330,7 +332,9 @@ function check_inputs(package_name, source_dir, target_dir, mode, extras, dry)
 end
 
 if ~exist(source_dir, 'dir')
-   throw(MException('DistPackage:DirNotFound', 'source_dir does not exist'));
+   throw(MException('DistPackage:DirNotFound', ...
+                    sprintf('source_dir "%s "does not exist', ...
+                            protect_path(source_dir))));
 end
 
 if ~exist(target_dir, 'dir')
@@ -378,25 +382,6 @@ function check_inputs(package_name, source_dir, target_dir, mode, extras, dry)
 end
 end
 
-function joined = strjoin_(toks, delimiter)
-% For compatibility
-if ~verLessThan('matlab', '8.2')
-    joined = strjoin(toks, delimiter);
-else
-    d = delimiter;
-    n = numel(toks);
-    if n == 0
-        joined = '';
-    elseif n == 1
-        joined = toks{1};
-    else
-        ss = cell(1, 2 * n - 1);
-        ss(1:2:end) = toks;
-        [ss{2:2:end}] = deal(d);
-        joined = [ss{:}];
-    end
-end
-end
 
 function ppath = protect_path(path)
 ppath = strrep(path, '\', '\\');

diff --git a/dist_tools/strjoin_.m b/dist_tools/strjoin_.m
@@ -0,0 +1,19 @@
+function joined = strjoin_(toks, delimiter)
+% For compatibility
+if ~verLessThan('matlab', '8.2')
+    joined = strjoin(toks, delimiter);
+else
+    d = delimiter;
+    n = numel(toks);
+    if n == 0
+        joined = '';
+    elseif n == 1
+        joined = toks{1};
+    else
+        ss = cell(1, 2 * n - 1);
+        ss(1:2:end) = toks;
+        [ss{2:2:end}] = deal(d);
+        joined = [ss{:}];
+    end
+end
+end
diff --git a/run_tests.m b/run_tests.m
@@ -8,7 +8,7 @@ function run_tests(to_run, stop_on_error, do_coverage, re_match_filter)
 % 
 install_error_msg = sprintf(['To run unit tests, nirstorm debug functions must be installed.\n'...
                             ' Use nst_install(''copy'', ''debug'') or ' ...
-                            'nst_install(''copy'', ''debug'') (linux only).\n'...
+                            'nst_install(''link'', ''debug'') (linux only).\n'...
                             'WARNING: these functions override brainstorm behavior.']);
 try
     if ~exist(fullfile(bst_get('BrainstormUserDir'), 'process', 'bst_error'), 'file')

diff --git a/test/InstallSourceTest.m b/test/InstallSourceTest.m
@@ -170,20 +170,22 @@ function test_package_install(testCase)
             testCase.assertTrue(all(~files_exist(target_dir, base_rel_fns)));
             testCase.assertTrue(~exist(uninstall_script_fn, 'file')>0);
 
-            % Test installation and uninstallation, link mode
-            install_package(package_name, root_src_dir, target_dir, 'link', {}, 0);
-            testCase.assertTrue(all(files_exist(testCase.tmp_dir, package_rel_files)));
-            testCase.assertTrue(all(files_exist(target_dir, base_rel_fns)));
-            testCase.assertTrue(all(files_are_symlinks(target_dir, base_rel_fns)));
-            testCase.assertTrue(all(~files_exist(target_dir, extra_rel_fns)));
-            testCase.assertTrue(all(~files_exist(target_dir,files_not_to_install)));
-            testCase.assertTrue(exist(uninstall_script_fn, 'file')>0);
-
-            uninstall_package(package_name, target_dir);
-            testCase.assertTrue(all(files_exist(testCase.tmp_dir, package_rel_files)));
-            testCase.assertTrue(all(~files_exist(target_dir, base_rel_fns)));
-            testCase.assertTrue(~exist(uninstall_script_fn, 'file')>0);
-
+            if isempty(strfind(computer, 'WIN'))
+                % Test installation and uninstallation, link mode
+                install_package(package_name, root_src_dir, target_dir, 'link', {}, 0);
+                testCase.assertTrue(all(files_exist(testCase.tmp_dir, package_rel_files)));
+                testCase.assertTrue(all(files_exist(target_dir, base_rel_fns)));
+                testCase.assertTrue(all(files_are_symlinks(target_dir, base_rel_fns)));
+                testCase.assertTrue(all(~files_exist(target_dir, extra_rel_fns)));
+                testCase.assertTrue(all(~files_exist(target_dir,files_not_to_install)));
+                testCase.assertTrue(exist(uninstall_script_fn, 'file')>0);
+
+                uninstall_package(package_name, target_dir);
+                testCase.assertTrue(all(files_exist(testCase.tmp_dir, package_rel_files)));
+                testCase.assertTrue(all(~files_exist(target_dir, base_rel_fns)));
+                testCase.assertTrue(~exist(uninstall_script_fn, 'file')>0);
+            end
+
             % Test installation with already existing items in target_dir 
             % -> should be backuped
             existing_target_fn = fullfile(target_dir, 'func1.m');
@@ -192,7 +194,7 @@ function test_package_install(testCase)
             fout = fopen(existing_target_fn, 'w');
             fprintf(fout, 'blah');
             fclose(fout);
-            install_package(package_name, root_src_dir, target_dir, 'link', {}, 0);
+            install_package(package_name, root_src_dir, target_dir, 'copy', {}, 0);
             testCase.assertTrue(exist(existing_target_backup_fn, 'file')>0);
             testCase.assertTrue(all(files_exist(testCase.tmp_dir, package_rel_files)));
             testCase.assertTrue(all(files_exist(target_dir, base_rel_fns)));
@@ -213,7 +215,7 @@ function test_package_install(testCase)
             fout = fopen(existing_target_fn, 'w');
             fprintf(fout, 'blah');
             fclose(fout);
-            install_package(package_name, root_src_dir, target_dir, 'link', {}, 0);
+            install_package(package_name, root_src_dir, target_dir, 'copy', {}, 0);
             testCase.assertTrue(exist(existing_target_backup_fn, 'file')>0);
             testCase.assertTrue(all(files_exist(testCase.tmp_dir, package_rel_files)));
             testCase.assertTrue(all(files_exist(target_dir, base_rel_fns)));
@@ -292,7 +294,7 @@ function test_package_install_errors(testCase)
             fclose(fout);
             exception_caught = 0;
             try
-                install_package(package_name, root_src_dir, target_dir, 'link', {}, 0);
+                install_package(package_name, root_src_dir, target_dir, 'copy', {}, 0);
             catch ME
                 testCase.assertTrue(strcmp(ME.identifier, 'DistPackage:TargetExists'))
                 testCase.assertTrue(~isempty(strfind(ME.message, existing_target_backup_fn)));
@@ -307,7 +309,7 @@ function test_package_install_errors(testCase)
             delete(version_fn)
             exception_caught = 0;
             try
-                install_package(package_name, root_src_dir, target_dir, 'link', {}, 0);
+                install_package(package_name, root_src_dir, target_dir, 'copy', {}, 0);
             catch ME
                 testCase.assertTrue(strcmp(ME.identifier, 'DistPackage:FileNotFound'))
                 testCase.assertTrue(~isempty(strfind(ME.message, 'VERSION file')));
@@ -324,7 +326,7 @@ function test_package_install_errors(testCase)
             write_file(version_fn, {version_tag});
             exception_caught = 0;
             try
-                install_package(package_name, root_src_dir, target_dir, 'link', {}, 0);
+                install_package(package_name, root_src_dir, target_dir, 'copy', {}, 0);
             catch ME
                 testCase.assertTrue(strcmp(ME.identifier, 'DistPackage:BadVersionTag'))
                 testCase.assertTrue(~isempty(strfind(ME.message, version_tag)));
@@ -340,7 +342,7 @@ function test_package_install_errors(testCase)
             write_file(version_fn, {version_tag});
             exception_caught = 0;
             try
-                install_package(package_name, root_src_dir, target_dir, 'link', {}, 0);
+                install_package(package_name, root_src_dir, target_dir, 'copy', {}, 0);
             catch ME
                 testCase.assertTrue(strcmp(ME.identifier, 'DistPackage:BadVersionTag'))
                 exception_caught = 1;
@@ -397,7 +399,7 @@ function test_uninstall_error(testCase)
             fprintf(fout, 'blah');
             fclose(fout);
 
-            install_package(package_name, root_src_dir, target_dir, 'link', {}, 0);
+            install_package(package_name, root_src_dir, target_dir, 'copy', {}, 0);
             delete(existing_target_backup_fn);
             delete(existing_target_fn);
             exception_caught = 0;
@@ -451,7 +453,7 @@ function write_file(fn, lines)
 
 function flags = files_are_symlinks(root_dir, rel_fns)
 if ~isempty(strfind(computer, 'WIN'))
-    flags = zeros(1, length(rel_fns))==0;
+    flags = zeros(1, length(rel_fns))==1;
 else
     flags = cellfun(@(rfn) unix(['test -L ' fullfile(root_dir, rfn)])==0, rel_fns); 
 end

diff --git a/test/bst_create_test_subject.m b/test/bst_create_test_subject.m
@@ -18,6 +18,9 @@
 
 sTemplates = bst_get('AnatomyDefaults');
 iTemplate = strcmpi('Colin27_4NIRS', {sTemplates.Name});
+if ~any(iTemplate)
+    error('Template Colin27_4NIRS not found');
+end
 db_set_template(iSubject, sTemplates(iTemplate), 0);
 db_save();
 sSubject = bst_get('Subject', subject_name);