fix copying of broken symlinks with copy/copy_file

Author: boegel

easybuild/tools/filetools.py

@@ -1924,7 +1924,12 @@ def copy_file(path, target_path, force_in_dry_run=False):
                 _log.info("Copied contents of file %s to %s", path, target_path)
             else:
                 mkdir(os.path.dirname(target_path), parents=True)
-                shutil.copy2(path, target_path)
+                if os.path.exists(path):
+                    shutil.copy2(path, target_path)
+                elif os.path.islink(path):
+                    # special care for copying broken symlinks
+                    link_target = os.readlink(path)
+                    symlink(link_target, target_path)
                 _log.info("%s copied to %s", path, target_path)
         except (IOError, OSError, shutil.Error) as err:
             raise EasyBuildError("Failed to copy file %s to %s: %s", path, target_path, err)
@@ -2029,7 +2034,8 @@ def copy(paths, target_path, force_in_dry_run=False, **kwargs):
         full_target_path = os.path.join(target_path, os.path.basename(path))
         mkdir(os.path.dirname(full_target_path), parents=True)
 
-        if os.path.isfile(path):
+        # copy broken symlinks only if 'symlinks=True' is used
+        if os.path.isfile(path) or (os.path.islink(path) and kwargs.get('symlinks')):
             copy_file(path, full_target_path, force_in_dry_run=force_in_dry_run)
         elif os.path.isdir(path):
             copy_dir(path, full_target_path, force_in_dry_run=force_in_dry_run, **kwargs)

test/framework/filetools.py

@@ -1518,6 +1518,36 @@ def ignore_func(_, names):
         self.assertEqual(sorted(os.listdir(testdir)), expected)
         self.assertFalse(os.path.exists(os.path.join(testdir, 'GCC-6.4.0-2.28.eb')))
 
+        # test copy_dir when broken symlinks are involved
+        srcdir = os.path.join(self.test_prefix, 'topdir_to_copy')
+        ft.mkdir(srcdir)
+        ft.write_file(os.path.join(srcdir, 'test.txt'), '123')
+        subdir = os.path.join(srcdir, 'subdir')
+        # introduce broken file symlink
+        foo_txt = os.path.join(subdir, 'foo.txt')
+        ft.write_file(foo_txt, 'bar')
+        ft.symlink(foo_txt, os.path.join(subdir, 'bar.txt'))
+        ft.remove_file(foo_txt)
+        # introduce broken dir symlink
+        subdir_tmp = os.path.join(srcdir, 'subdir_tmp')
+        ft.mkdir(subdir_tmp)
+        ft.symlink(subdir_tmp, os.path.join(srcdir, 'subdir_link'))
+        ft.remove_dir(subdir_tmp)
+
+        target_dir = os.path.join(self.test_prefix, 'target_to_copy_to')
+
+        # trying this without symlinks=True ends in tears, because bar.txt points to a non-existing file
+        self.assertErrorRegex(EasyBuildError, "Failed to copy directory", ft.copy_dir, srcdir, target_dir)
+        ft.remove_dir(target_dir)
+
+        ft.copy_dir(srcdir, target_dir, symlinks=True)
+
+        # copying directory with broken symlinks should also work if target directory already exists
+        ft.remove_dir(target_dir)
+        ft.mkdir(target_dir)
+        ft.mkdir(subdir)
+        ft.copy_dir(srcdir, target_dir, symlinks=True, dirs_exist_ok=True)
+
         # also test behaviour of copy_file under --dry-run
         build_options = {
             'extended_dry_run': True,
@@ -1535,7 +1565,7 @@ def ignore_func(_, names):
         self.mock_stdout(False)
 
         self.assertFalse(os.path.exists(target_dir))
-        self.assertTrue(re.search("^copied directory .*/GCC to .*/GCC", txt))
+        self.assertTrue(re.search("^copied directory .*/GCC to .*/%s" % os.path.basename(target_dir), txt))
 
         # forced copy, even in dry run mode
         self.mock_stdout(True)