imported copy_tree from master

assembler/src/spades_pipeline/stages/correction_stage.py

@@ -10,7 +10,6 @@
 import os
 import shutil
 import sys
-from distutils import dir_util
 from site import addsitedir
 
 from stages import stage
@@ -71,7 +70,7 @@ def generate_config(self, cfg):
  dst_configs = os.path.join(self.cfg.output_dir, "configs")
  if os.path.isdir(dst_configs):
  shutil.rmtree(dst_configs)
- dir_util.copy_tree(os.path.join(self.tmp_configs_dir, "corrector"), dst_configs, preserve_times=False)
+ support.copy_tree(os.path.join(self.tmp_configs_dir, "corrector"), dst_configs, preserve_times=False)
  cfg_file_name = os.path.join(dst_configs, "corrector.info")
 
  self.cfg.tmp_dir = support.get_tmp_dir(prefix="corrector_")

assembler/src/spades_pipeline/stages/error_correction_stage.py

@@ -10,7 +10,6 @@
 import os
 import shutil
 import sys
-from distutils import dir_util
 from site import addsitedir
 
 import commands_parser
@@ -63,10 +62,10 @@ def generate_config(self, cfg):
  if os.path.isdir(dst_configs):
  shutil.rmtree(dst_configs)
  if cfg.iontorrent:
- dir_util.copy_tree(os.path.join(self.tmp_configs_dir, "ionhammer"), dst_configs, preserve_times=False)
+ support.copy_tree(os.path.join(self.tmp_configs_dir, "ionhammer"), dst_configs, preserve_times=False)
  cfg_file_name = os.path.join(dst_configs, "ionhammer.cfg")
  else:
- dir_util.copy_tree(os.path.join(self.tmp_configs_dir, "hammer"), dst_configs, preserve_times=False)
+ support.copy_tree(os.path.join(self.tmp_configs_dir, "hammer"), dst_configs, preserve_times=False)
  cfg_file_name = os.path.join(dst_configs, "config.info")
 
  cfg.tmp_dir = support.get_tmp_dir(prefix="hammer_")

assembler/src/spades_pipeline/stages/pipeline.py

@@ -9,8 +9,8 @@
 
 import os
 import shutil
-from distutils import dir_util
 
+import support
 import options_storage
 
 class Pipeline(object):
@@ -22,10 +22,10 @@ def copy_configs(self, cfg, spades_home, tmp_configs_dir):
  shutil.rmtree(tmp_configs_dir)
  if not os.path.isdir(tmp_configs_dir):
  if options_storage.args.configs_dir:
- dir_util.copy_tree(options_storage.args.configs_dir, tmp_configs_dir, preserve_times=False,
+ support.copy_tree(options_storage.args.configs_dir, tmp_configs_dir, preserve_times=False,
  preserve_mode=False)
  else:
- dir_util.copy_tree(os.path.join(spades_home, "configs"), tmp_configs_dir, preserve_times=False,
+ support.copy_tree(os.path.join(spades_home, "configs"), tmp_configs_dir, preserve_times=False,
  preserve_mode=False)
 
  def add(self, stage):

assembler/src/spades_pipeline/stages/spades_iteration_stage.py

@@ -9,11 +9,11 @@
 
 import os
 import shutil
-from distutils import dir_util
 
 import commands_parser
 import options_storage
 from stages import stage
+import support
 import process_cfg
 from process_cfg import bool_to_str
 
@@ -139,9 +139,7 @@ def generate_config(self, cfg):
  if self.get_stage(self.short_name) == options_storage.BASE_STAGE:
  if not os.path.isdir(data_dir):
  os.makedirs(data_dir)
-
- dir_util._path_created = {} # see http://stackoverflow.com/questions/9160227/dir-util-copy-tree-fails-after-shutil-rmtree
- dir_util.copy_tree(os.path.join(self.tmp_configs_dir, "debruijn"), dst_configs, preserve_times=False)
+ support.copy_tree(os.path.join(self.tmp_configs_dir, "debruijn"), dst_configs, preserve_times=False)
 
  if self.prev_K:
  additional_contigs_dname = os.path.join(cfg.output_dir, "K%d" % self.prev_K, "simplified_contigs")

assembler/src/spades_pipeline/support.py

@@ -940,3 +940,30 @@ def is_int(value):
  return True
  except ValueError:
  return False
+
+
+# shutil.copyfile does not copy any metadata (time and permission), so one
+# cannot expect preserve_mode = False and preserve_times = True to work.
+def copy_tree(src, dst, preserve_times=True, preserve_mode=True):
+ if sys.version.split()[0][0] == '2':
+ from distutils import dir_util
+ dir_util._path_created = {} # see http://stackoverflow.com/questions/9160227/dir-util-copy-tree-fails-after-shutil-rmtree
+ dir_util.copy_tree(src, dst, preserve_times=preserve_times, preserve_mode=preserve_mode)
+ return
+
+ if not preserve_mode:
+ copy_fn = shutil.copyfile
+ else:
+ copy_fn = shutil.copy2
+
+ if os.path.exists(dst):
+ shutil.rmtree(dst)
+
+ # shutil.copytree preserves the timestamp, so we must update it afterwards.
+ shutil.copytree(src, dst, copy_function = copy_fn)
+
+ if not preserve_times:
+ for dirpath, _, filenames in os.walk(dst):
+ os.utime(dirpath, None)
+ for file in filenames:
+ os.utime(os.path.join(dirpath, file), None)