Fix more instances of issue #21 - use copyfile instead of move

dataworkspaces/__init__.py

@@ -1,3 +1,3 @@
 # Copyright 2018,2019 by MPI-SWS and Data-ken Research. Licensed under Apache 2.0. See LICENSE.txt.
 
-__version__ = '1.0.2'
+__version__ = '1.0.3'

dataworkspaces/resources/git_resource.py

@@ -7,6 +7,7 @@
 from os.path import realpath, basename, isdir, join, dirname, exists
 import stat
 import click
+import shutil
 
 from dataworkspaces.errors import ConfigurationError, InternalError
 from dataworkspaces.utils.subprocess_utils import \
@@ -137,7 +138,8 @@ def results_move_current_files(self, rel_dest_root, exclude_files,
 
     def add_results_file(self, temp_path, rel_dest_path):
         """Copy a results file from the temporary location to
-        the specified path in the resource.
+        the specified path in the resource. Caller responsible for
+        cleanup of temp_path.
         """
         assert exists(temp_path)
         assert self.role==ResourceRoles.RESULTS
@@ -146,7 +148,9 @@ def add_results_file(self, temp_path, rel_dest_path):
         parent_dir = dirname(abs_dest_path)
         if not exists(parent_dir):
             os.makedirs(parent_dir)
-        os.rename(temp_path, abs_dest_path)
+        # Need to use copy instead of move, because /tmp might be in a separate
+        # filesystem (see issue #21). Caller will do cleanup of temp file.
+        shutil.copyfile(temp_path, abs_dest_path)
         call_subprocess([GIT_EXE_PATH, 'add', rel_dest_path],
                         cwd=self.local_path, verbose=self.verbose)
         call_subprocess([GIT_EXE_PATH, 'commit',
@@ -425,14 +429,17 @@ def results_move_current_files(self, rel_dest_root, exclude_files,
 
     def add_results_file(self, temp_path, rel_dest_path):
         """Move a results file from the temporary location to
-        the specified path in the resource.
+        the specified path in the resource. Caller responsible
+        for cleanup of temp_path
         """
         assert exists(temp_path)
         abs_dest_path = join(self.local_path, rel_dest_path)
         parent_dir = dirname(abs_dest_path)
         if not exists(parent_dir):
             os.makedirs(parent_dir)
-        os.rename(temp_path, abs_dest_path)
+        # Need to use copy instead of move, because /tmp might be in a separate
+        # filesystem (see issue #21). Caller will do cleanup of temp file.
+        shutil.copyfile(temp_path, abs_dest_path)
         rel_path_in_repo = join(self.relative_path, rel_dest_path)
         call_subprocess([GIT_EXE_PATH, 'add', rel_path_in_repo],
                         cwd=self.workspace_dir, verbose=self.verbose)
@@ -529,7 +536,7 @@ def results_move_current_files(self, rel_dest_root, exclude_files,
 
     def add_results_file(self, temp_path, rel_dest_path):
         """Copy a results file from the temporary location to
-        the specified path in the resource.
+        the specified path in the resource. Caller responsible for cleanup.
         """
         raise InternalError("add_results_file should not be called for %s" %
                             self.__class__.__name__)

dataworkspaces/resources/local_file_resource.py

@@ -4,7 +4,8 @@
 """
 from errno import EEXIST
 import os
-import os.path 
+import os.path
+import shutil
 
 from dataworkspaces.errors import ConfigurationError
 from dataworkspaces.utils.subprocess_utils import call_subprocess
@@ -85,15 +86,16 @@ def snapshot(self):
 
     def add_results_file(self, temp_path, rel_dest_path):
         """Move a results file from the temporary location to
-        the specified path in the resource.
+        the specified path in the resource. Caller responsible
+        for cleanup.
         """
         assert self.role==ResourceRoles.RESULTS
         assert os.path.exists(temp_path)
         abs_dest_path = os.path.join(self.local_path, rel_dest_path)
         parent_dir = os.path.dirname(abs_dest_path)
         if not os.path.isdir(parent_dir):
             os.makedirs(parent_dir)
-        os.rename(temp_path, abs_dest_path)
+        shutil.copyfile(temp_path, abs_dest_path)
 
     def restore_prechecks(self, hashval):
         print("IN RESTORE")

dataworkspaces/resources/rclone_resource.py

@@ -6,6 +6,7 @@
 import os
 import os.path 
 import stat
+import shutil
 
 from dataworkspaces.errors import ConfigurationError
 from dataworkspaces.utils.subprocess_utils import call_subprocess
@@ -123,15 +124,16 @@ def snapshot(self):
 
     def add_results_file(self, temp_path, rel_dest_path):
         """Move a results file from the temporary location to
-        the specified path in the resource.
+        the specified path in the resource. Caller responsible
+        for cleanup.
         """
         assert self.role==ResourceRoles.RESULTS
         assert os.path.exists(temp_path)
         abs_dest_path = os.path.join(self.local_path, rel_dest_path)
         parent_dir = os.path.dirname(abs_dest_path)
         if not os.path.isdir(parent_dir):
             os.makedirs(parent_dir)
-        os.rename(temp_path, abs_dest_path)
+        shutil.copy(temp_path, abs_dest_path)
 
     def restore_prechecks(self, hashval):
         pass

dataworkspaces/resources/resource.py

@@ -127,7 +127,8 @@ def results_move_current_files(self, rel_dest_root, exclude_files,
 
     def add_results_file(self, temp_path, rel_dest_path):
         """Move a results file from the temporary location to
-        the specified path in the resource.
+        the specified path in the resource. Caller responsible for
+        cleanup of temp_path.
         """
         raise NotImplementedError(self.__class__.__name__)