opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-09-24 16:30:27 +08:00
Code Issues Packages Projects Releases Wiki Activity

Merge pull request #4539 from mvdbeek/purge_source

Browse Source 
Prevent in-place editing of uploaded files if files are imported from the FTP folder
This commit is contained in:
John Chilton
2017-09-07 10:11:04 -04:00
committed by GitHub
parent 696a1eda3c 06db29413e
commit 57ff68edd0
2 changed files with 33 additions and 25 deletions
Download Patch File Download Diff File Expand all files Collapse all files
tools/data_source/upload.py
+23 -21
View File
@@ -6,6 +6,7 @@
from __future__ import print_function
import codecs
import errno
import gzip
import os
import shutil
@@ -79,8 +80,13 @@ def add_file(dataset, registry, json_file, output_path):
converted_path = None
stdout = None
link_data_only = dataset.get('link_data_only', 'copy_files')
in_place = dataset.get('in_place', True)
run_as_real_user = in_place = dataset.get('in_place', True)
purge_source = dataset.get('purge_source', True)
# in_place is True if there is no external chmod in place,
# however there are other instances where modifications should not occur in_place:
# when a file is added from a directory on the local file system (ftp import folder or any other path).
if dataset.type in ('server_dir', 'path_paste', 'ftp_import'):
in_place = False
check_content = dataset.get('check_content' , True)
auto_decompress = dataset.get('auto_decompress', True)
try:
@@ -158,7 +164,7 @@ def add_file(dataset, registry, json_file, output_path):
os.close(fd)
gzipped_file.close()
# Replace the gzipped file with the decompressed file if it's safe to do so
if dataset.type in ('server_dir', 'path_paste') or not in_place:
if not in_place:
dataset.path = uncompressed
else:
shutil.move(uncompressed, dataset.path)
@@ -191,7 +197,7 @@ def add_file(dataset, registry, json_file, output_path):
os.close(fd)
bzipped_file.close()
# Replace the bzipped file with the decompressed file if it's safe to do so
if dataset.type in ('server_dir', 'path_paste') or not in_place:
if not in_place:
dataset.path = uncompressed
else:
shutil.move(uncompressed, dataset.path)
@@ -248,7 +254,7 @@ def add_file(dataset, registry, json_file, output_path):
z.close()
# Replace the zipped file with the decompressed file if it's safe to do so
if uncompressed is not None:
if dataset.type in ('server_dir', 'path_paste') or not in_place:
if not in_place:
dataset.path = uncompressed
else:
shutil.move(uncompressed, dataset.path)
@@ -280,12 +286,9 @@ def add_file(dataset, registry, json_file, output_path):
file_err('The uploaded file contains inappropriate HTML content', dataset, json_file)
return
if data_type != 'binary':
if link_data_only == 'copy_files':
if dataset.type in ('server_dir', 'path_paste') and data_type not in ['gzip', 'bz2', 'zip']:
in_place = False
# Convert universal line endings to Posix line endings, but allow the user to turn it off,
# so that is becomes possible to upload gzip, bz2 or zip files with binary data without
# corrupting the content of those files.
if link_data_only == 'copy_files' and data_type not in ('gzip', 'bz2', 'zip'):
# Convert universal line endings to Posix line endings if to_posix_lines is True
# and the data is not binary or gzip-, bz2- or zip-compressed.
if dataset.to_posix_lines:
tmpdir = output_adjacent_tmpdir(output_path)
tmp_prefix = 'data_id_%s_convert_' % dataset.dataset_id
@@ -313,19 +316,18 @@ def add_file(dataset, registry, json_file, output_path):
'<b>Copy files into Galaxy</b> instead of <b>Link to files without copying into Galaxy</b> so grooming can be performed.'
file_err(err_msg, dataset, json_file)
return
if link_data_only == 'copy_files' and dataset.type in ('server_dir', 'path_paste') and data_type not in ['gzip', 'bz2', 'zip']:
if link_data_only == 'copy_files' and converted_path:
# Move the dataset to its "real" path
if converted_path is not None:
shutil.copy(converted_path, output_path)
try:
os.remove(converted_path)
except:
pass
else:
# This should not happen, but it's here just in case
shutil.copy(dataset.path, output_path)
try:
shutil.move(converted_path, output_path)
except OSError as e:
# We may not have permission to remove converted_path
if e.errno != errno.EACCES:
raise
elif link_data_only == 'copy_files':
if purge_source:
if purge_source and not run_as_real_user:
# if the upload tool runs as a real user the real user
# can't move dataset.path as this path is owned by galaxy.
shutil.move(dataset.path, output_path)
else:
shutil.copy(dataset.path, output_path)