Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 14497719ba6d3a9727563d15dbeacf2b537551f3 https://github.com/galaxyproject/galaxy/commit/14497719ba6d3a9727563d15dbeac... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-09-03 (Sun, 03 Sep 2017) Changed paths: M lib/galaxy/tools/actions/upload_common.py M tools/data_source/upload.py Log Message: ----------- Prevent in-place editing if purge_source is false When importing files from the FTP folder the admin can choose to prevent purging of imported files. In this case the source file should not be modified in-place by galaxy. This also modifies relevant bare `except:` statements and modifies the meaning of `in_place` in upload.py from no external chown script to do not edit files in place if we keep the source file. This fixes https://github.com/galaxyproject/galaxy/issues/4527. Commit: 62ef8b52aedb9b9b34403db83703083a0cddbaf9 https://github.com/galaxyproject/galaxy/commit/62ef8b52aedb9b9b34403db837030... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-09-03 (Sun, 03 Sep 2017) Changed paths: M tools/data_source/upload.py Log Message: ----------- Fix sniffing for non-binary files Commit: 06db29413e838fd88a2ec84ede347f097be161e2 https://github.com/galaxyproject/galaxy/commit/06db29413e838fd88a2ec84ede347... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-09-03 (Sun, 03 Sep 2017) Changed paths: M tools/data_source/upload.py Log Message: ----------- Move instead of copying converted datasets when possible shutil.move tries to move files by renaming them. If that fails with OSError (due to permission or cross-filesystem rename) it falls back to copying files followed by removing them (https://github.com/python/cpython/blob/2.7/Lib/shutil.py#L279). By using shutil.move and catching permission problems we avoid an unnecessary copy if source and destination are on the same filesystem. Also avoids shutil.move if the upload tool is run as real-user which should fix https://github.com/galaxyproject/galaxy/issues/4300. Commit: 57ff68edd0627a58c1bdce645d666ad3243df8d2 https://github.com/galaxyproject/galaxy/commit/57ff68edd0627a58c1bdce645d666... Author: John Chilton <jmchilton@gmail.com> Date: 2017-09-07 (Thu, 07 Sep 2017) Changed paths: M lib/galaxy/tools/actions/upload_common.py M tools/data_source/upload.py Log Message: ----------- Merge pull request #4539 from mvdbeek/purge_source Prevent in-place editing of uploaded files if files are imported from the FTP folder Compare: https://github.com/galaxyproject/galaxy/compare/696a1eda3ca5...57ff68edd062