Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 00e8d4ee76c65652e6a0b208f44d957c79db40b1 https://github.com/galaxyproject/galaxy/commit/00e8d4ee76c65652e6a0b208f44d9... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-08-13 (Mon, 13 Aug 2018)
Changed paths: M tools/stats/filtering.xml
Log Message: ----------- Quote Filter1 input and output
Commit: 819ee07af36d10734b32474fa832ce9e09e1b376 https://github.com/galaxyproject/galaxy/commit/819ee07af36d10734b32474fa832c... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-08-13 (Mon, 13 Aug 2018)
Changed paths: M lib/galaxy/model/__init__.py
Log Message: ----------- Respect unavilable peek when serializing HDA
Also call display_peek() just once.
That fixes the following exception that occurs when running the Filter1 tool through the API:
``` galaxy.datatypes.tabular ERROR 2018-08-12 22:53:42,939 make_html_peek_rows failed on HDA 64 Traceback (most recent call last): File "/Users/mvandenb/src/galaxy/lib/galaxy/datatypes/tabular.py", line 186, in make_html_peek_rows dataset.set_peek() File "/Users/mvandenb/src/galaxy/lib/galaxy/model/__init__.py", line 2264, in set_peek return self.datatype.set_peek(self) File "/Users/mvandenb/src/galaxy/lib/galaxy/datatypes/tabular.py", line 57, in set_peek super(TabularData, self).set_peek(dataset, line_count=line_count, WIDTH=WIDTH, skipchars=skipchars, line_wrap=False) File "/Users/mvandenb/src/galaxy/lib/galaxy/datatypes/data.py", line 813, in set_peek dataset.peek = get_file_peek(dataset.file_name, WIDTH=WIDTH, skipchars=skipchars, line_wrap=line_wrap) File "/Users/mvandenb/src/galaxy/lib/galaxy/datatypes/data.py", line 1029, in get_file_peek with compression_utils.get_fileobj(file_name, "U") as temp: File "/Users/mvandenb/src/galaxy/lib/galaxy/util/compression_utils.py", line 29, in get_fileobj return get_fileobj_raw(filename, mode, compressed_formats)[1] File "/Users/mvandenb/src/galaxy/lib/galaxy/util/compression_utils.py", line 58, in get_fileobj_raw return compressed_format, io.open(filename, mode, encoding='utf-8') FileNotFoundError: [Errno 2] No such file or directory: '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpan_4qaow/tmpfzus9jhv/tmplqjtbp5c/database/files/000/dataset_40.dat' ```
This is because we serialize the HDA just after the job has been created, meaning the file may not exist yet.
Commit: f4343d876f13e55e92ca228582b4430dcd01e4aa https://github.com/galaxyproject/galaxy/commit/f4343d876f13e55e92ca228582b44... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-08-13 (Mon, 13 Aug 2018)
Changed paths: M lib/galaxy/jobs/__init__.py
Log Message: ----------- Clarify set_peek setting when finishing job
Commit: 3d0763f71c795549e6c133f2734cf7ae5337c296 https://github.com/galaxyproject/galaxy/commit/3d0763f71c795549e6c133f2734cf... Author: Dannon dannon.baker@gmail.com Date: 2018-08-13 (Mon, 13 Aug 2018)
Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/model/__init__.py M tools/stats/filtering.xml
Log Message: ----------- Merge pull request #6594 from mvdbeek/respect_unavailable_display_peek
Respect unavailable display peek
Compare: https://github.com/galaxyproject/galaxy/compare/e853762fdbb2...3d0763f71c79 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
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