Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8255e722cd21bb1cee594db3212657c6a22aa730 https://github.com/galaxyproject/galaxy/commit/8255e722cd21bb1cee594db321265... Author: Nicola Soranzo nicola.soranzo@tgac.ac.uk Date: 2016-05-11 (Wed, 11 May 2016)

Changed paths: M lib/galaxy/tools/evaluation.py

Log Message: ----------- Do not pollute param_dict with a non JSONifiable dict

When running a data manager with a dataset parameter, the job fails with the following backtrace:

Traceback (most recent call last): File "/opt/galaxy/lib/galaxy/jobs/runners/__init__.py", line 166, in prepare_job job_wrapper.prepare() File "/opt/galaxy/lib/galaxy/jobs/__init__.py", line 885, in prepare tool_evaluator.set_compute_environment( compute_environment, get_special=get_special ) File "/opt/galaxy/lib/galaxy/tools/evaluation.py", line 107, in set_compute_environment self.tool.exec_before_job( self.app, inp_data, out_data, param_dict ) File "/opt/galaxy/lib/galaxy/tools/__init__.py", line 1956, in exec_before_job out.write( json.dumps( (json_params) ).encode('utf8') ) File "/usr/lib/python2.7/json/__init__.py", line 243, in dumps return _default_encoder.encode(obj) File "/usr/lib/python2.7/json/encoder.py", line 207, in encode chunks = self.iterencode(o, _one_shot=True) File "/usr/lib/python2.7/json/encoder.py", line 270, in iterencode return _iterencode(o, 0) TypeError: keys must be a string

The bug was introduced in PR #2029.

Commit: e28d305f3cda4377325190363057431f1f4f4d46 https://github.com/galaxyproject/galaxy/commit/e28d305f3cda43773251903630574... Author: Daniel Blankenberg dan.blankenberg@gmail.com Date: 2016-05-12 (Thu, 12 May 2016)

Changed paths: M lib/galaxy/tools/evaluation.py

Log Message: ----------- Merge pull request #2345 from nsoranzo/release_16.04_fix_for_2029

[16.04] Do not pollute param_dict with a non JSONifiable dict

Commit: bf7996087e8b3da9c40f7cd575691cf7123d760d https://github.com/galaxyproject/galaxy/commit/bf7996087e8b3da9c40f7cd575691... Author: Nicola Soranzo nicola.soranzo@tgac.ac.uk Date: 2016-05-12 (Thu, 12 May 2016)

Changed paths: M lib/galaxy/tools/evaluation.py

Log Message: ----------- Merge branch 'release_16.04' into dev

Compare: https://github.com/galaxyproject/galaxy/compare/366056c0b70a...bf7996087e8b