Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: bd69278f0bcc67afc1eb827a8a7bc80ae7766072 https://github.com/galaxyproject/galaxy/commit/bd69278f0bcc67afc1eb827a8a7bc... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-03-02 (Fri, 02 Mar 2018) Changed paths: M test/functional/tools/multi_output_recurse.xml Log Message: ----------- Add a testcase for optional output discovery This test correctly fails with: ``` galaxy.jobs.runners.local ERROR 2018-03-02 17:55:32,396 Job wrapper finish method failed Traceback (most recent call last): File "/Users/mvandenb/src/galaxy/lib/galaxy/jobs/runners/local.py", line 152, in queue_job self._finish_or_resubmit_job(job_state, stdout, stderr, exit_code) File "/Users/mvandenb/src/galaxy/lib/galaxy/jobs/runners/__init__.py", line 432, in _finish_or_resubmit_job job_state.job_wrapper.finish(stdout, stderr, exit_code, check_output_detected_state=check_output_detected_state) File "/Users/mvandenb/src/galaxy/lib/galaxy/jobs/__init__.py", line 1381, in finish 'primary': self.tool.collect_primary_datasets(out_data, self.get_tool_provided_job_metadata(), tool_working_directory, input_ext, input_dbkey) File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/__init__.py", line 1614, in collect_primary_datasets return output_collect.collect_primary_datasets(self, output, tool_provided_metadata, job_working_directory, input_ext, input_dbkey=input_dbkey) File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/parameters/output_collect.py", line 372, in collect_primary_datasets for discovered_file in discover_files(name, tool_provided_metadata, dataset_collectors, job_working_directory, outdata): File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/parameters/output_collect.py", line 490, in discover_files for (match, collector) in walk_over_file_collectors(extra_file_collectors, job_working_directory, matchable): File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/parameters/output_collect.py", line 507, in walk_over_file_collectors for match in walk_over_extra_files(extra_file_collector.directory, extra_file_collector, job_working_directory, matchable): File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/parameters/output_collect.py", line 519, in walk_over_extra_files for filename in os.listdir(directory): OSError: [Errno 2] No such file or directory: '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp5Tz0m9/tmpfUHHl6/tmpVBcnfI/database/job_working_directory_LJioiW/000/2/working/i_do_not_exist' ``` Commit: d21d7d9d2e10d9c09bdbadbf328fd3eef84630e6 https://github.com/galaxyproject/galaxy/commit/d21d7d9d2e10d9c09bdbadbf328fd... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-03-02 (Fri, 02 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/output_collect.py Log Message: ----------- Fix output discovery when directory doesn't exist This broke in 8b76a5a698fd3bc13d4acc38194221def9ed5163. Checking if `directory` is a directory is what we had done previously. Commit: 7ed81e18101c33a1e83bb5e72851698910a118e9 https://github.com/galaxyproject/galaxy/commit/7ed81e18101c33a1e83bb5e728516... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-03-02 (Fri, 02 Mar 2018) Changed paths: M test/functional/tools/multi_output_recurse.xml Log Message: ----------- Move `optional` tag to the output data element Thx @nsoranzo! Commit: da867852ae6437c02c64287521dde0b8aa1e8109 https://github.com/galaxyproject/galaxy/commit/da867852ae6437c02c64287521dde... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-03-02 (Fri, 02 Mar 2018) Changed paths: M test/functional/tools/multi_output_recurse.xml Log Message: ----------- Drop optional="true" altogther Commit: d77845268a9243535e2b77383bc4ed3d433e2e7a https://github.com/galaxyproject/galaxy/commit/d77845268a9243535e2b77383bc4e... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-04 (Sun, 04 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/output_collect.py M test/functional/tools/multi_output_recurse.xml Log Message: ----------- Merge pull request #5635 from mvdbeek/fix_optional_output_discovery [18.01] Fix output discovery if dir doesn't exist Compare: https://github.com/galaxyproject/galaxy/compare/e01f9fa1b89e...d77845268a92