Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f05c9518be52ecaa9cb13885aeec3f57054e976a https://github.com/galaxyproject/galaxy/commit/f05c9518be52ecaa9cb13885aeec3... Author: guerler <aysam.guerler@gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dynamic_options.py Log Message: ----------- Remove unvalidated values Commit: 89ba002475695d09542dbe85886c6d69e6f54307 https://github.com/galaxyproject/galaxy/commit/89ba002475695d09542dbe85886c6... Author: guerler <aysam.guerler@gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Remove late validation handling Commit: 49026134443e49c81d5b071817bb7a018357f945 https://github.com/galaxyproject/galaxy/commit/49026134443e49c81d5b071817bb7... Author: guerler <aysam.guerler@gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/util/dbkeys.py Log Message: ----------- Use bunch instead of trans Commit: 12f2571d975ca89548259e1322882e87dbb5b17e https://github.com/galaxyproject/galaxy/commit/12f2571d975ca89548259e1322882... Author: guerler <aysam.guerler@gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Use self.app in tools Commit: 52b6881f017e38ea5969c5adb70b5c83d6753cd3 https://github.com/galaxyproject/galaxy/commit/52b6881f017e38ea5969c5adb70b5... Author: guerler <aysam.guerler@gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/grouping.py Log Message: ----------- Revise history handling Commit: 34f46c98c7bdace6af9126b44534fd41c9121002 https://github.com/galaxyproject/galaxy/commit/34f46c98c7bdace6af9126b44534f... Author: guerler <aysam.guerler@gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/tools/parameters/grouping.py Log Message: ----------- Remove comments Commit: 7eb6cc7b8247689d1bfef12c99a9514610bbd0bb https://github.com/galaxyproject/galaxy/commit/7eb6cc7b8247689d1bfef12c99a95... Author: guerler <aysam.guerler@gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/validation.py Log Message: ----------- Revise validate signature Commit: a272bff066516019ca74ee0012b2ae6fe02c21bc https://github.com/galaxyproject/galaxy/commit/a272bff066516019ca74ee0012b2a... Author: guerler <aysam.guerler@gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Use consistently other_values Commit: 550102915866ab4448a3e8a070437c80772320da https://github.com/galaxyproject/galaxy/commit/550102915866ab4448a3e8a070437... Author: guerler <aysam.guerler@gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Revise validate signature Commit: 4b6172299e2adc4edd117c505e5c7ddcde38c24b https://github.com/galaxyproject/galaxy/commit/4b6172299e2adc4edd117c505e5c7... Author: guerler <aysam.guerler@gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/work/context.py Log Message: ----------- Use workcontext Commit: eaf02029d43620db309e2860d4502e0f830bc2a9 https://github.com/galaxyproject/galaxy/commit/eaf02029d43620db309e2860d4502... Author: guerler <aysam.guerler@gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix remaining self.app, use workcontext app Commit: 5a72480719055ac4a6d04ff690f69d5a118b5c81 https://github.com/galaxyproject/galaxy/commit/5a72480719055ac4a6d04ff690f69... Author: guerler <aysam.guerler@gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix dataset selection Commit: 7cc505019d2b2af938b61efe0e00bd25a13af91b https://github.com/galaxyproject/galaxy/commit/7cc505019d2b2af938b61efe0e00b... Author: guerler <aysam.guerler@gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/util/dbkeys.py Log Message: ----------- Use sa_session of workcontext Commit: b56574115fa9ae32f2d4703f0b257991ad2f4c26 https://github.com/galaxyproject/galaxy/commit/b56574115fa9ae32f2d4703f0b257... Author: guerler <aysam.guerler@gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/util/dbkeys.py Log Message: ----------- Fix trans usage Commit: 93dbf742b36b614bacbb7a806431532567203b70 https://github.com/galaxyproject/galaxy/commit/93dbf742b36b614bacbb7a8064315... Author: guerler <aysam.guerler@gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/tools/evaluation.py Log Message: ----------- Reinsert last validation Commit: 7c69227c8cde400df37f5e9390fdd88e51f64f2a https://github.com/galaxyproject/galaxy/commit/7c69227c8cde400df37f5e9390fdd... Author: guerler <aysam.guerler@gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix db_builds Commit: 269ce36d3f5212b2d98315a67b25cc6db5a3429c https://github.com/galaxyproject/galaxy/commit/269ce36d3f5212b2d98315a67b25c... Author: guerler <aysam.guerler@gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/execute.py M lib/galaxy/workflow/modules.py Log Message: ----------- Fix check params Commit: 3acdee5143586d0224f896d2bfc5c085e3409349 https://github.com/galaxyproject/galaxy/commit/3acdee5143586d0224f896d2bfc5c... Author: guerler <aysam.guerler@gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/jobs/runners/__init__.py Log Message: ----------- Show validation error for workflow step preparation Commit: b38479c4a49efcf2c56e400b56d1da4f5eb4a02d https://github.com/galaxyproject/galaxy/commit/b38479c4a49efcf2c56e400b56d1d... Author: guerler <aysam.guerler@gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py M lib/galaxy/work/context.py M lib/galaxy/workflow/extract.py Log Message: ----------- Remove unvalidated value handling in workflow extraction Commit: 6939c99f1bb06532e5c4cb4c2a4ef936075b4569 https://github.com/galaxyproject/galaxy/commit/6939c99f1bb06532e5c4cb4c2a4ef... Author: guerler <aysam.guerler@gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/workflow/extract.py Log Message: ----------- Remove more unvalidated value hacks Commit: 539ddd4d90bda5400c3006ab4c574bebd353d280 https://github.com/galaxyproject/galaxy/commit/539ddd4d90bda5400c3006ab4c574... Author: guerler <aysam.guerler@gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/tools/evaluation.py Log Message: ----------- Remove optional parameter from request context initialization Commit: cc2cfe8d6adb264df41e18b4c33781712bb12cbb https://github.com/galaxyproject/galaxy/commit/cc2cfe8d6adb264df41e18b4c3378... Author: guerler <aysam.guerler@gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Use request context instead of trans in to_json Commit: a7117574268ab907fb27483a485d5d9e501b7e5e https://github.com/galaxyproject/galaxy/commit/a7117574268ab907fb27483a485d5... Author: guerler <aysam.guerler@gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/validation.py Log Message: ----------- Remove unused error handler, error is handled consistently through full validation Commit: 0ca9c7027b5ee3cd8ba433a4e8bc3e5ad57a5d7f https://github.com/galaxyproject/galaxy/commit/0ca9c7027b5ee3cd8ba433a4e8bc3... Author: guerler <aysam.guerler@gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/workflow/extract.py Log Message: ----------- Use request context in handle inputs Commit: 193c5293d9552d53a2358254fa2a25b236a31511 https://github.com/galaxyproject/galaxy/commit/193c5293d9552d53a2358254fa2a2... Author: guerler <aysam.guerler@gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M tools/data_source/upload.xml Log Message: ----------- Remove invalid validator from upload.xml Commit: 0fc8726414bfedcc234d7c4738ebff3a1b37e3d4 https://github.com/galaxyproject/galaxy/commit/0fc8726414bfedcc234d7c4738ebf... Author: guerler <aysam.guerler@gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Fix prefixed_label concatenation Commit: 0521644bb37336f31577c8bd73ac1fef6c936016 https://github.com/galaxyproject/galaxy/commit/0521644bb37336f31577c8bd73ac1... Author: guerler <aysam.guerler@gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix select validator Commit: 8bd4cabdde922f23c06c64f95f50ea4d81caa940 https://github.com/galaxyproject/galaxy/commit/8bd4cabdde922f23c06c64f95f50e... Author: guerler <aysam.guerler@gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/workflow/modules.py Log Message: ----------- Use request context for parameter helper Commit: b3f3f81a7d0d221e4a698dbd9a586a92cd6662af https://github.com/galaxyproject/galaxy/commit/b3f3f81a7d0d221e4a698dbd9a586... Author: guerler <aysam.guerler@gmail.com> Date: 2016-01-27 (Wed, 27 Jan 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M templates/webapps/galaxy/workflow/editor_tool_form.mako M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Remove unused to_html helper Commit: 8b6e4c9f2584d5768926836ee08607aeae0bb501 https://github.com/galaxyproject/galaxy/commit/8b6e4c9f2584d5768926836ee0860... Author: guerler <aysam.guerler@gmail.com> Date: 2016-01-27 (Wed, 27 Jan 2016) Changed paths: M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/grouping.py Log Message: ----------- Remove unused filter value helper Commit: 27df773c5a8823fff2d0dd68a8bd162147336bed https://github.com/galaxyproject/galaxy/commit/27df773c5a8823fff2d0dd68a8bd1... Author: guerler <aysam.guerler@gmail.com> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Always display discarded datasets on rerun Commit: f8e3fa51f4b2fbaab54becd869ede40e43c5067a https://github.com/galaxyproject/galaxy/commit/f8e3fa51f4b2fbaab54becd869ede... Author: guerler <aysam.guerler@gmail.com> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/tools/parameters/basic.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_execution.py M test/unit/tools/test_select_parameters.py M test/unit/tools_support.py Log Message: ----------- Apply suggested fixes, fix test cases Commit: 72370b251723eac746bd1720a85df539cd96e78a https://github.com/galaxyproject/galaxy/commit/72370b251723eac746bd1720a85df... Author: guerler <aysam.guerler@gmail.com> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Fix paused workflow step resubmission Commit: 41a3a1676245284fa01e9697bd91710244ddde83 https://github.com/galaxyproject/galaxy/commit/41a3a1676245284fa01e9697bd917... Author: John Chilton <jmchilton@gmail.com> Date: 2016-02-01 (Mon, 01 Feb 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/work/context.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/modules.py M templates/webapps/galaxy/workflow/editor_tool_form.mako M templates/webapps/galaxy/workflow/run.mako M test/unit/tools/test_data_parameters.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_execution.py M test/unit/tools/test_select_parameters.py M test/unit/tools_support.py M tools/data_source/upload.xml Log Message: ----------- Merge pull request #1572 from guerler/fix_unvalidated_008 Fix parameter validation Compare: https://github.com/galaxyproject/galaxy/compare/dacb91907af7...41a3a1676245