- galaxy-commits - lists.galaxyproject.org

[galaxyproject/usegalaxy-playbook] 292816: Revert "update TTS"
by GitHub 24 Nov '15

24 Nov '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 292816b71a8244991500f52b87128067e73bb48c https://github.com/galaxyproject/usegalaxy-playbook/commit/292816b71a824499… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-24 (Tue, 24 Nov 2015) Changed paths: M stage/group_vars/toolshedservers.yml Log Message: ----------- Revert "update TTS" This reverts commit 7fb048393b5682c1139be2c3e927788659966d80.

1 0

[galaxyproject/galaxy] 1ea68f: Save a query per output during tool execution.
by GitHub 24 Nov '15

24 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1ea68f938408b72f8f0f4ebe2545550baea85037 https://github.com/galaxyproject/galaxy/commit/1ea68f938408b72f8f0f4ebe2545… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-24 (Tue, 24 Nov 2015) Changed paths: M lib/galaxy/security/__init__.py M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Save a query per output during tool execution. Commit: 42d006162c095669a2c7afe1ab0f1fb67b000798 https://github.com/galaxyproject/galaxy/commit/42d006162c095669a2c7afe1ab0f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-24 (Tue, 24 Nov 2015) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Another tool dataset creation optimization... Rather than using three transactions to create an HDA, a dataset, and its roles - do this all in one transaction. Commit: 01c57908eaf8bd589ce8738fdab14d415543d072 https://github.com/galaxyproject/galaxy/commit/01c57908eaf8bd589ce8738fdab1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-24 (Tue, 24 Nov 2015) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Another tool execution optimization... Prefetch all groups, roles, and associations when using User.all_users(). This reduces three queries down to one if the user has no groups or group roles and only belongs to the private user role, obviously the number of queries saved would increase more and more if the user belonged to multiple roles or groups. Commit: 11edf3559d7092c9e3fada3f04d9291bea64f2f0 https://github.com/galaxyproject/galaxy/commit/11edf3559d7092c9e3fada3f04d9… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-11-24 (Tue, 24 Nov 2015) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Merge pull request #1166 from jmchilton/tool_opts_2 Another set of tool execution optimizations Compare: https://github.com/galaxyproject/galaxy/compare/853efcea14d1...11edf3559d70

1 0

[galaxyproject/usegalaxy-playbook] 7fb048: update TTS
by GitHub 24 Nov '15

24 Nov '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 7fb048393b5682c1139be2c3e927788659966d80 https://github.com/galaxyproject/usegalaxy-playbook/commit/7fb048393b5682c1… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-24 (Tue, 24 Nov 2015) Changed paths: M stage/group_vars/toolshedservers.yml Log Message: ----------- update TTS

1 0

[galaxyproject/galaxy] 32728e: Small optimizations to running tools.
by GitHub 24 Nov '15

24 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 32728e23921553c75fda61acadb4f5dc82a4f915 https://github.com/galaxyproject/galaxy/commit/32728e23921553c75fda61acadb4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-24 (Tue, 24 Nov 2015) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Small optimizations to running tools. Commit: 853efcea14d1ce11961d171324dbce03e6694117 https://github.com/galaxyproject/galaxy/commit/853efcea14d1ce11961d171324db… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-11-24 (Tue, 24 Nov 2015) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Merge pull request #1163 from jmchilton/tool_opts_1 Small optimizations to running tools. Compare: https://github.com/galaxyproject/galaxy/compare/77166a7295b1...853efcea14d1

1 0

[galaxyproject/galaxy] 9cc8e0: add local grunt-cli dependency for qunit tests
by GitHub 23 Nov '15

23 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9cc8e08537291a85885ee3ad52daeb36b95b4f8e https://github.com/galaxyproject/galaxy/commit/9cc8e08537291a85885ee3ad52da… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-23 (Mon, 23 Nov 2015) Changed paths: M test/qunit/package.json Log Message: ----------- add local grunt-cli dependency for qunit tests Commit: 77166a7295b1fe13f366414361b1752e6c0dd953 https://github.com/galaxyproject/galaxy/commit/77166a7295b1fe13f366414361b1… Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com> Date: 2015-11-23 (Mon, 23 Nov 2015) Changed paths: M test/qunit/package.json Log Message: ----------- Merge pull request #1159 from martenson/local-grunt-cli-dep add local grunt-cli dependency for qunit tests Compare: https://github.com/galaxyproject/galaxy/compare/3cadcdffb51f...77166a7295b1

1 0

[galaxyproject/galaxy] b6451d: Fix bugs in test and code introduced in PR #1113.
by GitHub 23 Nov '15

23 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b6451d0be60a3bf2ca7c65c7700cb7361cb50754 https://github.com/galaxyproject/galaxy/commit/b6451d0be60a3bf2ca7c65c7700c… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-11-23 (Mon, 23 Nov 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py M test/functional/tools/output_format_collection.xml M test/unit/tools/test_actions.py Log Message: ----------- Fix bugs in test and code introduced in PR #1113. Commit: 3cadcdffb51f3994ed6ca0f4a9508f31fba1c4a6 https://github.com/galaxyproject/galaxy/commit/3cadcdffb51f3994ed6ca0f4a950… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-23 (Mon, 23 Nov 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py M test/functional/tools/output_format_collection.xml M test/unit/tools/test_actions.py Log Message: ----------- Merge pull request #1155 from nsoranzo/fix_for_1113 Fix bugs in test and code introduced in PR #1113. Compare: https://github.com/galaxyproject/galaxy/compare/11f9fed4acb3...3cadcdffb51f

1 0

[galaxyproject/galaxy] 82ce62: Fix for re-installing an uninstalled TS repository...
by GitHub 23 Nov '15

23 Nov '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: 82ce6244653fe96f01f4b01bb4ecd366a1b45db0 https://github.com/galaxyproject/galaxy/commit/82ce6244653fe96f01f4b01bb4ec… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2015-11-23 (Mon, 23 Nov 2015) Changed paths: M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Fix for re-installing an uninstalled TS repository with a dependency where both the repository and the dependency were updated in the TS after the repository was uninstalled.

1 0

[galaxyproject/galaxy] a16cb0: Fix for re-installing an uninstalled TS repository...
by GitHub 23 Nov '15

23 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a16cb06705676aa49e725c8ab58521c239dfea4d https://github.com/galaxyproject/galaxy/commit/a16cb06705676aa49e725c8ab585… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2015-11-22 (Sun, 22 Nov 2015) Changed paths: M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Fix for re-installing an uninstalled TS repository with a dependency where both the repository and the dependency were updated in the TS after the repository was uninstalled. Commit: 11f9fed4acb3fb912bc0e0e5c0232fb85c974f2f https://github.com/galaxyproject/galaxy/commit/11f9fed4acb3fb912bc0e0e5c023… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-22 (Sun, 22 Nov 2015) Changed paths: M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Merge pull request #1154 from gregvonkuster/dev Fix for re-installing an uninstalled TS repository with a dependency Compare: https://github.com/galaxyproject/galaxy/compare/2e510bd5e12a...11f9fed4acb3

1 0

[galaxyproject/galaxy] 312746: Allow accessing collection elements in format_sour...
by GitHub 22 Nov '15

22 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 312746d1698e99e13b9a60db881d0093da6cc4c0 https://github.com/galaxyproject/galaxy/commit/312746d1698e99e13b9a60db881d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-17 (Tue, 17 Nov 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py A test/functional/tools/output_format_collection.xml M test/functional/tools/samples_tool_conf.xml M test/unit/tools/test_actions.py Log Message: ----------- Allow accessing collection elements in format_source. Can do it by numeric index or element name, e.g. input[0] or input["forward"]. Only works for 1-D collections. Implements #699. Run new and most relevant existing tests with the following commands: ``` nosetests test/unit/tools/test_actions.py ./run_tests.sh -framework -id output_format_collection ./run_tests.sh -framework -id output_format ``` Commit: 2e510bd5e12ab5e2c401e835e0f84f29376766db https://github.com/galaxyproject/galaxy/commit/2e510bd5e12ab5e2c401e835e0f8… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-21 (Sat, 21 Nov 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py A test/functional/tools/output_format_collection.xml M test/functional/tools/samples_tool_conf.xml M test/unit/tools/test_actions.py Log Message: ----------- Merge pull request #1113 from jmchilton/format_source_collection Allow accessing collection elements in format_source. Compare: https://github.com/galaxyproject/galaxy/compare/ab0829f2e8df...2e510bd5e12a

1 0

[galaxyproject/galaxy] b4c77b: Introduce "Format 2" workflow definitions.
by GitHub 21 Nov '15

21 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b4c77b761799b3a8752a6fec500717b1a6f3818b https://github.com/galaxyproject/galaxy/commit/b4c77b761799b3a8752a6fec5007… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: M test/api/test_workflow_extraction.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py A test/api/workflows_format_2/README.txt A test/api/workflows_format_2/__init__.py A test/api/workflows_format_2/converter.py A test/api/workflows_format_2/interface.py A test/api/workflows_format_2/main.py R test/api/yaml_to_workflow.py M test/functional/tools/simple_constructs.yml M test/unit/tools/test_parsing.py Log Message: ----------- Introduce "Format 2" workflow definitions. This is a slight tightening up of the ad-hoc, experimental workflow YAML definition used by the test framework (and by Kyle, but lets just admit Kyle is part of Galaxy's test framework). This format is still defined entirely client side by transcoding the YAML or python object description into real (or format 1) Galaxy workflows - so these cannot realisticaly be declared part of Galaxy's public interface and can remain experimental and subject to change. In addition to refactoring the code implementing these workflows for upstream modifications to explore new features, the format itself has been made slightly more stringent in two ways: - 'steps' must now be explicit (previously converted auto-convert list to dict). - Ensure the workflow declared a 'class' is defined and the class is 'GalaxyWorkflow'. This will help with discovery of workflow objects with downstream tooling (planemo for workflows?) and brings the Galaxy definition slightly more inline with the CWL definition for workflows (very slightly). Commit: ab0829f2e8df480d467f3b575c18a1ace38543cd https://github.com/galaxyproject/galaxy/commit/ab0829f2e8df480d467f3b575c18… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M test/api/test_workflow_extraction.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py A test/api/workflows_format_2/README.txt A test/api/workflows_format_2/__init__.py A test/api/workflows_format_2/converter.py A test/api/workflows_format_2/interface.py A test/api/workflows_format_2/main.py R test/api/yaml_to_workflow.py M test/functional/tools/simple_constructs.yml M test/unit/tools/test_parsing.py Log Message: ----------- Merge pull request #1096 from jmchilton/format_2 Outline "Format 2" workflow definitions. Compare: https://github.com/galaxyproject/galaxy/compare/a664deeee76b...ab0829f2e8df

1 0