galaxy-commits July 2017

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[galaxyproject/galaxy] cc18d5: Prevent early dataset state changes
by GitHub 28 Jul '17

28 Jul '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: cc18d5bfbf05a6684e6b59c4ace9571e577619aa https://github.com/galaxyproject/galaxy/commit/cc18d5bfbf05a6684e6b59c4ace9… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-07-25 (Tue, 25 Jul 2017) Changed paths: M lib/galaxy/jobs/runners/cli.py Log Message: ----------- Prevent early dataset state changes This prevents a (rare) problem when running a workflow, where a "step 2" requires tool metadata from the output of "step 1". Calling `job_wrapper.state_change()` too early will cause the next job to run, which will fail due to missing metadata. Note that other job runners do not explicitly call `job_wrapper.change_state()` when the state is OK. Commit: a930e54021f702eedb7b21385c060249030c3984 https://github.com/galaxyproject/galaxy/commit/a930e54021f702eedb7b21385c06… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-07-25 (Tue, 25 Jul 2017) Changed paths: M lib/galaxy/jobs/runners/cli.py Log Message: ----------- Simplify check_watched_items logic Commit: e1c54f37d904127aeebc5ce7010d3cfc45fcb921 https://github.com/galaxyproject/galaxy/commit/e1c54f37d904127aeebc5ce7010d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-07-28 (Fri, 28 Jul 2017) Changed paths: M lib/galaxy/jobs/runners/cli.py Log Message: ----------- Merge pull request #4343 from mvdbeek/clirunner_fix_metadata Prevent early dataset state changes in the ShellJobRunner Compare: https://github.com/galaxyproject/galaxy/compare/55ad61c28fd0...e1c54f37d904

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[galaxyproject/galaxy] 6c6c80: When a page is involved, the ID will be wrong
by GitHub 28 Jul '17

28 Jul '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: 6c6c804ab63866c6239299f4221fa436dd4a9591 https://github.com/galaxyproject/galaxy/commit/6c6c804ab63866c6239299f4221f… Author: E Rasche <hxr(a)hx42.org> Date: 2017-07-28 (Fri, 28 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- When a page is involved, the ID will be wrong Commit: 33a0c7fac3a0624d26efd8d08dabbca5f7e8c226 https://github.com/galaxyproject/galaxy/commit/33a0c7fac3a0624d26efd8d08dab… Author: E Rasche <hxr(a)hx42.org> Date: 2017-07-28 (Fri, 28 Jul 2017) Changed paths: A static/maps/mvc/job/job-params.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map A static/scripts/mvc/job/job-params.js M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Make client Commit: a2229783177b76786f581cc78040b059cbd2aab5 https://github.com/galaxyproject/galaxy/commit/a2229783177b76786f581cc78040… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-07-28 (Fri, 28 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js A static/maps/mvc/job/job-params.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map A static/scripts/mvc/job/job-params.js M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge pull request #4355 from erasche/patch-wrong-folder-id [release_17.05] Patch bug preventing creation of dataset library folders Compare: https://github.com/galaxyproject/galaxy/compare/d4d558b27a09...a2229783177b

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[galaxyproject/galaxy] 961c9f: Fix default output labels for subworkflows
by GitHub 28 Jul '17

28 Jul '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 961c9ffc36dba17e96e7116c9a48b910121015e5 https://github.com/galaxyproject/galaxy/commit/961c9ffc36dba17e96e7116c9a48… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-07-27 (Thu, 27 Jul 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Fix default output labels for subworkflows And do not display input or input_collection modules as subworkflow outputs. This should fix https://github.com/galaxyproject/galaxy/issues/3120 Commit: 80d5f9bb9d9471cfbdaaaedef7315f1fe7902916 https://github.com/galaxyproject/galaxy/commit/80d5f9bb9d9471cfbdaaaedef731… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-07-27 (Thu, 27 Jul 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Change label to output_name if label is NoneType this deals with empty strings as labels (i.e if the user has deleted a label). Commit: 6b13129b93abe15147c9aca644405cad792a8b52 https://github.com/galaxyproject/galaxy/commit/6b13129b93abe15147c9aca64440… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-07-27 (Thu, 27 Jul 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Fix inputs without label Commit: d6807b7aa8f72ca1f02bd021f4deca1dce8f51cf https://github.com/galaxyproject/galaxy/commit/d6807b7aa8f72ca1f02bd021f4de… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-07-27 (Thu, 27 Jul 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Fix run workflow selection for input module Commit: 55ad61c28fd081f53a8fdd3df69ce97ce5c63b94 https://github.com/galaxyproject/galaxy/commit/55ad61c28fd081f53a8fdd3df69c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-07-28 (Fri, 28 Jul 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #4346 from mvdbeek/subworkflow_ux_improvements Fix default output labels for subworkflows Compare: https://github.com/galaxyproject/galaxy/compare/6d1b90e70a79...55ad61c28fd0

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[galaxyproject/galaxy] c2107c: Fix some French errors
by GitHub 27 Jul '17

27 Jul '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c2107c916a05e5e88716e5069456f1a418a26a95 https://github.com/galaxyproject/galaxy/commit/c2107c916a05e5e88716e5069456… Author: Loraine Guéguen <loraine-gueguen(a)users.noreply.github.com> Date: 2017-07-24 (Mon, 24 Jul 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js Log Message: ----------- Fix some French errors Commit: 6d1b90e70a794184387e6b3580be81c62a54bb88 https://github.com/galaxyproject/galaxy/commit/6d1b90e70a794184387e6b3580be… Author: Eric Rasche <hxr(a)hx42.org> Date: 2017-07-27 (Thu, 27 Jul 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js Log Message: ----------- Merge pull request #4337 from loraine-gueguen/loraine-gueguen-patch-french_locale Fix some French errors Compare: https://github.com/galaxyproject/galaxy/compare/7d1fd6c8f02e...6d1b90e70a79

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[galaxyproject/galaxy] 71c258: Updated the version requirements
by GitHub 27 Jul '17

27 Jul '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 71c2586538836a2988422aa286fabde61784706f https://github.com/galaxyproject/galaxy/commit/71c2586538836a2988422aa286fa… Author: Vahid <VJalili(a)users.noreply.github.com> Date: 2017-07-25 (Tue, 25 Jul 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Updated the version requirements Update the version of `Babel` and `requests` packages to the minimum required versions for `CloudBridge` wheel. Commit: 1767cbedba52fb89df5dc77d03a6ca9a3cf73b19 https://github.com/galaxyproject/galaxy/commit/1767cbedba52fb89df5dc77d03a6… Author: Vahid <VJalili(a)users.noreply.github.com> Date: 2017-07-26 (Wed, 26 Jul 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Updated `Babel` package to a latest version. Commit: 7d1fd6c8f02e7a1a51f3d97ec318dbf96cb568c4 https://github.com/galaxyproject/galaxy/commit/7d1fd6c8f02e7a1a51f3d97ec318… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-07-27 (Thu, 27 Jul 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Merge pull request #4342 from VJalili/patch-2 Updated the version requirements Compare: https://github.com/galaxyproject/galaxy/compare/e43a12ad3e6f...7d1fd6c8f02e

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[galaxyproject/usegalaxy-playbook] 494920: Add static inventory for Main
by GitHub 24 Jul '17

24 Jul '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 4949204e3e3c0325ee92c6181b6157c7a4aa14f9 https://github.com/galaxyproject/usegalaxy-playbook/commit/4949204e3e3c0325… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-07-24 (Mon, 24 Jul 2017) Changed paths: A env/main/inventory.static Log Message: ----------- Add static inventory for Main Commit: 4e0343a0470d8162d2619adf4dde79dbccce379b https://github.com/galaxyproject/usegalaxy-playbook/commit/4e0343a0470d8162… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-07-24 (Mon, 24 Jul 2017) Changed paths: M env/main/group_vars/galaxywebservers.yml M env/test/group_vars/galaxyservers/vars.yml Log Message: ----------- Decrease memory requirements slightly for GIEs (the requirements didn't fit on a single node) Commit: 3ea4cacef5185b6b3821dc36e8a264c86b3c909e https://github.com/galaxyproject/usegalaxy-playbook/commit/3ea4cacef5185b6b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-07-24 (Mon, 24 Jul 2017) Changed paths: M env/test/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Run Unicycler in the multi partition on Test Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/11d253edd6e5...…

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[galaxyproject/galaxy] 68433b: Force uniqueness of preserved tags (so, don't allo...
by GitHub 24 Jul '17

24 Jul '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: 68433b1eff0a93704544a49f3d8f3a912d97c285 https://github.com/galaxyproject/galaxy/commit/68433b1eff0a93704544a49f3d8f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-05-25 (Thu, 25 May 2017) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Force uniqueness of preserved tags (so, don't allow many inputs with a 'name:foo' tag to add a ton of 'name:foo' tags to a dataset; just use one) Commit: b6e8d3e8acd00c1a595f15f2654c1b7809ecc831 https://github.com/galaxyproject/galaxy/commit/b6e8d3e8acd00c1a595f15f2654c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-05-26 (Fri, 26 May 2017) Changed paths: M lib/galaxy/managers/collections.py M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Slight refactoring to use a dict for unique'ing preserved tags. TODO: enhance object builtins to compare correctly so we can use a set, maybe. Not a big deal unless/until we have a second type of preserved tag though. Commit: dd06a01746f2ace048b9e1e604756e648a6ef1fd https://github.com/galaxyproject/galaxy/commit/dd06a01746f2ace048b9e1e60475… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-05-26 (Fri, 26 May 2017) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Handle *both* paths for tag appending using the now-dict correctly. Commit: 2ac04bbf095573f2621ffeea0e2fdeb59b21da53 https://github.com/galaxyproject/galaxy/commit/2ac04bbf095573f2621ffeea0e2f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-05-26 (Fri, 26 May 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/hdca-li.js M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/history/hdca-li.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/history/hdca-li.js Log Message: ----------- Uniqueify hashtag display Commit: 3d16319a15b7ac2f947eca24c36957894ae00afe https://github.com/galaxyproject/galaxy/commit/3d16319a15b7ac2f947eca24c369… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-05-27 (Sat, 27 May 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/hdca-li.js M lib/galaxy/managers/collections.py M lib/galaxy/tools/actions/__init__.py M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/history/hdca-li.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/history/hdca-li.js Log Message: ----------- Merge pull request #4114 from dannon/force_uniqueness_preserved_tags [17.05] Force uniqueness of preserved tags Commit: 55336d2c3142051f605231e6db1cb6a45639417c https://github.com/galaxyproject/galaxy/commit/55336d2c3142051f605231e6db1c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-05-28 (Sun, 28 May 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix legacy Python path for genome diversity tools from miller lab. Fixes #4108. Commit: 96e1cf58f480549cf5b39647c8772863405f582f https://github.com/galaxyproject/galaxy/commit/96e1cf58f480549cf5b39647c877… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-05-29 (Mon, 29 May 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #4117 from jmchilton/genome_diversity_fixes [17.01] Fix legacy Python path for genome diversity tools from miller lab. Commit: 42e274d3342720037d441222b9fb1bbcbce2d7c1 https://github.com/galaxyproject/galaxy/commit/42e274d3342720037d441222b9fb… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-30 (Tue, 30 May 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #4122 from galaxyproject/release_17.01 [17.05] merge Release 17.01 Commit: c409572ef8510e0c4322d835c5ba90f32bc9c653 https://github.com/galaxyproject/galaxy/commit/c409572ef8510e0c4322d835c5ba… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-05-31 (Wed, 31 May 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Handle potential regex expression in workflow parameter names Commit: a9d0d3671afc2be90509517b53b96af694ff22e5 https://github.com/galaxyproject/galaxy/commit/a9d0d3671afc2be90509517b53b9… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2017-05-31 (Wed, 31 May 2017) Changed paths: M lib/galaxy/util/compression_utils.py Log Message: ----------- Fix for returning a fileobject in compression_utils.py when handling a zipfile. Will return the first named object in the archive. zipfile.os_zipfile does not exist... Commit: f6ced00ef0de0fa67e2ecd06fa2db204e73f25ad https://github.com/galaxyproject/galaxy/commit/f6ced00ef0de0fa67e2ecd06fa2d… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-31 (Wed, 31 May 2017) Changed paths: M lib/galaxy/util/compression_utils.py Log Message: ----------- Merge pull request #4135 from blankenberg/17.05_zipfile [17.05] Fix for returning a fileobject in compression_utils.py when handling a zipfile. Commit: 75028ac1eec7de53a197217921ebd5b7dac4daac https://github.com/galaxyproject/galaxy/commit/75028ac1eec7de53a197217921eb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-05-31 (Wed, 31 May 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Merge pull request #4133 from guerler/escape_regex [17.05] Properly escape potential regex expression in workflow parameters Commit: c260e0b0c8ec1b8c479ab2aa2f60b7dfd533b324 https://github.com/galaxyproject/galaxy/commit/c260e0b0c8ec1b8c479ab2aa2f60… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-06-01 (Thu, 01 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/hdca-li.js M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/history/hda-li.js.map M static/maps/mvc/history/hdca-li.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/history/hda-li.js M static/scripts/mvc/history/hdca-li.js Log Message: ----------- Sort tags for display (note, this is stupid to have in 3 places -- refactor) Commit: 967c363786f36a4d4aab020a073b7c5e7eefbce6 https://github.com/galaxyproject/galaxy/commit/967c363786f36a4d4aab020a073b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-06-01 (Thu, 01 Jun 2017) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Filter tags for empties (fixes #4127) Commit: 0c43954e8d09f9f6dc7ac3af02b14821e8fc53ae https://github.com/galaxyproject/galaxy/commit/0c43954e8d09f9f6dc7ac3af02b1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-06-01 (Thu, 01 Jun 2017) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Slight tweak of logic in tag filtering PJA Commit: 12905321ca8083e4b41eb0fe03193463b8efb019 https://github.com/galaxyproject/galaxy/commit/12905321ca8083e4b41eb0fe0319… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-06-01 (Thu, 01 Jun 2017) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Allow hashtag usage in workflow PJA tag addition mechanism Commit: 0954290e5dfe74ab4d7a658dca9e2896e7aa020e https://github.com/galaxyproject/galaxy/commit/0954290e5dfe74ab4d7a658dca9e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-06-01 (Thu, 01 Jun 2017) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Combine list comprehensions, slightly tweak logic. Commit: c2348340cfa865ac33ed38311f22c0e8043c89ae https://github.com/galaxyproject/galaxy/commit/c2348340cfa865ac33ed38311f22… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2017-06-01 (Thu, 01 Jun 2017) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Fix for Data Tables loaded from a URL. Commit: b0c46cc4d0ec554d10186050c91a5c8a4880a8ff https://github.com/galaxyproject/galaxy/commit/b0c46cc4d0ec554d10186050c91a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-06-01 (Thu, 01 Jun 2017) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Merge pull request #4140 from blankenberg/17.05_data_tables_URL_fix [17.05] Fix for Data Tables loaded from a URL. Commit: 0272e188a81b89d743c22956c88e6cdac433b8db https://github.com/galaxyproject/galaxy/commit/0272e188a81b89d743c22956c88e… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2017-06-02 (Fri, 02 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/hdca-li.js M lib/galaxy/jobs/actions/post.py M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/history/hda-li.js.map M static/maps/mvc/history/hdca-li.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/history/hda-li.js M static/scripts/mvc/history/hdca-li.js Log Message: ----------- Merge pull request #4139 from dannon/tag_sorting [17.05] Tag fixes Commit: fdc712fb8884ada20373eab548144d4179aa0461 https://github.com/galaxyproject/galaxy/commit/fdc712fb8884ada20373eab54814… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-02 (Fri, 02 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M static/maps/mvc/form/form-input.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/form/form-input.js Log Message: ----------- Hide error highlighting if user interacts with highlighted field Commit: 9d0f9efbbaf52b81baed355e9b88afd9b29a7472 https://github.com/galaxyproject/galaxy/commit/9d0f9efbbaf52b81baed355e9b88… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-02 (Fri, 02 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M static/maps/mvc/form/form-input.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-input.js Log Message: ----------- Disable feature for forms which auto refresh with a server validation Commit: cbe9944815d0e543247824969b2c6aa5212b971b https://github.com/galaxyproject/galaxy/commit/cbe9944815d0e543247824969b2c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-06-04 (Sun, 04 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M static/maps/mvc/form/form-input.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/form/form-input.js Log Message: ----------- Merge pull request #4147 from martenson/fix_hide_error [17.05] Hide error highlighting if user interacts with highlighted field Commit: 0b1eaf3269ed5ccbfba7807826e822b38f57778e https://github.com/galaxyproject/galaxy/commit/0b1eaf3269ed5ccbfba7807826e8… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-06-06 (Tue, 06 Jun 2017) Changed paths: M config/plugins/webhooks/demo/search/config/searchover.yaml M config/plugins/webhooks/demo/tool_list/config/tool_list.yml M test/functional/webhooks/trans_object/config/trans_object.yaml Log Message: ----------- fix - remove extra slash Commit: d39b955e8a5d6c54852d3b32cd9cd1e7e2d3e519 https://github.com/galaxyproject/galaxy/commit/d39b955e8a5d6c54852d3b32cd9c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-06-06 (Tue, 06 Jun 2017) Changed paths: M config/plugins/webhooks/demo/search/config/searchover.yaml M config/plugins/webhooks/demo/tool_list/config/tool_list.yml M test/functional/webhooks/trans_object/config/trans_object.yaml Log Message: ----------- Merge pull request #4158 from martenson/webhooks-fix-prefix [17.05] fix webhooks loading url Commit: c90b94311e5427da95a36a9661c1d0eb19e16fc2 https://github.com/galaxyproject/galaxy/commit/c90b94311e5427da95a36a9661c1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-06-13 (Tue, 13 Jun 2017) Changed paths: M lib/galaxy/jobs/actions/post.py M lib/galaxy/managers/tags.py Log Message: ----------- Instead of setting the tags from a list, workflow PJAs will now append tags, so propagating tags will work alongside this feature. Commit: 01510af8f57508877dda205cb0afdc144bfa73c2 https://github.com/galaxyproject/galaxy/commit/01510af8f57508877dda205cb0af… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-06-13 (Tue, 13 Jun 2017) Changed paths: M lib/galaxy/managers/tags.py Log Message: ----------- Consistent spacing (not a fan of the rule, but consistency is better) Commit: 472ff8ce520a6327179dd54c301db763ea7e979b https://github.com/galaxyproject/galaxy/commit/472ff8ce520a6327179dd54c301d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-06-13 (Tue, 13 Jun 2017) Changed paths: M lib/galaxy/managers/tags.py Log Message: ----------- Fix for when item.tags is undefined Commit: b32c1cf1a3143804b0c4f12f6f7235a87801a74d https://github.com/galaxyproject/galaxy/commit/b32c1cf1a3143804b0c4f12f6f72… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-16 (Fri, 16 Jun 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Check name export in legacy export section Commit: f7ba7295102c9ce9969c634ee89e26f02c2801ea https://github.com/galaxyproject/galaxy/commit/f7ba7295102c9ce9969c634ee89e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-06-19 (Mon, 19 Jun 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Merge pull request #4203 from guerler/fix_name_export [17.05] Check name type in legacy export section Commit: 268ee7f1b7e65dde514098e0779b80b7589d26b5 https://github.com/galaxyproject/galaxy/commit/268ee7f1b7e65dde514098e0779b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-21 (Wed, 21 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Improve resilience of tool url building Commit: 69e76f98fa90782c37a2697de0204e4ff7945f09 https://github.com/galaxyproject/galaxy/commit/69e76f98fa90782c37a2697de020… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-21 (Wed, 21 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Remove redundancy of tool_id parameter Commit: a498390bef74301816945551a9832f38747fd4fc https://github.com/galaxyproject/galaxy/commit/a498390bef74301816945551a983… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-21 (Wed, 21 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Fix basic version changes for reloaded tools Commit: 9dca211e2fe59eaad1f7b95c8d51608b2afa05af https://github.com/galaxyproject/galaxy/commit/9dca211e2fe59eaad1f7b95c8d51… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-06-22 (Thu, 22 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Merge pull request #4214 from guerler/revise_tool_url [17.05] Improve resilience of tool url building Commit: 368be188d0918adaa0d7f752883c24bb79f261ec https://github.com/galaxyproject/galaxy/commit/368be188d0918adaa0d7f752883c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-26 (Mon, 26 Jun 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Unescape tool id before parsing to tool form builder Commit: 0ff61d9ffc93063f8c2e6261a1ea6c36c1176d77 https://github.com/galaxyproject/galaxy/commit/0ff61d9ffc93063f8c2e6261a1ea… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-06-26 (Mon, 26 Jun 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Fix Registry.get_datatype_by_extension() to return None if ext is unknown Without this fix, the Cheetah expression: $dataset.is_of_type('unknown_ext') in a tool command would be equivalent to: $dataset.is_of_type('txt') meaning that if the dataset datatype is a subclass of Text, the expression would evaluate to True without any warning. xref. https://github.com/galaxyproject/tools-iuc/issues/1373 Also add missing `xml` datatype to `test/functional/tools/sample_datatypes_conf.xml` which is needed by 3 test tools. Commit: f439fd30eb1f803daf8e1898bc1648c8cee131f8 https://github.com/galaxyproject/galaxy/commit/f439fd30eb1f803daf8e1898bc16… Author: Andrea Bagnacani <andrea.bagnacani(a)uni-rostock.de> Date: 2017-06-26 (Mon, 26 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/tours.js M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tours.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tours.js Log Message: ----------- conditional postclick execution onNext Commit: c8eff858d68cdbea85524c4e366cc479ba556dcd https://github.com/galaxyproject/galaxy/commit/c8eff858d68cdbea85524c4e366c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-26 (Mon, 26 Jun 2017) Changed paths: M client/galaxy/style/less/ui.less M static/style/blue/base.css Log Message: ----------- Remove float style from color picker label Commit: bd2d52800e7776ead1c8c7af53995d13cd288397 https://github.com/galaxyproject/galaxy/commit/bd2d52800e7776ead1c8c7af5399… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M client/galaxy/style/less/ui.less M static/style/blue/base.css Log Message: ----------- Merge pull request #4233 from guerler/fix_color_picker_release [17.05] Remove float style from color picker label Commit: 5a39d47b0adde675fc195c5d8b9c82c13917a233 https://github.com/galaxyproject/galaxy/commit/5a39d47b0adde675fc195c5d8b9c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Merge pull request #4230 from nsoranzo/release_16.07_backport_4224 [16.07] Backport #4224 Commit: fada8d2a60e625cf16fce7e20715422f86d6f40c https://github.com/galaxyproject/galaxy/commit/fada8d2a60e625cf16fce7e20715… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Merge branch 'release_16.07' into release_16.10 Commit: bfb3ce6e79074c42803444701e814c65631ac0cd https://github.com/galaxyproject/galaxy/commit/bfb3ce6e79074c42803444701e81… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Merge branch 'release_16.10' into release_17.01 Conflicts: test/functional/tools/sample_datatypes_conf.xml Commit: d0893b91ae281a17b3ae1bc210f197c6f259103c https://github.com/galaxyproject/galaxy/commit/d0893b91ae281a17b3ae1bc210f1… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Merge branch 'release_17.01' into release_17.05 Commit: fc613d2d60c126b3b37c9ebe3ddbd9cc58803643 https://github.com/galaxyproject/galaxy/commit/fc613d2d60c126b3b37c9ebe3ddb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M lib/galaxy/jobs/actions/post.py M lib/galaxy/managers/tags.py Log Message: ----------- Merge pull request #4188 from dannon/workflow_pja_add_not_set_tags [17.05] Hashtags w/ workflow-defined tags fix Commit: e58b24db6133720edf442ca85702e4bba050e9c9 https://github.com/galaxyproject/galaxy/commit/e58b24db6133720edf442ca85702… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-07-10 (Mon, 10 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/tours.js M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tours.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tours.js Log Message: ----------- Merge pull request #4228 from bagnacan/release_17.05_backport_4062 [17.05] conditional postclick execution onNext Commit: d4d558b27a09f684be8311f3cfb659b16545e167 https://github.com/galaxyproject/galaxy/commit/d4d558b27a09f684be8311f3cfb6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-07-17 (Mon, 17 Jul 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Merge remote-tracking branch 'guerler/fix_id_encoding' into release_17.05 Includes client rebuild. Commit: 4a7045c8d2102d2e6188df222e5b128b8fbe7534 https://github.com/galaxyproject/galaxy/commit/4a7045c8d2102d2e6188df222e5b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-07-24 (Mon, 24 Jul 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/style/less/ui.less M config/plugins/webhooks/demo/search/config/searchover.yaml M config/plugins/webhooks/demo/tool_list/config/tool_list.yml M lib/galaxy/datatypes/registry.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/tags.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py M lib/galaxy/util/compression_utils.py M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/history/hda-li.js.map M static/maps/mvc/history/hdca-li.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tours.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/history/hda-li.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tours.js M static/style/blue/base.css M test/functional/tools/sample_datatypes_conf.xml M test/functional/webhooks/trans_object/config/trans_object.yaml Log Message: ----------- Merge remote-tracking branch 'origin/release_17.05' Compare: https://github.com/galaxyproject/galaxy/compare/796168bfa76b...4a7045c8d210

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[galaxyproject/galaxy] 08fec8: Some formatting
by GitHub 23 Jul '17

23 Jul '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 08fec8770afade0ad0748b55d67784ea1f531b3e https://github.com/galaxyproject/galaxy/commit/08fec8770afade0ad0748b55d677… Author: Vahid <VJalili(a)users.noreply.github.com> Date: 2017-07-21 (Fri, 21 Jul 2017) Changed paths: M lib/galaxy/model/mapping.py Log Message: ----------- Some formatting Fixed some formatting inconsistencies by adding missing spaces between open/close parenthesis and arguments. Commit: e43a12ad3e6fbc0835e40dc92555908eb0264dfa https://github.com/galaxyproject/galaxy/commit/e43a12ad3e6fbc0835e40dc92555… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-07-23 (Sun, 23 Jul 2017) Changed paths: M lib/galaxy/model/mapping.py Log Message: ----------- Merge pull request #4333 from VJalili/patch-1 Some formatting Compare: https://github.com/galaxyproject/galaxy/compare/fe038dcb4e97...e43a12ad3e6f

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[galaxyproject/usegalaxy-playbook] 11d253: New cert for new usegalaxy.org VMs
by GitHub 22 Jul '17

22 Jul '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 11d253edd6e5fa508bd8379563b79f2dcda4ae13 https://github.com/galaxyproject/usegalaxy-playbook/commit/11d253edd6e5fa50… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-07-22 (Sat, 22 Jul 2017) Changed paths: M env/common/files/ssl/usegalaxy.org_cert.pem M env/common/group_vars/sslservers/vault.yml Log Message: ----------- New cert for new usegalaxy.org VMs

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[galaxyproject/usegalaxy-playbook] a17b38: Fix dynamic rule typo
by GitHub 20 Jul '17

20 Jul '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: a17b38614a7ee4c7b33a6fb6fb8fd6e77c1c10b7 https://github.com/galaxyproject/usegalaxy-playbook/commit/a17b38614a7ee4c7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-07-20 (Thu, 20 Jul 2017) Changed paths: M env/common/files/galaxy/dynamic_rules/multi_dynamic_walltime.py Log Message: ----------- Fix dynamic rule typo

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