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October 2015

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[galaxyproject/galaxy] 57d062: Fix for missing included files on history export a...
by GitHub 22 Oct '15

22 Oct '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: 57d0620292d3272b3bd6f8f7e9ec3833931c62be https://github.com/galaxyproject/galaxy/commit/57d0620292d3272b3bd6f8f7e9ec… Author: Vimalkumar Velayudhan <vimalkumarvelayudhan(a)gmail.com> Date: 2015-10-22 (Thu, 22 Oct 2015) Changed paths: M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/export_history.py Log Message: ----------- Fix for missing included files on history export and import. Notes: If a history was exported previously, galaxy would just serve the cached version. In that case, it is better to make some changes to the history for example, by re-running the last job and then exporting it. Export of histories that haven't been exported previously should work without problems. (cherry picked from commit 9ea0fee48aa57361147e9145be8deaaafb2a0960) Commit: dfb59002ba78373dac32d8aebefd7b2de324260b https://github.com/galaxyproject/galaxy/commit/dfb59002ba78373dac32d8aebefd… Author: Vimalkumar Velayudhan <vimalkumarvelayudhan(a)gmail.com> Date: 2015-10-22 (Thu, 22 Oct 2015) Changed paths: M lib/galaxy/tools/imp_exp/__init__.py Log Message: ----------- Use object store for imported history datasets and included files (cherry picked from commit ea89dd8f149778b6c2f0f3f4a34c8b21f7033af7) Commit: dab1ce3f03c25d35604d0ed75fc8aa6e3702c26d https://github.com/galaxyproject/galaxy/commit/dab1ce3f03c25d35604d0ed75fc8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-22 (Thu, 22 Oct 2015) Changed paths: M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/export_history.py Log Message: ----------- Merge pull request #973 from natefoo/composite-history-import-export [15.10] Fix for missing included files on history export and import Compare: https://github.com/galaxyproject/galaxy/compare/3fe148dd1981...dab1ce3f03c2

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[galaxyproject/galaxy] 9ea0fe: Fix for missing included files on history export a...
by GitHub 22 Oct '15

22 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9ea0fee48aa57361147e9145be8deaaafb2a0960 https://github.com/galaxyproject/galaxy/commit/9ea0fee48aa57361147e9145be8d… Author: Vimalkumar Velayudhan <vimalkumarvelayudhan(a)gmail.com> Date: 2015-07-02 (Thu, 02 Jul 2015) Changed paths: M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/export_history.py Log Message: ----------- Fix for missing included files on history export and import. Notes: If a history was exported previously, galaxy would just serve the cached version. In that case, it is better to make some changes to the history for example, by re-running the last job and then exporting it. Export of histories that haven't been exported previously should work without problems. Commit: ea89dd8f149778b6c2f0f3f4a34c8b21f7033af7 https://github.com/galaxyproject/galaxy/commit/ea89dd8f149778b6c2f0f3f4a34c… Author: Vimalkumar Velayudhan <vimalkumarvelayudhan(a)gmail.com> Date: 2015-07-20 (Mon, 20 Jul 2015) Changed paths: M lib/galaxy/tools/imp_exp/__init__.py Log Message: ----------- Use object store for imported history datasets and included files Commit: 53f924fbaf07979913e0ad3829cc5c9708549140 https://github.com/galaxyproject/galaxy/commit/53f924fbaf07979913e0ad3829cc… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-22 (Thu, 22 Oct 2015) Changed paths: M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/export_history.py Log Message: ----------- Merge pull request #417 from vimalkumarvelayudhan/dev Fix for missing included files on history export and import. Compare: https://github.com/galaxyproject/galaxy/compare/cbc87383db0c...53f924fbaf07

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[galaxyproject/galaxy] ee3277: Fix workflow extraction from history
by GitHub 22 Oct '15

22 Oct '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: ee327702d75415261085796af1e5c1ff5b1308ee https://github.com/galaxyproject/galaxy/commit/ee327702d75415261085796af1e5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-10-21 (Wed, 21 Oct 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix workflow extraction from history Fix history extraction by returning value dictionary Remove previous fix Commit: 9d3893ed632d95d8b70fdbc8a95ba9c44a9a5207 https://github.com/galaxyproject/galaxy/commit/9d3893ed632d95d8b70fdbc8a95b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-10-21 (Wed, 21 Oct 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Undo commit, wrong branch Commit: 8a0a445ec334d5c98ef601d80fff1bf111b6c453 https://github.com/galaxyproject/galaxy/commit/8a0a445ec334d5c98ef601d80fff… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-10-21 (Wed, 21 Oct 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix workflow extraction from history Commit: 3fe148dd1981b516452df9ace6db75e95879df03 https://github.com/galaxyproject/galaxy/commit/3fe148dd1981b516452df9ace6db… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-22 (Thu, 22 Oct 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #970 from guerler/fix_history_extract_001 [15.10] Fix workflow extraction from history Compare: https://github.com/galaxyproject/galaxy/compare/82e96140a17e...3fe148dd1981

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[galaxyproject/galaxy] c9d4d0: Fix base panels to include scripts as the last ele...
by GitHub 22 Oct '15

22 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c9d4d0000bc545526aba9759f3c1ee7b0654a9ca https://github.com/galaxyproject/galaxy/commit/c9d4d0000bc545526aba9759f3c1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-20 (Tue, 20 Oct 2015) Changed paths: M templates/base/base_panels.mako Log Message: ----------- Fix base panels to include scripts as the last element of the body, instead of after the body closing (which is not valid). Resolves a scary IE message. This should probably be swapped to async/defer as appropriate. Commit: cbc87383db0cf9cb2ac99fdecf0234825c913e3d https://github.com/galaxyproject/galaxy/commit/cbc87383db0cf9cb2ac99fdecf02… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-10-22 (Thu, 22 Oct 2015) Changed paths: M templates/base/base_panels.mako Log Message: ----------- Merge pull request #969 from dannon/ie_explorations Fix base panels to include scripts as the last element of the body, Compare: https://github.com/galaxyproject/galaxy/compare/8716eefc9e72...cbc87383db0c

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[galaxyproject/galaxy] f3bfa2: remove the autorefresh on Reports app
by GitHub 22 Oct '15

22 Oct '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: f3bfa2f56bb71f737ff8faa622271102652c7592 https://github.com/galaxyproject/galaxy/commit/f3bfa2f56bb71f737ff8faa62227… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-21 (Wed, 21 Oct 2015) Changed paths: M client/galaxy/scripts/reports_webapp/run_stats.js M static/maps/reports_webapp/run_stats.js.map M static/scripts/reports_webapp/run_stats.js Log Message: ----------- remove the autorefresh on Reports app because of how long each page takes on Main the request for a subpage would timeout because new autorefresh request would be automatically issued Commit: 82e96140a17e75a0766c45a9071eb73d4b58a0e7 https://github.com/galaxyproject/galaxy/commit/82e96140a17e75a0766c45a9071e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-22 (Thu, 22 Oct 2015) Changed paths: M client/galaxy/scripts/reports_webapp/run_stats.js M static/maps/reports_webapp/run_stats.js.map M static/scripts/reports_webapp/run_stats.js Log Message: ----------- Merge pull request #967 from martenson/remove-reports-autorefresh [15.10] remove the autorefresh on Reports app homepage Compare: https://github.com/galaxyproject/galaxy/compare/ab7ec7b3abbb...82e96140a17e

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[galaxyproject/galaxy] a02e0f: Set <options sanitize="False"> for genomespace_imp...
by GitHub 21 Oct '15

21 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a02e0f19c80c6fe8f0f9405607b3e6e8a012a77e https://github.com/galaxyproject/galaxy/commit/a02e0f19c80c6fe8f0f9405607b3… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-10-21 (Wed, 21 Oct 2015) Changed paths: M tools/genomespace/genomespace_importer.xml Log Message: ----------- Set <options sanitize="False"> for genomespace_importer.xml Commit: ab7ec7b3abbba0e0dd8892d504e6d1b2511d9b55 https://github.com/galaxyproject/galaxy/commit/ab7ec7b3abbba0e0dd8892d504e6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-21 (Wed, 21 Oct 2015) Changed paths: M tools/genomespace/genomespace_importer.xml Log Message: ----------- Merge pull request #963 from blankenberg/gs_release_15.10 [15.10] Set <options sanitize="False"> for genomespace_importer.xml Commit: 8716eefc9e727902fc2d67df49488e1d63282e6a https://github.com/galaxyproject/galaxy/commit/8716eefc9e727902fc2d67df4948… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-21 (Wed, 21 Oct 2015) Changed paths: M tools/genomespace/genomespace_importer.xml Log Message: ----------- Merge branch 'master' into dev Compare: https://github.com/galaxyproject/galaxy/compare/a5814e8f3bd6...8716eefc9e72

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[galaxyproject/galaxy] a02e0f: Set <options sanitize="False"> for genomespace_imp...
by GitHub 21 Oct '15

21 Oct '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: a02e0f19c80c6fe8f0f9405607b3e6e8a012a77e https://github.com/galaxyproject/galaxy/commit/a02e0f19c80c6fe8f0f9405607b3… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-10-21 (Wed, 21 Oct 2015) Changed paths: M tools/genomespace/genomespace_importer.xml Log Message: ----------- Set <options sanitize="False"> for genomespace_importer.xml Commit: ab7ec7b3abbba0e0dd8892d504e6d1b2511d9b55 https://github.com/galaxyproject/galaxy/commit/ab7ec7b3abbba0e0dd8892d504e6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-21 (Wed, 21 Oct 2015) Changed paths: M tools/genomespace/genomespace_importer.xml Log Message: ----------- Merge pull request #963 from blankenberg/gs_release_15.10 [15.10] Set <options sanitize="False"> for genomespace_importer.xml Compare: https://github.com/galaxyproject/galaxy/compare/92666cdf6691...ab7ec7b3abbb

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[galaxyproject/galaxy] a02e0f: Set <options sanitize="False"> for genomespace_imp...
by GitHub 21 Oct '15

21 Oct '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: a02e0f19c80c6fe8f0f9405607b3e6e8a012a77e https://github.com/galaxyproject/galaxy/commit/a02e0f19c80c6fe8f0f9405607b3… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-10-21 (Wed, 21 Oct 2015) Changed paths: M tools/genomespace/genomespace_importer.xml Log Message: ----------- Set <options sanitize="False"> for genomespace_importer.xml Commit: ab7ec7b3abbba0e0dd8892d504e6d1b2511d9b55 https://github.com/galaxyproject/galaxy/commit/ab7ec7b3abbba0e0dd8892d504e6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-21 (Wed, 21 Oct 2015) Changed paths: M tools/genomespace/genomespace_importer.xml Log Message: ----------- Merge pull request #963 from blankenberg/gs_release_15.10 [15.10] Set <options sanitize="False"> for genomespace_importer.xml Compare: https://github.com/galaxyproject/galaxy/compare/92666cdf6691...ab7ec7b3abbb

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[galaxyproject/galaxy] 60a1b4: make lib search case insensitive
by GitHub 21 Oct '15

21 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 60a1b45704c4794e6fcac2e9ab6001484a801ca6 https://github.com/galaxyproject/galaxy/commit/60a1b45704c4794e6fcac2e9ab60… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-08 (Thu, 08 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-model.js M static/maps/mvc/library/library-model.js.map M static/scripts/mvc/library/library-model.js Log Message: ----------- make lib search case insensitive Commit: 2d4bd2e6f5c64162ab2c1de6d6b1e338bafb4b16 https://github.com/galaxyproject/galaxy/commit/2d4bd2e6f5c64162ab2c1de6d6b1… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-08 (Thu, 08 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/style/less/library.less M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/scripts/mvc/library/library-librarytoolbar-view.js M static/style/blue/base.css M static/style/blue/library.css Log Message: ----------- fix the ordering and margins of lib toolbar items Commit: 39f5b7adf1cb835eed7b450806b249200c2a9cbe https://github.com/galaxyproject/galaxy/commit/39f5b7adf1cb835eed7b450806b2… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-08 (Thu, 08 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M static/maps/mvc/library/library-librarylist-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js Log Message: ----------- show proper message when search has no results Commit: 775ee33d4dbf7cb763e9f25430aae645d2df4c65 https://github.com/galaxyproject/galaxy/commit/775ee33d4dbf7cb763e9f25430aa… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-08 (Thu, 08 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M static/maps/mvc/library/library-librarylist-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js Log Message: ----------- fix options default order to fix bug with improper page being rendered also add missing comma for previous commit Commit: fe8dbd8183fe5706e041686ee57a683d1fd63c9e https://github.com/galaxyproject/galaxy/commit/fe8dbd8183fe5706e041686ee57a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-08 (Thu, 08 Oct 2015) Changed paths: M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M static/maps/galaxy.library.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-librarylist-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/scripts/galaxy.library.js M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js Log Message: ----------- fix problems with multiple bindings of view events; drop attempts at caching the libraries - need to study more for that Commit: 251f390f7c45f5d02af90f01f7b892b207950cb6 https://github.com/galaxyproject/galaxy/commit/251f390f7c45f5d02af90f01f7b8… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-08 (Thu, 08 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- fix the ordering of folder controls to match library's also fix the active area of 'include deleted' checkbox Commit: 6c5f6e3f692c2b151afab39126a068f56971708d https://github.com/galaxyproject/galaxy/commit/6c5f6e3f692c2b151afab39126a0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-12 (Mon, 12 Oct 2015) Changed paths: M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/library/library-model.js M client/galaxy/style/less/library.less M static/maps/galaxy.library.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-librarylist-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/maps/mvc/library/library-model.js.map M static/scripts/galaxy.library.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/library/library-model.js M static/style/blue/base.css M static/style/blue/library.css Log Message: ----------- Merge pull request #878 from martenson/datalib-fixes-release [15.10] Release Fixes for Data Libraries Commit: b470843c89af119b9800d6fb68323338c7020fb6 https://github.com/galaxyproject/galaxy/commit/b470843c89af119b9800d6fb6832… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-10-13 (Tue, 13 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-analysis.js M static/maps/mvc/app/app-analysis.js.map M static/scripts/mvc/app/app-analysis.js Log Message: ----------- UI, histories: fix multiview button to be logged-in users only Commit: 99fab6f342f6f50536b1a5544b8b07f769805497 https://github.com/galaxyproject/galaxy/commit/99fab6f342f6f50536b1a5544b8b… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-10-13 (Tue, 13 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/history/history-panel.js M client/galaxy/scripts/mvc/list/list-panel.js M static/maps/mvc/history/history-panel.js.map M static/maps/mvc/list/list-panel.js.map M static/scripts/mvc/history/history-panel.js M static/scripts/mvc/list/list-panel.js Log Message: ----------- UI, histories: on first history search, use current searchFor value at callback and not value when ajax began Commit: 34a11d1187127face6dd0c780051458b2b5d7430 https://github.com/galaxyproject/galaxy/commit/34a11d1187127face6dd0c780051… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-10-13 (Tue, 13 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/history/multi-panel.js M static/maps/mvc/history/multi-panel.js.map M static/scripts/mvc/history/multi-panel.js Log Message: ----------- UI, histories: fix default empty message for lazy loaded panels in multi-view Commit: 41069e8ba6dcd6328864eabb104e36a2a70e6140 https://github.com/galaxyproject/galaxy/commit/41069e8ba6dcd6328864eabb104e… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-10-13 (Tue, 13 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/history/multi-panel.js M static/maps/mvc/history/multi-panel.js.map M static/scripts/mvc/history/multi-panel.js Log Message: ----------- UI, histories: fix/reverse order for drag and drop dataset copy Commit: 03c7aae512d010a3100a547af3c194e6f8957e35 https://github.com/galaxyproject/galaxy/commit/03c7aae512d010a3100a547af3c1… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-10-13 (Tue, 13 Oct 2015) Changed paths: M client/galaxy/style/less/list-item.less M static/style/blue/base.css Log Message: ----------- UI, histories: disable user-select on dataset selectors to prevent text select/highlight when using shift to select a range Commit: ee42fd05319171a79791803d5c0adc168ef2cced https://github.com/galaxyproject/galaxy/commit/ee42fd05319171a79791803d5c0a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-analysis.js M client/galaxy/scripts/mvc/history/history-panel.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/list/list-panel.js M client/galaxy/style/less/list-item.less M static/maps/mvc/app/app-analysis.js.map M static/maps/mvc/history/history-panel.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/list/list-panel.js.map M static/scripts/mvc/app/app-analysis.js M static/scripts/mvc/history/history-panel.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/list/list-panel.js M static/style/blue/base.css Log Message: ----------- Merge pull request #910 from carlfeberhard/release_15.10 [15.10] Some minor fixes to the history UI Commit: 120ec61264dadb90b0386e46bd4c33a2f6481c52 https://github.com/galaxyproject/galaxy/commit/120ec61264dadb90b0386e46bd4c… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M tools/filters/cutWrapper.xml Log Message: ----------- Fix command quoting and remove size from text input for Cut tool. Commit: cf59e8bd3c52f52ae717ca9755e6b10f48382b07 https://github.com/galaxyproject/galaxy/commit/cf59e8bd3c52f52ae717ca9755e6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M tools/filters/cutWrapper.xml Log Message: ----------- Merge pull request #913 from blankenberg/cut_15.10 [15.10] Fix command quoting and remove size from text input for Cut tool. Commit: a742198a36d700f299019ef8929a9dc55d58c17a https://github.com/galaxyproject/galaxy/commit/a742198a36d700f299019ef8929a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Fixes for switching history (standard as well as multiview) when using IE11. Intentionally minimal fix for 15.10, more comprehensive refactoring+solution forthcoming for dev. Commit: 11d17b3e7b305a28aaa0fb8392424dbb650e70d6 https://github.com/galaxyproject/galaxy/commit/11d17b3e7b305a28aaa0fb839242… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-15 (Thu, 15 Oct 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Merge pull request #920 from dannon/release_15.10 [15.10] IE11 history-stuck fix Commit: 15a8c594bd8041c17512a719eab6185c6b478f19 https://github.com/galaxyproject/galaxy/commit/15a8c594bd8041c17512a719eab6… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-16 (Fri, 16 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-librarylist-view.js M static/maps/mvc/library/library-librarylist-view.js.map M static/scripts/mvc/library/library-librarylist-view.js Log Message: ----------- fix the filter on deleted libraries to not show the public deleted libs by default Commit: 47ce939322111da71b914976170dd9ad41c0fe7d https://github.com/galaxyproject/galaxy/commit/47ce939322111da71b914976170d… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-16 (Fri, 16 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-librarylist-view.js M static/maps/mvc/library/library-librarylist-view.js.map M static/scripts/mvc/library/library-librarylist-view.js Log Message: ----------- remove log Commit: b7dfeb4174183135f8ac7c858d6ce33ba69286c0 https://github.com/galaxyproject/galaxy/commit/b7dfeb4174183135f8ac7c858d6c… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-10-19 (Mon, 19 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-librarylist-view.js M static/maps/mvc/library/library-librarylist-view.js.map M static/scripts/mvc/library/library-librarylist-view.js Log Message: ----------- Merge pull request #934 from martenson/fix-showing-deleted-libs [15.10] fix the filter on search results to not show the public deleted libs Commit: dd2d6960db3cd14238a9b10595cc0f5840e8f92b https://github.com/galaxyproject/galaxy/commit/dd2d6960db3cd14238a9b10595cc… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-10-20 (Tue, 20 Oct 2015) Changed paths: M client/galaxy/style/less/base.less M static/style/blue/base.css Log Message: ----------- Fixed missing trackster navigation pane (issue #946) Please enter the commit message for your changes. Lines starting Commit: 0f9067d2444575760f138e7fe9c4b6302b172ace https://github.com/galaxyproject/galaxy/commit/0f9067d2444575760f138e7fe9c4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-20 (Tue, 20 Oct 2015) Changed paths: M client/galaxy/style/less/base.less M static/style/blue/base.css Log Message: ----------- Merge pull request #957 from guerler/fix_trackster_001 [15.10] Fixed missing trackster navigation pane (issue #946) Commit: 732b4f5b1f45a6e676ff70590944f3b6dcf8a77f https://github.com/galaxyproject/galaxy/commit/732b4f5b1f45a6e676ff70590944… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-20 (Tue, 20 Oct 2015) Changed paths: M templates/webapps/galaxy/root/index.mako Log Message: ----------- fix missing analytics on the analysis page we abandoned base_panels for this page so the script was missing Commit: d53e13a4a997beec3cef5532ce39558296f54977 https://github.com/galaxyproject/galaxy/commit/d53e13a4a997beec3cef5532ce39… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-20 (Tue, 20 Oct 2015) Changed paths: M templates/webapps/galaxy/root/index.mako Log Message: ----------- Merge pull request #958 from martenson/fix-google-analytics [15.10] Fix google analytics on the analysis page Commit: 6f5aafe6279337b318149058e90b749e94838eaa https://github.com/galaxyproject/galaxy/commit/6f5aafe6279337b318149058e90b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-21 (Wed, 21 Oct 2015) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- For require_login=True, redirect directly to login without showing empty (and broken) looking panels, and potentially hitting an endless reload cycle. Commit: 92666cdf66914e98535567cd46946b745d02673e https://github.com/galaxyproject/galaxy/commit/92666cdf66914e98535567cd4694… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-10-21 (Wed, 21 Oct 2015) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- Merge pull request #965 from dannon/login_req [15.10] Fix endless redirect cycle when login is required Commit: a5814e8f3bd66799f1941ed47ffc94498a56e471 https://github.com/galaxyproject/galaxy/commit/a5814e8f3bd66799f1941ed47ffc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-21 (Wed, 21 Oct 2015) Changed paths: M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/mvc/app/app-analysis.js M client/galaxy/scripts/mvc/history/history-panel.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/library/library-model.js M client/galaxy/scripts/mvc/list/list-panel.js M client/galaxy/style/less/library.less M client/galaxy/style/less/list-item.less M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/galaxy.library.js.map M static/maps/mvc/app/app-analysis.js.map M static/maps/mvc/history/history-panel.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-librarylist-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/maps/mvc/library/library-model.js.map M static/maps/mvc/list/list-panel.js.map M static/scripts/galaxy.library.js M static/scripts/mvc/app/app-analysis.js M static/scripts/mvc/history/history-panel.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/library/library-model.js M static/scripts/mvc/list/list-panel.js M static/style/blue/base.css M static/style/blue/library.css M templates/webapps/galaxy/root/index.mako M tools/filters/cutWrapper.xml Log Message: ----------- Merge master-> dev. Resolved one conflict on style build. Compare: https://github.com/galaxyproject/galaxy/compare/0f0d14ae5130...a5814e8f3bd6

1 0

[galaxyproject/galaxy] 7e0ccb: Apply patch
by GitHub 21 Oct '15

21 Oct '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: 7e0ccbe2146e51dc4cd44c56fec352c0e0b34857 https://github.com/galaxyproject/galaxy/commit/7e0ccbe2146e51dc4cd44c56fec3… Author: Airistotal <daniel.bouchard(a)phac-aspc.gc.ca> Date: 2015-06-16 (Tue, 16 Jun 2015) Changed paths: A client/galaxy/scripts/libs/jquery.sparklines.js A static/maps/libs/jquery.sparklines.js.map A templates/spark_base.mako Log Message: ----------- Apply patch Commit: 82456bb1347a054050789d02a4b5a03bad6f8bfe https://github.com/galaxyproject/galaxy/commit/82456bb1347a054050789d02a4b5… Author: Airistotal <daniel.bouchard(a)phac-aspc.gc.ca> Date: 2015-06-16 (Tue, 16 Jun 2015) Changed paths: M lib/galaxy/webapps/reports/controllers/jobs.py M templates/base.mako M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_all.mako M templates/webapps/reports/jobs_specified_month_in_error.mako M templates/webapps/reports/jobs_tool_per_month.mako M templates/webapps/reports/jobs_user_per_month.mako Log Message: ----------- Apply Patch Commit: 55eadd41f42fb8ddf9c46a21e5c1e3f8e2fe6d91 https://github.com/galaxyproject/galaxy/commit/55eadd41f42fb8ddf9c46a21e5c1… Author: Airistotal <daniel.bouchard(a)phac-aspc.gc.ca> Date: 2015-06-16 (Tue, 16 Jun 2015) Changed paths: A static/scripts/libs/jquery.sparklines.js Log Message: ----------- Build with grunt Commit: 041a7df4a220e797a447a3ba2c857a745069f89c https://github.com/galaxyproject/galaxy/commit/041a7df4a220e797a447a3ba2c85… Author: Airistotal <daniel.bouchard(a)phac-aspc.gc.ca> Date: 2015-06-16 (Tue, 16 Jun 2015) Changed paths: M lib/galaxy/webapps/reports/controllers/jobs.py Log Message: ----------- Bug fix for page crash Commit: eca0329d26b607fa208bd9c07240d8511dfa7d3d https://github.com/galaxyproject/galaxy/commit/eca0329d26b607fa208bd9c07240… Author: Airistotal <daniel.bouchard(a)phac-aspc.gc.ca> Date: 2015-06-17 (Wed, 17 Jun 2015) Changed paths: M lib/galaxy/webapps/reports/controllers/jobs.py M templates/webapps/reports/jobs_specified_month_all.mako M templates/webapps/reports/jobs_specified_month_in_error.mako Log Message: ----------- Refactoring the creation of tool tips Commit: 597a2b61e2a6a0f9f6c50e4a9095e7cf50012642 https://github.com/galaxyproject/galaxy/commit/597a2b61e2a6a0f9f6c50e4a9095… Author: Airistotal <daniel.bouchard(a)phac-aspc.gc.ca> Date: 2015-06-17 (Wed, 17 Jun 2015) Changed paths: M lib/galaxy/webapps/reports/controllers/jobs.py M templates/sorting_base.mako M templates/webapps/reports/jobs_specified_month_all.mako Log Message: ----------- Added pagintation to Jobs_per_month_all Commit: 4db40ff6b505dba663bbf381161d58374ce617dd https://github.com/galaxyproject/galaxy/commit/4db40ff6b505dba663bbf381161d… Author: Airistotal <daniel.bouchard(a)phac-aspc.gc.ca> Date: 2015-06-18 (Thu, 18 Jun 2015) Changed paths: M lib/galaxy/webapps/reports/controllers/jobs.py A templates/page_base.mako M templates/webapps/reports/jobs_specified_month_all.mako Log Message: ----------- Added pagination to jobs_specified_month_all Commit: f6baadbefa742907e9e43f3e02b9ac44f0b51a1e https://github.com/galaxyproject/galaxy/commit/f6baadbefa742907e9e43f3e02b9… Author: Airistotal <daniel.bouchard(a)phac-aspc.gc.ca> Date: 2015-06-19 (Fri, 19 Jun 2015) Changed paths: M lib/galaxy/webapps/reports/controllers/jobs.py M templates/page_base.mako M templates/webapps/reports/jobs_specified_month_all.mako Log Message: ----------- Added the ability to choose the amount of rows desired Commit: 465661bc2c01a3d955d795e64e4b8693244618f9 https://github.com/galaxyproject/galaxy/commit/465661bc2c01a3d955d795e64e4b… Author: Airistotal <daniel.bouchard(a)phac-aspc.gc.ca> Date: 2015-06-19 (Fri, 19 Jun 2015) Changed paths: M templates/page_base.mako M templates/webapps/reports/jobs_specified_month_all.mako Log Message: ----------- Small aesthetic changes and refactoring Commit: 6b021b1c989e3b62e24d11fff86d73c66ee019b2 https://github.com/galaxyproject/galaxy/commit/6b021b1c989e3b62e24d11fff86d… Author: Airistotal <daniel.bouchard(a)phac-aspc.gc.ca> Date: 2015-06-22 (Mon, 22 Jun 2015) Changed paths: M lib/galaxy/webapps/reports/controllers/jobs.py Log Message: ----------- Added type checking and casting for certain errors Commit: bc69acb8a99ea93b0179d2c2495c9d37e85464e9 https://github.com/galaxyproject/galaxy/commit/bc69acb8a99ea93b0179d2c2495c… Author: Airistotal <daniel.bouchard(a)phac-aspc.gc.ca> Date: 2015-06-22 (Mon, 22 Jun 2015) Changed paths: M lib/galaxy/webapps/reports/controllers/jobs.py Log Message: ----------- Added whitespace to pass Travis CI. Commit: 3a9ff2a1dd8b6e9f997335742532a511ae7c04b8 https://github.com/galaxyproject/galaxy/commit/3a9ff2a1dd8b6e9f997335742532… Author: Airistotal <daniel.bouchard(a)phac-aspc.gc.ca> Date: 2015-06-22 (Mon, 22 Jun 2015) Changed paths: M lib/galaxy/webapps/reports/controllers/jobs.py M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako Log Message: ----------- Added compatibility for postgres, bug fix where sparklines broke when no jobs were done in the past 50 days(arbitrary amount decided in code) Commit: d870a24071341a4e874d9367cc22088264a1e683 https://github.com/galaxyproject/galaxy/commit/d870a24071341a4e874d9367cc22… Author: Airistotal <daniel.bouchard(a)phac-aspc.gc.ca> Date: 2015-06-22 (Mon, 22 Jun 2015) Changed paths: M lib/galaxy/webapps/reports/controllers/jobs.py M templates/spark_base.mako M templates/webapps/reports/index.mako M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako Log Message: ----------- Added option for how long sparklines jobs per user, jobs per tool and errors per tool are Commit: e286c14f6b718853124ae1ab5b83d7e2f07be5e9 https://github.com/galaxyproject/galaxy/commit/e286c14f6b718853124ae1ab5b83… Author: Airistotal <daniel.bouchard(a)phac-aspc.gc.ca> Date: 2015-06-22 (Mon, 22 Jun 2015) Changed paths: M lib/galaxy/webapps/reports/controllers/jobs.py Log Message: ----------- Added whitespace for CI Commit: 895d09cd9b3682e99e1f365fa87970f0a425ff47 https://github.com/galaxyproject/galaxy/commit/895d09cd9b3682e99e1f365fa879… Author: Airistotal <daniel.bouchard(a)phac-aspc.gc.ca> Date: 2015-06-22 (Mon, 22 Jun 2015) Changed paths: M lib/galaxy/webapps/reports/controllers/jobs.py Log Message: ----------- Fixed bug on Jobs per month page where postgres was showing all jobs on same day in sparkline Commit: 08049542aacf23acff2c53b13bc7775d342bba16 https://github.com/galaxyproject/galaxy/commit/08049542aacf23acff2c53b13bc7… Author: Airistotal <daniel.bouchard(a)phac-aspc.gc.ca> Date: 2015-06-22 (Mon, 22 Jun 2015) Changed paths: M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako Log Message: ----------- Small bug fix in sparklines tool tip where it said day even though it was measured in weeks/months/years Commit: 1c7017cf4b44f55d94bdbb9d3e2dbbd8f757d032 https://github.com/galaxyproject/galaxy/commit/1c7017cf4b44f55d94bdbb9d3e2d… Author: Airistotal <daniel.bouchard(a)phac-aspc.gc.ca> Date: 2015-06-25 (Thu, 25 Jun 2015) Changed paths: M lib/galaxy/webapps/reports/controllers/jobs.py M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_tool_per_month.mako M templates/webapps/reports/jobs_user_per_month.mako Log Message: ----------- Fixed a bug where the queries truncated the days so the sparklines didn't display correctly Commit: 88471eb21b6b22c416ae9f6dd19cca8322b3e75c https://github.com/galaxyproject/galaxy/commit/88471eb21b6b22c416ae9f6dd19c… Author: Airistotal <daniel.bouchard(a)phac-aspc.gc.ca> Date: 2015-06-26 (Fri, 26 Jun 2015) Changed paths: M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/reports/controllers/workflows.py M templates/webapps/reports/index.mako M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_user_per_month.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako M templates/webapps/reports/workflows_user_per_month.mako Log Message: ----------- Fix where days/weeks/... reverted to days when sorting columns. Refactored time_period code into function. Applied sparklines to workflows pages. Commit: 263f6341274b06d60eb7e08d8bd834ad0b567c41 https://github.com/galaxyproject/galaxy/commit/263f6341274b06d60eb7e08d8bd8… Author: Airistotal <daniel.bouchard(a)phac-aspc.gc.ca> Date: 2015-06-26 (Fri, 26 Jun 2015) Changed paths: M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/reports/controllers/workflows.py Log Message: ----------- Fixed up whitespaces Commit: 328da98823722bb28ab09aa1caa00ca6085327c6 https://github.com/galaxyproject/galaxy/commit/328da98823722bb28ab09aa1caa0… Author: Airistotal <daniel.bouchard(a)phac-aspc.gc.ca> Date: 2015-06-30 (Tue, 30 Jun 2015) Changed paths: M client/galaxy/style/less/base.less M static/style/blue/base.css M templates/spark_base.mako M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_all.mako M templates/webapps/reports/jobs_specified_month_in_error.mako M templates/webapps/reports/jobs_tool_per_month.mako M templates/webapps/reports/jobs_user_per_month.mako M templates/webapps/reports/registered_users_per_month.mako M templates/webapps/reports/registered_users_specified_month.mako M templates/webapps/reports/requests_per_month_all.mako M templates/webapps/reports/requests_per_user.mako M templates/webapps/reports/requests_user_per_month.mako M templates/webapps/reports/users_last_access_date.mako M templates/webapps/reports/users_user_disk_usage.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako M templates/webapps/reports/workflows_user_per_month.mako Log Message: ----------- Refactored and added styling Commit: 9ab2f656995bed4d06818270d90fb37c9835c39d https://github.com/galaxyproject/galaxy/commit/9ab2f656995bed4d06818270d90f… Author: Airistotal <daniel.bouchard(a)phac-aspc.gc.ca> Date: 2015-06-30 (Tue, 30 Jun 2015) Changed paths: M .ci/flake8_wrapper.sh M .ci/pep8_sources.txt A CONTRIBUTORS.md M LICENSE.txt M README.rst R client/galaxy/scripts/galaxy.workflow_editor.canvas.js R client/galaxy/scripts/galaxy.workflows.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-view.js R client/galaxy/scripts/mvc/groups/group-detail-view.js R client/galaxy/scripts/mvc/groups/group-list-view.js R client/galaxy/scripts/mvc/groups/group-listrow-view.js R client/galaxy/scripts/mvc/groups/group-model.js M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/scripts/mvc/tools/tools-form-workflow.js A client/galaxy/scripts/mvc/workflow/workflow-canvas.js A client/galaxy/scripts/mvc/workflow/workflow-connector.js A client/galaxy/scripts/mvc/workflow/workflow-manager.js A client/galaxy/scripts/mvc/workflow/workflow-node.js A client/galaxy/scripts/mvc/workflow/workflow-terminals.js A client/galaxy/scripts/mvc/workflow/workflow-view-data.js A client/galaxy/scripts/mvc/workflow/workflow-view-node.js A client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js A client/galaxy/scripts/mvc/workflow/workflow-view.js R client/galaxy/scripts/toolshed.groups.js A client/toolshed/scripts/mvc/groups/group-detail-view.js A client/toolshed/scripts/mvc/groups/group-list-view.js A client/toolshed/scripts/mvc/groups/group-listrow-view.js A client/toolshed/scripts/mvc/groups/group-model.js R client/toolshed/scripts/test-file.js A client/toolshed/scripts/toolshed.groups.js M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced M config/object_store_conf.xml.sample M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/tool_shed.ini.sample M cron/parse_builds.py M display_applications/ensembl/ensembl_bam.xml M display_applications/ensembl/ensembl_gff.xml M display_applications/ensembl/ensembl_interval_as_bed.xml M display_applications/gbrowse/gbrowse_gff.xml M display_applications/gbrowse/gbrowse_interval_as_bed.xml M display_applications/gbrowse/gbrowse_wig.xml M display_applications/igb/bam.xml M display_applications/igb/bb.xml M display_applications/igb/bed.xml M display_applications/igb/bedgraph.xml M display_applications/igb/bigwig.xml M display_applications/igb/gtf.xml M display_applications/igb/wig.xml M display_applications/igv/bam.xml M display_applications/igv/gff.xml M display_applications/igv/interval_as_bed.xml M display_applications/igv/vcf.xml M display_applications/rviewer/bed.xml M display_applications/rviewer/vcf.xml A doc/source/api_doc.rst M doc/source/conf.py M doc/source/index.rst R doc/source/lib/fpconst.rst M doc/source/lib/galaxy.actions.rst A doc/source/lib/galaxy.auth.providers.rst A doc/source/lib/galaxy.auth.rst A doc/source/lib/galaxy.dataset_collections.rst A doc/source/lib/galaxy.dataset_collections.types.rst M doc/source/lib/galaxy.datatypes.converters.rst A doc/source/lib/galaxy.datatypes.dataproviders.rst M doc/source/lib/galaxy.datatypes.display_applications.rst M doc/source/lib/galaxy.datatypes.rst M doc/source/lib/galaxy.datatypes.util.rst M doc/source/lib/galaxy.eggs.rst M doc/source/lib/galaxy.exceptions.rst M doc/source/lib/galaxy.external_services.result_handlers.rst M doc/source/lib/galaxy.external_services.rst M doc/source/lib/galaxy.forms.rst M doc/source/lib/galaxy.jobs.actions.rst M doc/source/lib/galaxy.jobs.deferred.rst A doc/source/lib/galaxy.jobs.metrics.collectl.rst A doc/source/lib/galaxy.jobs.metrics.instrumenters.rst A doc/source/lib/galaxy.jobs.metrics.rst M doc/source/lib/galaxy.jobs.rst R doc/source/lib/galaxy.jobs.runners.cli_job.rst R doc/source/lib/galaxy.jobs.runners.cli_shell.rst A doc/source/lib/galaxy.jobs.runners.lwr_client.rst A doc/source/lib/galaxy.jobs.runners.lwr_client.staging.rst A 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lib/tool_shed/scripts/api/common.py M lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_tool_shed.sh M lib/tool_shed/scripts/deprecate_repositories_without_metadata.py M lib/tool_shed/util/workflow_util.py M scripts/api/common.py M scripts/functional_tests.py M scripts/tool_shed/build_ts_whoosh_index.py R static/maps/galaxy.workflow_editor.canvas.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/tools/tools-form-workflow.js.map A static/maps/mvc/workflow/workflow-canvas.js.map A static/maps/mvc/workflow/workflow-connector.js.map A static/maps/mvc/workflow/workflow-manager.js.map A static/maps/mvc/workflow/workflow-node.js.map A static/maps/mvc/workflow/workflow-terminals.js.map A static/maps/mvc/workflow/workflow-view-data.js.map A static/maps/mvc/workflow/workflow-view-node.js.map A static/maps/mvc/workflow/workflow-view-terminals.js.map A static/maps/mvc/workflow/workflow-view.js.map A static/maps/mvc/workflow/workflow.js.map R static/scripts/galaxy.workflow_editor.canvas.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-view.js R static/scripts/mvc/groups/group-detail-view.js R static/scripts/mvc/groups/group-groupdetail-view.js R static/scripts/mvc/groups/group-grouprow-view.js R static/scripts/mvc/groups/group-list-view.js R static/scripts/mvc/groups/group-listrow-view.js R static/scripts/mvc/groups/group-model.js R static/scripts/mvc/groups/group.model.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/tools/tools-form-workflow.js A static/scripts/mvc/workflow/workflow-canvas.js A static/scripts/mvc/workflow/workflow-connector.js A static/scripts/mvc/workflow/workflow-manager.js A static/scripts/mvc/workflow/workflow-node.js A static/scripts/mvc/workflow/workflow-terminals.js A static/scripts/mvc/workflow/workflow-view-data.js A static/scripts/mvc/workflow/workflow-view-node.js A static/scripts/mvc/workflow/workflow-view-terminals.js A static/scripts/mvc/workflow/workflow-view.js A static/scripts/mvc/workflow/workflow.js R static/scripts/toolshed.groups.js A static/toolshed/maps/mvc/groups/group-detail-view.js.map A static/toolshed/maps/mvc/groups/group-list-view.js.map A static/toolshed/maps/mvc/groups/group-listrow-view.js.map A static/toolshed/maps/mvc/groups/group-model.js.map A static/toolshed/maps/test-file.js.map A static/toolshed/maps/toolshed.groups.js.map A static/toolshed/scripts/mvc/groups/group-detail-view.js A static/toolshed/scripts/mvc/groups/group-list-view.js A static/toolshed/scripts/mvc/groups/group-listrow-view.js A static/toolshed/scripts/mvc/groups/group-model.js A static/toolshed/scripts/toolshed.groups.js M templates/webapps/galaxy/history/display_structured.mako M templates/webapps/galaxy/workflow/display.mako M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/galaxy/workflow/editor_tool_form.mako M templates/webapps/galaxy/workflow/run.mako M templates/webapps/tool_shed/group/index.mako M templates/webapps/tool_shed/repository/manage_repository.mako M templates/webapps/tool_shed/repository/view_repository.mako M test/api/test_workflows.py M test/functional/tools/code_file.py A test/functional/tools/environment_variables.xml M test/functional/tools/samples_tool_conf.xml M test/qunit/test-common.js M test/qunit/tests/workflow_editor_tests.js M test/unit/jobs/test_job_configuration.py M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_runner_local.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_tool_dependency_description.py M test/unit/tools/test_tool_deps.py M test/unit/tools/test_tool_loader.py M tools/data_source/upload.py M tools/evolution/codingSnps_filter.py Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into Reports_TTClean Commit: 860c39b48c37ca4bb37c2be555b983d1cd95f8a7 https://github.com/galaxyproject/galaxy/commit/860c39b48c37ca4bb37c2be555b9… Author: Airistotal <daniel.bouchard(a)phac-aspc.gc.ca> Date: 2015-06-30 (Tue, 30 Jun 2015) Changed paths: M lib/galaxy/webapps/reports/controllers/workflows.py M templates/webapps/reports/index.mako A templates/webapps/reports/workflows_per_workflow.mako Log Message: ----------- Added new Runs per workflow page Commit: 428559e0bcd47d64d2e710c414933c1dbd5af50c https://github.com/galaxyproject/galaxy/commit/428559e0bcd47d64d2e710c41493… Author: Airistotal <daniel.bouchard(a)phac-aspc.gc.ca> Date: 2015-06-30 (Tue, 30 Jun 2015) Changed paths: M .ci/pep8_sources.txt A client/galaxy/scripts/libs/jquery.sparklines.js M client/galaxy/style/less/base.less M config/object_store_conf.xml.sample A doc/source/api_doc.rst M doc/source/conf.py M doc/source/index.rst R doc/source/lib/fpconst.rst M doc/source/lib/galaxy.actions.rst A doc/source/lib/galaxy.auth.providers.rst A doc/source/lib/galaxy.auth.rst A doc/source/lib/galaxy.dataset_collections.rst A doc/source/lib/galaxy.dataset_collections.types.rst M doc/source/lib/galaxy.datatypes.converters.rst A doc/source/lib/galaxy.datatypes.dataproviders.rst M doc/source/lib/galaxy.datatypes.display_applications.rst M doc/source/lib/galaxy.datatypes.rst M doc/source/lib/galaxy.datatypes.util.rst M doc/source/lib/galaxy.eggs.rst M doc/source/lib/galaxy.exceptions.rst M doc/source/lib/galaxy.external_services.result_handlers.rst M doc/source/lib/galaxy.external_services.rst M doc/source/lib/galaxy.forms.rst M doc/source/lib/galaxy.jobs.actions.rst M doc/source/lib/galaxy.jobs.deferred.rst A doc/source/lib/galaxy.jobs.metrics.collectl.rst A doc/source/lib/galaxy.jobs.metrics.instrumenters.rst A doc/source/lib/galaxy.jobs.metrics.rst M doc/source/lib/galaxy.jobs.rst R doc/source/lib/galaxy.jobs.runners.cli_job.rst R doc/source/lib/galaxy.jobs.runners.cli_shell.rst A 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doc/source/lib/galaxy.webapps.community.controllers.rst R doc/source/lib/galaxy.webapps.community.framework.middleware.rst R doc/source/lib/galaxy.webapps.community.framework.rst R doc/source/lib/galaxy.webapps.community.model.migrate.rst R doc/source/lib/galaxy.webapps.community.model.rst R doc/source/lib/galaxy.webapps.community.rst R doc/source/lib/galaxy.webapps.community.security.rst R doc/source/lib/galaxy.webapps.community.util.rst M doc/source/lib/galaxy.webapps.galaxy.api.rst M doc/source/lib/galaxy.webapps.galaxy.controllers.rst M doc/source/lib/galaxy.webapps.galaxy.rst M doc/source/lib/galaxy.webapps.reports.controllers.rst M doc/source/lib/galaxy.webapps.reports.rst M doc/source/lib/galaxy.webapps.rst M doc/source/lib/galaxy.webapps.tool_shed.api.rst M doc/source/lib/galaxy.webapps.tool_shed.controllers.rst M doc/source/lib/galaxy.webapps.tool_shed.framework.middleware.rst M doc/source/lib/galaxy.webapps.tool_shed.framework.rst M doc/source/lib/galaxy.webapps.tool_shed.model.migrate.rst M doc/source/lib/galaxy.webapps.tool_shed.model.rst M doc/source/lib/galaxy.webapps.tool_shed.rst A doc/source/lib/galaxy.webapps.tool_shed.search.rst M doc/source/lib/galaxy.webapps.tool_shed.security.rst M doc/source/lib/galaxy.webapps.tool_shed.util.rst A doc/source/lib/galaxy.work.rst M doc/source/lib/galaxy.workflow.rst A doc/source/lib/galaxy.workflow.schedulers.rst A doc/source/lib/galaxy_ext.metadata.rst A doc/source/lib/galaxy_ext.rst M doc/source/lib/galaxy_utils.rst M doc/source/lib/galaxy_utils.sequence.rst M doc/source/lib/log_tempfile.rst M doc/source/lib/mimeparse.rst M doc/source/lib/modules.rst M doc/source/lib/pkg_resources.rst M doc/source/lib/psyco_full.rst A doc/source/lib/pulsar.client.rst A doc/source/lib/pulsar.client.staging.rst A doc/source/lib/pulsar.client.transport.rst A doc/source/lib/pulsar.rst A doc/source/lib/tool_shed.capsule.rst A doc/source/lib/tool_shed.dependencies.repository.rst A doc/source/lib/tool_shed.dependencies.rst A doc/source/lib/tool_shed.dependencies.tool.rst A doc/source/lib/tool_shed.galaxy_install.datatypes.rst M doc/source/lib/tool_shed.galaxy_install.grids.rst A doc/source/lib/tool_shed.galaxy_install.metadata.rst M doc/source/lib/tool_shed.galaxy_install.migrate.rst A doc/source/lib/tool_shed.galaxy_install.repository_dependencies.rst M doc/source/lib/tool_shed.galaxy_install.rst A doc/source/lib/tool_shed.galaxy_install.tool_dependencies.recipe.rst M doc/source/lib/tool_shed.galaxy_install.tool_dependencies.rst A doc/source/lib/tool_shed.galaxy_install.tools.rst A doc/source/lib/tool_shed.galaxy_install.utility_containers.rst M doc/source/lib/tool_shed.grids.rst A doc/source/lib/tool_shed.managers.rst A doc/source/lib/tool_shed.metadata.rst A doc/source/lib/tool_shed.repository_types.rst M doc/source/lib/tool_shed.rst A doc/source/lib/tool_shed.tools.rst M doc/source/lib/tool_shed.util.rst A doc/source/lib/tool_shed.utility_containers.rst M doc/source/releases/15.05.rst M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/histories.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/s3.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/visualization/data_providers/registry.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/reports/controllers/workflows.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/api/tools.py M lib/galaxy/webapps/tool_shed/search/repo_search.py M lib/galaxy/webapps/tool_shed/search/tool_search.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py A static/maps/libs/jquery.sparklines.js.map A static/scripts/libs/jquery.sparklines.js M static/style/blue/base.css M templates/base.mako A templates/spark_base.mako M templates/webapps/reports/index.mako M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_all.mako M templates/webapps/reports/jobs_specified_month_in_error.mako M templates/webapps/reports/jobs_tool_per_month.mako M templates/webapps/reports/jobs_user_per_month.mako M templates/webapps/reports/registered_users_per_month.mako M templates/webapps/reports/registered_users_specified_month.mako M templates/webapps/reports/requests_per_month_all.mako M templates/webapps/reports/requests_per_user.mako M templates/webapps/reports/requests_user_per_month.mako M templates/webapps/reports/users_last_access_date.mako M templates/webapps/reports/users_user_disk_usage.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako M templates/webapps/reports/workflows_user_per_month.mako Log Message: ----------- Merge branch 'Reports_newpage' of https://github.com/Airistotal/galaxy into Reports_newpage Commit: 33154aaac535fcac0c1a1b6ee9aa0617736862ba https://github.com/galaxyproject/galaxy/commit/33154aaac535fcac0c1a1b6ee9aa… Author: Airistotal <daniel.bouchard(a)phac-aspc.gc.ca> Date: 2015-06-30 (Tue, 30 Jun 2015) Changed paths: M lib/galaxy/webapps/reports/controllers/workflows.py Log Message: ----------- Fixed formatting Commit: 7b794600d10f1591334a6fcf268905a7a92d3526 https://github.com/galaxyproject/galaxy/commit/7b794600d10f1591334a6fcf2689… Author: kaktus42 <vowinkel.alexander(a)gmail.com> Date: 2015-07-03 (Fri, 03 Jul 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- add error message for bad dependency declaration I got crazy identifying this error. The only error was a generic "KeyError" This will help others to detect the problem in their tool files. Commit: 679924ac86eae46e91388b8760662d42afc4507a https://github.com/galaxyproject/galaxy/commit/679924ac86eae46e91388b876066… Author: kaktus42 <vowinkel.alexander(a)gmail.com> Date: 2015-07-03 (Fri, 03 Jul 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- improve error message Commit: 9805294f9773968b2a9707a814fc41dbf596a8a0 https://github.com/galaxyproject/galaxy/commit/9805294f9773968b2a9707a814fc… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-07-12 (Sun, 12 Jul 2015) Changed paths: M .ci/pep8_sources.txt M lib/galaxy/__init__.py M lib/galaxy/dataset_collections/subcollections.py M lib/galaxy/dataset_collections/types/__init__.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/bed_to_gff_converter.py M lib/galaxy/datatypes/converters/bgzip.py M lib/galaxy/datatypes/converters/fasta_to_len.py M lib/galaxy/datatypes/converters/fasta_to_tabular_converter.py M 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lib/galaxy/webapps/galaxy/api/requests.py M lib/galaxy/webapps/galaxy/api/roles.py M lib/galaxy/webapps/galaxy/api/samples.py M lib/galaxy/webapps/galaxy/api/tool_data.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/visualizations.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/biostar.py M lib/galaxy/webapps/galaxy/controllers/data_manager.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/error.py M lib/galaxy/webapps/galaxy/controllers/external_service.py M lib/galaxy/webapps/galaxy/controllers/external_services.py M lib/galaxy/webapps/galaxy/controllers/forms.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library.py M 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lib/galaxy/webapps/tool_shed/model/migrate/versions/0022_add_repository_admin_roles.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0024_password_reset.py M lib/galaxy/webapps/tool_shed/search/repo_search.py M lib/galaxy/webapps/tool_shed/search/tool_search.py M lib/galaxy/webapps/tool_shed/security/__init__.py M lib/galaxy/webapps/tool_shed/util/hgweb_config.py M lib/galaxy/webapps/tool_shed/util/ratings_util.py M lib/galaxy/workflow/modules.py M lib/galaxy_ext/metadata/__init__.py M lib/galaxy_ext/metadata/set_metadata.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M test/api/test_dataset_collections.py M test/api/test_datasets.py M test/api/test_histories.py M test/api/test_workflow_extraction.py M test/api/test_workflows.py M test/api/yaml_to_workflow.py M test/base/twilltestcase.py M test/unit/jobs/test_job_output_checker.py M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_rules/20_instance.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HistoryManager.py M test/unit/managers/test_UserManager.py M test/unit/test_galaxy_mapping.py M test/unit/test_objectstore.py M test/unit/test_routes.py M test/unit/test_sockets.py M test/unit/tool_shed_unit_tests/test_fabric_util.py M test/unit/tool_shed_unit_tests/test_td_common_util.py M test/unit/workflows/test_extract_summary.py Log Message: ----------- Revert "Revert "[WIP] Mega flake8 linting"" This reverts commit 37f1976d38c21eb08fe38a348d6cbf435c5afd8e. Commit: 1dab5f9384fd2d7ba52a0328f3549f84ebda0645 https://github.com/galaxyproject/galaxy/commit/1dab5f9384fd2d7ba52a0328f354… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2015-07-12 (Sun, 12 Jul 2015) Changed paths: M lib/galaxy/model/migrate/versions/0001_initial_tables.py M lib/galaxy/model/migrate/versions/0002_metadata_file_table.py M lib/galaxy/model/migrate/versions/0003_security_and_libraries.py M lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py M lib/galaxy/model/migrate/versions/0027_request_events.py M lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py Log Message: ----------- revert changes to model/migrate/versions/ Commit: f1fa2ab3166d5d85cabe3e7f61cdb50226a4e222 https://github.com/galaxyproject/galaxy/commit/f1fa2ab3166d5d85cabe3e7f61cd… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2015-07-12 (Sun, 12 Jul 2015) Changed paths: M lib/galaxy/datatypes/converters/bed_to_gff_converter.py M lib/galaxy/datatypes/converters/fasta_to_len.py M lib/galaxy/datatypes/converters/fasta_to_tabular_converter.py M lib/galaxy/datatypes/converters/fastq_to_fqtoc.py M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py M lib/galaxy/datatypes/converters/gff_to_bed_converter.py M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py M lib/galaxy/datatypes/converters/interval_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/interval_to_fli.py M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py M lib/galaxy/datatypes/converters/lped_to_fped_converter.py M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py M lib/galaxy/datatypes/converters/maf_to_fasta_converter.py M lib/galaxy/datatypes/converters/maf_to_interval_converter.py M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/tool_shed/api/tools.py M lib/log_tempfile.py M lib/mimeparse.py M lib/psyco_full.py Log Message: ----------- additional linting of datatypes to make it more strict Commit: cdf089e322a74c0f8853483eda56a4d0d6a61dc0 https://github.com/galaxyproject/galaxy/commit/cdf089e322a74c0f8853483eda56… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2015-07-12 (Sun, 12 Jul 2015) Changed paths: M lib/galaxy/datatypes/converters/interval_to_coverage.py Log Message: ----------- remove unsued import Commit: f318379d67c4d31d1dd78a1f4659b9b5bd9c5ea6 https://github.com/galaxyproject/galaxy/commit/f318379d67c4d31d1dd78a1f4659… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2015-07-12 (Sun, 12 Jul 2015) Changed paths: M setup.cfg Log Message: ----------- add E402 to the exclude rules, until we can fix this Commit: 1bbff415f24d5117f9b1b83822cdc884164468f8 https://github.com/galaxyproject/galaxy/commit/1bbff415f24d5117f9b1b83822cd… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2015-07-12 (Sun, 12 Jul 2015) Changed paths: M test/functional/test_admin_features.py M test/functional/test_data_managers.py M test/functional/test_data_security.py M test/functional/test_get_data.py M test/functional/test_library_features.py M test/functional/test_library_security.py M test/functional/test_library_templates.py M test/functional/test_metadata_editing.py M test/functional/test_sample_tracking.py M test/functional/test_toolbox.py M test/functional/test_ucsc_table_browser.py M test/functional/test_user_info.py M test/functional/workflow.py Log Message: ----------- lint fixes for test/functional/ Commit: 626871c2b4d41be87c77d11d305adc48b4e4caad https://github.com/galaxyproject/galaxy/commit/626871c2b4d41be87c77d11d305a… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-07-12 (Sun, 12 Jul 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/forms.py Log Message: ----------- Fix for 6135cb5764597aa9459f3fed16fddd8701c4807f "linting lib/galaxy/webapps" . Commit: 2c61543d72490cf9ad9bec67be274e062d925018 https://github.com/galaxyproject/galaxy/commit/2c61543d72490cf9ad9bec67be27… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-07-13 (Mon, 13 Jul 2015) Changed paths: M cron/add_manual_builds.py M cron/build_chrom_db.py M cron/parse_builds_3_sites.py Log Message: ----------- Lint cron/ . Commit: 43aa5fa482dbbaca15183ca518472b94e2d831e7 https://github.com/galaxyproject/galaxy/commit/43aa5fa482dbbaca15183ca51847… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-07-13 (Mon, 13 Jul 2015) Changed paths: M client/galaxy/scripts/templates/compile_templates.py M client/galaxy/style/source_material/circle.py M lib/galaxy_ext/metadata/set_metadata.py M static/scripts/templates/compile_templates.py M tool_list.py Log Message: ----------- Lint various Python files. Commit: 5e149d01baa73ad6bb9d1018b192c92dc245dd31 https://github.com/galaxyproject/galaxy/commit/5e149d01baa73ad6bb9d1018b192… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2015-07-13 (Mon, 13 Jul 2015) Changed paths: M .ci/flake8_wrapper.sh M .ci/pep8_sources.txt Log Message: ----------- Switch over to a blacklist for linting. Commit: ab45efaba97bef7b2fec5e2e215f8a93793c8147 https://github.com/galaxyproject/galaxy/commit/ab45efaba97bef7b2fec5e2e215f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-13 (Mon, 13 Jul 2015) Changed paths: M lib/galaxy/jobs/handler.py M lib/galaxy/webapps/galaxy/api/histories.py Log Message: ----------- Fix broken sqlalchemy identity logic. Example: ``` In [3]: sa_session.query(galaxy.model.User).filter(galaxy.model.User.deleted is False).all() Out[3]: [] In [4]: sa_session.query(galaxy.model.User).filter(galaxy.model.User.deleted == False).all() Out[4]: [<galaxy.model.User at 0x1094e1610>] ``` Commit: 97ac587fedf1058b95f892531b862a3228bb896f https://github.com/galaxyproject/galaxy/commit/97ac587fedf1058b95f892531b86… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-13 (Mon, 13 Jul 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- One more sqlalchemy identity/value comparison fix. Commit: a34c5460a49a69e7d722649d9e1bdfe52d563a47 https://github.com/galaxyproject/galaxy/commit/a34c5460a49a69e7d722649d9e1b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-13 (Mon, 13 Jul 2015) Changed paths: M lib/galaxy/managers/libraries.py Log Message: ----------- Remove noqas in library manager Commit: db6786e41312dd8dbb3990d6a3a1667654d2d6d3 https://github.com/galaxyproject/galaxy/commit/db6786e41312dd8dbb3990d6a3a1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-13 (Mon, 13 Jul 2015) Changed paths: M lib/galaxy/managers/sharable.py Log Message: ----------- Remove noqas from sharable manager Commit: 2c100d715babf2f1802a0b42ea088c8f718eebbb https://github.com/galaxyproject/galaxy/commit/2c100d715babf2f1802a0b42ea08… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-13 (Mon, 13 Jul 2015) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Remove noqas from model Commit: f623e28ae9342ca30750c9c0b08120a0f24e2b4e https://github.com/galaxyproject/galaxy/commit/f623e28ae9342ca30750c9c0b081… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-13 (Mon, 13 Jul 2015) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Fix alignment in model Commit: 3df6daa52c91721c07e12dfe63c64b9c4df6d465 https://github.com/galaxyproject/galaxy/commit/3df6daa52c91721c07e12dfe63c6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-13 (Mon, 13 Jul 2015) Changed paths: M lib/galaxy/security/__init__.py Log Message: ----------- Various fixes and removal of noqas in security module Commit: cb5593f840d51be2802cb5603dda21b67bb94e0b https://github.com/galaxyproject/galaxy/commit/cb5593f840d51be2802cb5603dda… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-13 (Mon, 13 Jul 2015) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Noqa sqlalchemy fix in base controller. Commit: 8a031fb2906d301f0c524b3b8a228760212793b9 https://github.com/galaxyproject/galaxy/commit/8a031fb2906d301f0c524b3b8a22… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-13 (Mon, 13 Jul 2015) Changed paths: M lib/galaxy/web/base/controllers/admin.py Log Message: ----------- sqlalchemy expressions in admin controller Commit: e68e81dc675468aff96060e8005ca4afb93265b7 https://github.com/galaxyproject/galaxy/commit/e68e81dc675468aff96060e8005c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-13 (Mon, 13 Jul 2015) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- sqlalchemy expressions in grids helper Commit: 589dad6205f4a2c9870a8cd78a39b20099909597 https://github.com/galaxyproject/galaxy/commit/589dad6205f4a2c9870a8cd78a39… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-13 (Mon, 13 Jul 2015) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- pep8'd and noqa removal of framework/webapp Commit: b8b34cef60470a215c97c422be921bbf7f333841 https://github.com/galaxyproject/galaxy/commit/b8b34cef60470a215c97c422be92… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-13 (Mon, 13 Jul 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/groups.py Log Message: ----------- noqa removal in api/groups Commit: e0d38ae662a1b5d1016f01691a026b7828d68075 https://github.com/galaxyproject/galaxy/commit/e0d38ae662a1b5d1016f01691a02… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-13 (Mon, 13 Jul 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/histories.py Log Message: ----------- noqa removal in api/histories Commit: e1bbbe5ae800237bbfc4bbfa874b5299f3d0e0cf https://github.com/galaxyproject/galaxy/commit/e1bbbe5ae800237bbfc4bbfa874b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-13 (Mon, 13 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/style/less/trackster.less M lib/galaxy/tools/deps/__init__.py M lib/galaxy/util/streamball.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/tools.py M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/viz/trackster/tracks.js.map M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/viz/trackster/tracks.js M static/style/blue/trackster.css M tools/stats/grouping.py Log Message: ----------- Merge branch 'dev' into lint-additions Commit: 1f62be4e1aec00a82b4c66209d486ebda695554a https://github.com/galaxyproject/galaxy/commit/1f62be4e1aec00a82b4c66209d48… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-13 (Mon, 13 Jul 2015) Changed paths: M .ci/pep8_sources.txt M lib/galaxy/datatypes/converters/lped_to_fped_converter.py M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py Log Message: ----------- Fix lped converters and remove from flake8 blacklist Commit: 29c4f1ae8537cea25bb43e02d4bbf697697b3e65 https://github.com/galaxyproject/galaxy/commit/29c4f1ae8537cea25bb43e02d4bb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-13 (Mon, 13 Jul 2015) Changed paths: M .ci/pep8_sources.txt M lib/galaxy/model/mapping.py Log Message: ----------- Clean up model.mapping. TODO: this made it compliant, still needs a pass to make it consistent. Commit: 6569c2dcc37f880c0628d320932fb96e01ee8930 https://github.com/galaxyproject/galaxy/commit/6569c2dcc37f880c0628d320932f… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-07-13 (Mon, 13 Jul 2015) Changed paths: M .ci/pep8_sources.txt M scripts/build_toolbox.py M scripts/build_universe_config.py M scripts/check_eggs.py M scripts/check_galaxy.py M scripts/check_python.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.py M scripts/cleanup_datasets/populate_uuid.py M scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py M scripts/cleanup_datasets/rename_purged_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M scripts/cleanup_datasets/update_metadata.py M scripts/db_shell.py M scripts/dist-scramble.py M scripts/drmaa_external_killer.py M scripts/drmaa_external_runner.py M scripts/edam_mapping.py M scripts/egg_packager_template.py M scripts/external_chown_script.py M scripts/extract_dataset_part.py M scripts/extract_toolbox_sections.py M scripts/fetch_eggs.py M scripts/functional_tests.py M scripts/get_platforms.py M scripts/helper.py M scripts/make_egg_packager.py M scripts/metagenomics/convert_title.py M scripts/migrate_tools/migrate_tools.py M scripts/nosetests.py M scripts/paster.py M scripts/runtime_stats.py M scripts/scramble.py M scripts/set_dataset_sizes.py M scripts/set_metadata.py M scripts/set_user_disk_usage.py M scripts/sync_reports_config.py M scripts/test_dist_egg.py M scripts/update_shed_config_path.py Log Message: ----------- Partially lint scripts/ . Commit: be6cce14dc147c27827d96c427b54385427cd376 https://github.com/galaxyproject/galaxy/commit/be6cce14dc147c27827d96c427b5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-13 (Mon, 13 Jul 2015) Changed paths: M tools/stats/grouping.py Log Message: ----------- Merge branch 'dev' into lint-additions Commit: bbd31f70f165c860100bff4d892f8d96d7236e75 https://github.com/galaxyproject/galaxy/commit/bbd31f70f165c860100bff4d892f… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-07-14 (Tue, 14 Jul 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Add regex_replace tool dependency action. Commit: 34d93884562c0bd37c27278bed55a030a0ebc9d1 https://github.com/galaxyproject/galaxy/commit/34d93884562c0bd37c27278bed55… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-07-14 (Tue, 14 Jul 2015) Changed paths: M lib/galaxy/eggs/__init__.py M lib/tool_shed/scripts/api/common.py M scripts/api/common.py M scripts/bootstrap_history.py M scripts/check_eggs.py M scripts/check_galaxy.py M scripts/cleanup_datasets/pgcleanup.py M scripts/cleanup_datasets/update_metadata.py M scripts/db_shell.py M scripts/dist-scramble.py M scripts/edam_mapping.py M scripts/fetch_eggs.py M scripts/get_platforms.py M scripts/helper.py M scripts/make_egg_packager.py M scripts/scramble.py M scripts/scramble/lib/scramble_lib.py M scripts/scramble/scripts/DRMAA_python-macosx.py M scripts/scramble/scripts/DRMAA_python-solaris.py M scripts/scramble/scripts/DRMAA_python.py M scripts/scramble/scripts/MySQL_python-solaris.py M scripts/scramble/scripts/MySQL_python.py M scripts/scramble/scripts/PyRods.py M scripts/scramble/scripts/bx_python-solaris.py M scripts/scramble/scripts/generic.py M scripts/scramble/scripts/pbs_python.py M scripts/scramble/scripts/psycopg2-linux.py M scripts/scramble/scripts/psycopg2-macosx.py M scripts/scramble/scripts/psycopg2-solaris.py M scripts/scramble/scripts/psycopg2.py M scripts/scramble/scripts/pysam-solaris.py M scripts/scramble/scripts/pysqlite.py M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.py M scripts/summarize_timings.py M scripts/test_dist_egg.py M scripts/transfer.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M tools/data_source/data_source.py Log Message: ----------- Use os.pardir everywhere instead of '..' . Commit: f80c7f88f96fd4a8e0c23599bef43477dd3909f5 https://github.com/galaxyproject/galaxy/commit/f80c7f88f96fd4a8e0c23599bef4… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-07-14 (Tue, 14 Jul 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Add documentation to the execute_step method. Commit: 938361cee04436c78b0729aed87f2646a34913dd https://github.com/galaxyproject/galaxy/commit/938361cee04436c78b0729aed87f… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-07-14 (Tue, 14 Jul 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Improved memory usage for regex_replace action. Commit: cc9b0bed85696191f4a1acf94e5da7fd6bb278f4 https://github.com/galaxyproject/galaxy/commit/cc9b0bed85696191f4a1acf94e5d… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-07-14 (Tue, 14 Jul 2015) Changed paths: M .ci/pep8_sources.txt M contrib/nagios/check_galaxy.py M doc/patch.py M lib/galaxy/managers/libraries.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py M lib/galaxy/model/orm/__init__.py M lib/galaxy/model/orm/logging_connection_proxy.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/quotas.py M lib/galaxy/webapps/galaxy/api/requests.py M lib/galaxy/webapps/galaxy/api/roles.py M lib/galaxy/webapps/galaxy/api/samples.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/external_service.py M lib/galaxy/webapps/galaxy/controllers/forms.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library.py M lib/galaxy/webapps/galaxy/controllers/library_admin.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/request_type.py M lib/galaxy/webapps/galaxy/controllers/requests.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py M lib/galaxy/webapps/galaxy/controllers/requests_common.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/userskeys.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/reports/controllers/sample_tracking.py M lib/galaxy/webapps/reports/controllers/system.py M lib/galaxy/webapps/reports/controllers/users.py M lib/galaxy/webapps/reports/controllers/workflows.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/api/repository_revisions.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/controllers/repository_review.py M lib/galaxy/webapps/tool_shed/model/mapping.py M lib/galaxy/webapps/tool_shed/security/__init__.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/installed_repository_manager.py M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/galaxy_install/update_repository_manager.py M lib/tool_shed/grids/admin_grids.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/repository_review_grids.py M lib/tool_shed/managers/groups.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/repository_registry.py M lib/tool_shed/scripts/check_repositories_for_functional_tests.py M lib/tool_shed/scripts/check_tool_dependency_definition_repositories.py M lib/tool_shed/scripts/deprecate_repositories_without_metadata.py M lib/tool_shed/tools/tool_version_manager.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/review_util.py M lib/tool_shed/util/search_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_dependency_util.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/microbes/BeautifulSoup.py M scripts/microbes/create_bacteria_table.py M test/base/test_db_util.py M test/base/twilltestcase.py M test/functional/test_metadata_editing.py M test/install_and_test_tool_shed_repositories/base/test_db_util.py M test/tool_shed/base/test_db_util.py M test/unit/managers/test_HistoryManager.py M tools/phenotype_association/pagetag.py M tools/phenotype_association/senatag.py Log Message: ----------- Fix all E712 errors. Standardize sqlalchemy imports. Commit: a46ddd12211b6a0a33f19204095ac077062975ef https://github.com/galaxyproject/galaxy/commit/a46ddd12211b6a0a33f19204095a… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-07-15 (Wed, 15 Jul 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Minor cleanup to regex_replace. - Iterate through the input file in a more pythonic way. - Flush the output file, just in case. Commit: f8f36620ecb0c9b686dca6054c5f7fdb6ae8eff6 https://github.com/galaxyproject/galaxy/commit/f8f36620ecb0c9b686dca6054c5f… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2015-07-15 (Wed, 15 Jul 2015) Changed paths: M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/ipython/templates/ipython.mako Log Message: ----------- Fix issue with docker not being able to mount tmp dir Commit: de1cb4773040a8bfbce6abafffc2e5a3b241d992 https://github.com/galaxyproject/galaxy/commit/de1cb4773040a8bfbce6abafffc2… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2015-07-15 (Wed, 15 Jul 2015) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- More verbose communication on running the docker container Commit: d31822e6d48d80c737bfa210eb7b3f4a81bb2c29 https://github.com/galaxyproject/galaxy/commit/d31822e6d48d80c737bfa210eb7b… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-07-15 (Wed, 15 Jul 2015) Changed paths: M client/galaxy/scripts/utils/config.js M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/tracks.js M static/maps/utils/config.js.map M static/maps/viz/trackster/painters.js.map M static/maps/viz/trackster/tracks.js.map M static/scripts/utils/config.js M static/scripts/viz/trackster/painters.js M static/scripts/viz/trackster/tracks.js Log Message: ----------- Trackster, chromosome interaction: fix display of chrint files in trackster, do not apply config default_value if explicitly set to undefined, clean line endings Commit: dab8f4219519cdfc3967f25215b4b5c351b4253b https://github.com/galaxyproject/galaxy/commit/dab8f4219519cdfc3967f25215b4… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-07-15 (Wed, 15 Jul 2015) Changed paths: A client/galaxy/scripts/libs/snap.svg.js A lib/galaxy/webapps/reports/controllers/home.py A static/maps/libs/snap.svg.js.map A static/scripts/libs/snap.svg.js M templates/base.mako M templates/webapps/reports/index.mako A templates/webapps/reports/run_stats.mako Log Message: ----------- Added tool tips Changed titles to be more descriptive Commit: fadd1990e6e7f32f3298014c1aa6dcee4b8bc063 https://github.com/galaxyproject/galaxy/commit/fadd1990e6e7f32f3298014c1aa6… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2015-07-15 (Wed, 15 Jul 2015) Changed paths: M config/plugins/interactive_environments/ipython/templates/ipython.mako M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- moved changes to lib/galaxy/web/base/interactive_environments.py Commit: faca35f5ab2810ca0bcf79f73c2539cd5a34d85b https://github.com/galaxyproject/galaxy/commit/faca35f5ab2810ca0bcf79f73c25… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2015-07-15 (Wed, 15 Jul 2015) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- fixed travis complains - i think Commit: a0cd5b7410c0136c874649bdc41f5c7e6a369e46 https://github.com/galaxyproject/galaxy/commit/a0cd5b7410c0136c874649bdc41f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-07-16 (Thu, 16 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/upload/upload-button.js A client/galaxy/scripts/mvc/upload/upload-view-default.js M client/galaxy/scripts/mvc/upload/upload-view.js M static/maps/mvc/upload/upload-button.js.map A static/maps/mvc/upload/upload-view-default.js.map M static/maps/mvc/upload/upload-view.js.map M static/scripts/mvc/upload/upload-button.js A static/scripts/mvc/upload/upload-view-default.js M static/scripts/mvc/upload/upload-view.js Log Message: ----------- [WIP] Separate upload modal and default upload view, insert tabs Commit: 4d0243e7153b7333a316f00257e357d837307adf https://github.com/galaxyproject/galaxy/commit/4d0243e7153b7333a316f00257e3… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-07-16 (Thu, 16 Jul 2015) Changed paths: M client/galaxy/style/less/base.less A static/images/reports_webapp/bases/home-icon-active.png A static/images/reports_webapp/bases/home-icon-hov.png A static/images/reports_webapp/bases/home-icon.png A static/images/reports_webapp/home-icon-active.png A static/images/reports_webapp/home-icon-hov.png A static/images/reports_webapp/home-icon.png M static/style/blue/base.css M templates/webapps/reports/index.mako M templates/webapps/reports/run_stats.mako Log Message: ----------- Added home button to go back to the homepage Commit: c900528fe27259282a66fc6a33c6526dbf94d109 https://github.com/galaxyproject/galaxy/commit/c900528fe27259282a66fc6a33c6… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-07-16 (Thu, 16 Jul 2015) Changed paths: M client/galaxy/style/less/base.less M static/style/blue/base.css M templates/webapps/reports/index.mako Log Message: ----------- Moved css style to base.less Commit: 923f7b085cdefc5073d3d00802e1e0f964c53414 https://github.com/galaxyproject/galaxy/commit/923f7b085cdefc5073d3d00802e1… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-07-16 (Thu, 16 Jul 2015) Changed paths: M lib/galaxy/webapps/reports/controllers/home.py M templates/webapps/reports/run_stats.mako Log Message: ----------- Fixed UTC vs. CST time problems Fixed formatting issues for charts Commit: 664897e9c6b19bdaa5376abc5940b1799bcb2bad https://github.com/galaxyproject/galaxy/commit/664897e9c6b19bdaa5376abc5940… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-07-16 (Thu, 16 Jul 2015) Changed paths: M .ci/pep8_sources.txt M lib/galaxy/webapps/reports/controllers/home.py Log Message: ----------- Added home.py to the flake test Fixed home.py to be compliant with flake tests Commit: 7019e32305c2a71ef9b20f327e78603b04612a8f https://github.com/galaxyproject/galaxy/commit/7019e32305c2a71ef9b20f327e78… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-17 (Fri, 17 Jul 2015) Changed paths: A lib/galaxy/auth/providers/pam_auth.py A lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parser/xml.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py A scripts/auth/pam_auth_helper.py M templates/show_params.mako A test/functional/tools/output_collection_filter.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge with dev Commit: 345c86d8ef4a742af33ddc337728b1841e31d213 https://github.com/galaxyproject/galaxy/commit/345c86d8ef4a742af33ddc337728… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-17 (Fri, 17 Jul 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- More fixes for toolshed step handler post-merge. Commit: c18887c0d193fbba9631081af88e54e626735621 https://github.com/galaxyproject/galaxy/commit/c18887c0d193fbba9631081af88e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-17 (Fri, 17 Jul 2015) Changed paths: M scripts/auth/pam_auth_helper.py Log Message: ----------- Clean up pam auth helper. Commit: 223583470bffb56571a41f10ea993126036e3de7 https://github.com/galaxyproject/galaxy/commit/223583470bffb56571a41f10ea99… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-17 (Fri, 17 Jul 2015) Changed paths: M .ci/flake8_wrapper.sh M .ci/pep8_sources.txt M client/galaxy/scripts/templates/compile_templates.py M client/galaxy/style/source_material/circle.py M contrib/nagios/check_galaxy.py M cron/add_manual_builds.py M cron/build_chrom_db.py M cron/parse_builds_3_sites.py M doc/patch.py M lib/galaxy/__init__.py M lib/galaxy/dataset_collections/subcollections.py M lib/galaxy/dataset_collections/types/__init__.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/bed_to_gff_converter.py M lib/galaxy/datatypes/converters/bgzip.py M lib/galaxy/datatypes/converters/fasta_to_len.py M lib/galaxy/datatypes/converters/fasta_to_tabular_converter.py M lib/galaxy/datatypes/converters/fastq_to_fqtoc.py M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py M lib/galaxy/datatypes/converters/gff_to_bed_converter.py M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py M lib/galaxy/datatypes/converters/interval_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/interval_to_fli.py M lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py M lib/galaxy/datatypes/converters/lped_to_fped_converter.py M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py M lib/galaxy/datatypes/converters/maf_to_fasta_converter.py M lib/galaxy/datatypes/converters/maf_to_interval_converter.py M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py M lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/dataproviders/__init__.py M lib/galaxy/datatypes/dataproviders/base.py M lib/galaxy/datatypes/dataproviders/chunk.py M lib/galaxy/datatypes/dataproviders/column.py M lib/galaxy/datatypes/dataproviders/dataset.py M lib/galaxy/datatypes/dataproviders/decorators.py M lib/galaxy/datatypes/dataproviders/external.py M lib/galaxy/datatypes/dataproviders/hierarchy.py M lib/galaxy/datatypes/dataproviders/line.py M lib/galaxy/datatypes/display_applications/application.py M lib/galaxy/datatypes/display_applications/parameters.py M lib/galaxy/datatypes/genetics.py M 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Log Message: ----------- Merge pull request #454 from bgruening/lint-additions General cleanup, flake8 monster PR Commit: 1b23081d41e28eccbd1f6dc4326e8f8340ba73c0 https://github.com/galaxyproject/galaxy/commit/1b23081d41e28eccbd1f6dc4326e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-07-17 (Fri, 17 Jul 2015) Changed paths: M client/galaxy/style/less/base.less A client/galaxy/style/less/reports.less M client/grunt-tasks/style.js M static/style/blue/base.css A static/style/blue/reports.css M templates/webapps/reports/base_panels.mako Log Message: ----------- Refactor reports styling out into its own less file. This was it doesn't need to be loaded for Galaxy. Commit: 7719ea7ea8f791968673d410bd7cb63b2104da71 https://github.com/galaxyproject/galaxy/commit/7719ea7ea8f791968673d410bd7c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-07-17 (Fri, 17 Jul 2015) Changed paths: M .ci/flake8_wrapper.sh M .ci/pep8_sources.txt M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/templates/compile_templates.py M client/galaxy/scripts/utils/config.js M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/style/less/trackster.less M client/galaxy/style/source_material/circle.py M config/datatypes_conf.xml.sample M config/object_store_conf.xml.sample M config/plugins/interactive_environments/ipython/templates/ipython.mako M config/plugins/visualizations/charts/static/build-app.js M config/plugins/visualizations/charts/static/charts/nvd3/histogram/config.js M config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/config.js M config/plugins/visualizations/charts/static/views/editor.js M config/plugins/visualizations/charts/static/views/viewport.js M contrib/nagios/check_galaxy.py M cron/add_manual_builds.py M cron/build_chrom_db.py M cron/parse_builds_3_sites.py M doc/patch.py A doc/source/api_doc.rst M doc/source/conf.py M doc/source/index.rst R doc/source/lib/fpconst.rst M doc/source/lib/galaxy.actions.rst A doc/source/lib/galaxy.auth.providers.rst A doc/source/lib/galaxy.auth.rst A doc/source/lib/galaxy.dataset_collections.rst A doc/source/lib/galaxy.dataset_collections.types.rst M doc/source/lib/galaxy.datatypes.converters.rst A doc/source/lib/galaxy.datatypes.dataproviders.rst M doc/source/lib/galaxy.datatypes.display_applications.rst M doc/source/lib/galaxy.datatypes.rst M doc/source/lib/galaxy.datatypes.util.rst M doc/source/lib/galaxy.eggs.rst M doc/source/lib/galaxy.exceptions.rst M doc/source/lib/galaxy.external_services.result_handlers.rst M doc/source/lib/galaxy.external_services.rst M doc/source/lib/galaxy.forms.rst M doc/source/lib/galaxy.jobs.actions.rst M doc/source/lib/galaxy.jobs.deferred.rst A doc/source/lib/galaxy.jobs.metrics.collectl.rst A doc/source/lib/galaxy.jobs.metrics.instrumenters.rst A doc/source/lib/galaxy.jobs.metrics.rst M doc/source/lib/galaxy.jobs.rst R doc/source/lib/galaxy.jobs.runners.cli_job.rst R doc/source/lib/galaxy.jobs.runners.cli_shell.rst A doc/source/lib/galaxy.jobs.runners.lwr_client.rst A doc/source/lib/galaxy.jobs.runners.lwr_client.staging.rst A doc/source/lib/galaxy.jobs.runners.lwr_client.transport.rst M doc/source/lib/galaxy.jobs.runners.rst A doc/source/lib/galaxy.jobs.runners.state_handlers.rst A doc/source/lib/galaxy.jobs.runners.util.cli.job.rst A doc/source/lib/galaxy.jobs.runners.util.cli.rst A doc/source/lib/galaxy.jobs.runners.util.cli.shell.rst A doc/source/lib/galaxy.jobs.runners.util.condor.rst A doc/source/lib/galaxy.jobs.runners.util.job_script.rst A doc/source/lib/galaxy.jobs.runners.util.rst M doc/source/lib/galaxy.jobs.splitters.rst M doc/source/lib/galaxy.managers.rst M doc/source/lib/galaxy.model.migrate.rst R doc/source/lib/galaxy.model.orm.ext.rst M doc/source/lib/galaxy.model.orm.rst M doc/source/lib/galaxy.model.rst A doc/source/lib/galaxy.model.tool_shed_install.migrate.rst A doc/source/lib/galaxy.model.tool_shed_install.rst M doc/source/lib/galaxy.objectstore.rst M doc/source/lib/galaxy.openid.rst M doc/source/lib/galaxy.quota.rst M doc/source/lib/galaxy.rst M doc/source/lib/galaxy.sample_tracking.rst M doc/source/lib/galaxy.security.rst M doc/source/lib/galaxy.tags.rst R doc/source/lib/galaxy.tool_shed.migrate.rst R doc/source/lib/galaxy.tool_shed.rst R doc/source/lib/galaxy.tool_shed.tool_dependencies.rst M doc/source/lib/galaxy.tools.actions.rst M doc/source/lib/galaxy.tools.data.rst A doc/source/lib/galaxy.tools.data_manager.rst A doc/source/lib/galaxy.tools.deps.resolvers.rst M doc/source/lib/galaxy.tools.deps.rst A doc/source/lib/galaxy.tools.filters.rst R doc/source/lib/galaxy.tools.genome_index.rst M doc/source/lib/galaxy.tools.imp_exp.rst A doc/source/lib/galaxy.tools.linters.rst M doc/source/lib/galaxy.tools.parameters.rst A doc/source/lib/galaxy.tools.parser.rst M doc/source/lib/galaxy.tools.rst M doc/source/lib/galaxy.tools.search.rst A doc/source/lib/galaxy.tools.toolbox.filters.rst A doc/source/lib/galaxy.tools.toolbox.lineages.rst A doc/source/lib/galaxy.tools.toolbox.rst M doc/source/lib/galaxy.tools.util.galaxyops.rst M doc/source/lib/galaxy.tools.util.rst M doc/source/lib/galaxy.util.backports.importlib.rst M doc/source/lib/galaxy.util.backports.rst A doc/source/lib/galaxy.util.log.rst A doc/source/lib/galaxy.util.pastescript.rst M doc/source/lib/galaxy.util.rst M doc/source/lib/galaxy.visualization.data_providers.phyloviz.rst M doc/source/lib/galaxy.visualization.data_providers.rst M doc/source/lib/galaxy.visualization.genome.rst A doc/source/lib/galaxy.visualization.plugins.rst M doc/source/lib/galaxy.visualization.rst M doc/source/lib/galaxy.visualization.tracks.rst M doc/source/lib/galaxy.web.base.controllers.rst M doc/source/lib/galaxy.web.base.rst M doc/source/lib/galaxy.web.framework.helpers.rst M doc/source/lib/galaxy.web.framework.middleware.rst M doc/source/lib/galaxy.web.framework.rst A doc/source/lib/galaxy.web.proxy.rst M doc/source/lib/galaxy.web.rst M doc/source/lib/galaxy.web.security.rst R doc/source/lib/galaxy.webapps.community.controllers.rst R doc/source/lib/galaxy.webapps.community.framework.middleware.rst R doc/source/lib/galaxy.webapps.community.framework.rst R doc/source/lib/galaxy.webapps.community.model.migrate.rst R doc/source/lib/galaxy.webapps.community.model.rst R doc/source/lib/galaxy.webapps.community.rst R doc/source/lib/galaxy.webapps.community.security.rst R doc/source/lib/galaxy.webapps.community.util.rst M doc/source/lib/galaxy.webapps.galaxy.api.rst M doc/source/lib/galaxy.webapps.galaxy.controllers.rst M doc/source/lib/galaxy.webapps.galaxy.rst M doc/source/lib/galaxy.webapps.reports.controllers.rst M doc/source/lib/galaxy.webapps.reports.rst M doc/source/lib/galaxy.webapps.rst M doc/source/lib/galaxy.webapps.tool_shed.api.rst M doc/source/lib/galaxy.webapps.tool_shed.controllers.rst M doc/source/lib/galaxy.webapps.tool_shed.framework.middleware.rst M doc/source/lib/galaxy.webapps.tool_shed.framework.rst M doc/source/lib/galaxy.webapps.tool_shed.model.migrate.rst M doc/source/lib/galaxy.webapps.tool_shed.model.rst M doc/source/lib/galaxy.webapps.tool_shed.rst A doc/source/lib/galaxy.webapps.tool_shed.search.rst M doc/source/lib/galaxy.webapps.tool_shed.security.rst M doc/source/lib/galaxy.webapps.tool_shed.util.rst A doc/source/lib/galaxy.work.rst M doc/source/lib/galaxy.workflow.rst A doc/source/lib/galaxy.workflow.schedulers.rst A doc/source/lib/galaxy_ext.metadata.rst A doc/source/lib/galaxy_ext.rst M doc/source/lib/galaxy_utils.rst M doc/source/lib/galaxy_utils.sequence.rst M doc/source/lib/log_tempfile.rst M doc/source/lib/mimeparse.rst M doc/source/lib/modules.rst M doc/source/lib/pkg_resources.rst M doc/source/lib/psyco_full.rst A doc/source/lib/pulsar.client.rst A doc/source/lib/pulsar.client.staging.rst A doc/source/lib/pulsar.client.transport.rst A doc/source/lib/pulsar.rst A doc/source/lib/tool_shed.capsule.rst A doc/source/lib/tool_shed.dependencies.repository.rst A doc/source/lib/tool_shed.dependencies.rst A doc/source/lib/tool_shed.dependencies.tool.rst A doc/source/lib/tool_shed.galaxy_install.datatypes.rst M doc/source/lib/tool_shed.galaxy_install.grids.rst A doc/source/lib/tool_shed.galaxy_install.metadata.rst M doc/source/lib/tool_shed.galaxy_install.migrate.rst A 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M test/functional/workflow.py M test/install_and_test_tool_shed_repositories/base/test_db_util.py M test/tool_shed/base/test_db_util.py M test/unit/jobs/test_job_output_checker.py M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_rules/20_instance.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HistoryManager.py M test/unit/managers/test_UserManager.py M test/unit/test_galaxy_mapping.py M test/unit/test_objectstore.py M test/unit/test_routes.py M test/unit/test_sockets.py M test/unit/tool_shed_unit_tests/test_fabric_util.py M test/unit/tool_shed_unit_tests/test_td_common_util.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/workflows/test_extract_summary.py M tool_list.py M tools/data_source/data_source.py M tools/phenotype_association/pagetag.py M tools/phenotype_association/senatag.py M tools/stats/grouping.py Log Message: ----------- Merge remote-tracking branch 'galaxyproject/dev' into Reports_homepage Conflicts: .ci/pep8_sources.txt Commit: 9e2e909d3e5a10e6fc08ae4b82a98273d21481af https://github.com/galaxyproject/galaxy/commit/9e2e909d3e5a10e6fc08ae4b82a9… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-07-17 (Fri, 17 Jul 2015) Changed paths: M client/galaxy/style/less/base.less M client/galaxy/style/less/galaxy_bootstrap/variables.less M client/galaxy/style/less/history.less M client/grunt-tasks/style.js M client/package.json M static/style/blue/autocomplete_tagging.css M static/style/blue/base.css M static/style/blue/circster.css M static/style/blue/embed_item.css M static/style/blue/iphone.css M static/style/blue/library.css M static/style/blue/masthead.css M static/style/blue/sprite-fugue.png M static/style/blue/sprite-history-buttons.png M static/style/blue/sprite-history-states.png M static/style/blue/trackster.css Log Message: ----------- Client build: update style tools: grunt-contrib-less to 1.0, grunt-spritesmith to 4.7, fixes NameError with grunt style on node > 0.10, update galaxy_bootstrap/variables for different(?) lighten/saturate Commit: 70ef7e55615d7f5ffc0660ff06c9d122a07ceb35 https://github.com/galaxyproject/galaxy/commit/70ef7e55615d7f5ffc0660ff06c9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-07-17 (Fri, 17 Jul 2015) Changed paths: M client/galaxy/scripts/utils/config.js M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/tracks.js M static/maps/utils/config.js.map M static/maps/viz/trackster/painters.js.map M static/maps/viz/trackster/tracks.js.map M static/scripts/utils/config.js M static/scripts/viz/trackster/painters.js M static/scripts/viz/trackster/tracks.js Log Message: ----------- Merge pull request #463 from carlfeberhard/fix.trackster-chrint Trackster, chromosome interaction: fix display of chrint files in tra… Commit: be3bd7a2964dfaa052016f2687cb5dcd39e8aa77 https://github.com/galaxyproject/galaxy/commit/be3bd7a2964dfaa052016f2687cb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-07-17 (Fri, 17 Jul 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #419 from kaktus42/error_specification add error message for bad dependency declaration Commit: ef55279d58eced4b90632a572a8fc5a227ceefb9 https://github.com/galaxyproject/galaxy/commit/ef55279d58eced4b90632a572a8f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-07-17 (Fri, 17 Jul 2015) Changed paths: M client/galaxy/style/less/base.less M client/galaxy/style/less/galaxy_bootstrap/variables.less M client/galaxy/style/less/history.less M client/grunt-tasks/style.js M client/package.json M static/style/blue/autocomplete_tagging.css M static/style/blue/base.css M static/style/blue/circster.css M static/style/blue/embed_item.css M static/style/blue/iphone.css M static/style/blue/library.css M static/style/blue/masthead.css M static/style/blue/sprite-fugue.png M static/style/blue/sprite-history-buttons.png M static/style/blue/sprite-history-states.png M static/style/blue/trackster.css Log Message: ----------- Merge pull request #473 from carlfeberhard/update.spritesmith-less Client build: update style tools: grunt-contrib-less to 1.0, grunt-sp… Commit: 6ab9c524843f5f8b863a77fc8e76c9ddbcff436a https://github.com/galaxyproject/galaxy/commit/6ab9c524843f5f8b863a77fc8e76… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-07-17 (Fri, 17 Jul 2015) Changed paths: R client/galaxy/scripts/libs/snap.svg.js A client/galaxy/scripts/reports_webapp/run_stats.js M client/galaxy/style/less/base.less R static/maps/libs/snap.svg.js.map A static/maps/reports_webapp/run_stats.js.map R static/scripts/libs/snap.svg.js A static/scripts/reports_webapp/run_stats.js M static/style/blue/base.css M templates/base.mako M templates/webapps/reports/run_stats.mako Log Message: ----------- Removed Snap.svg.js Moved style to correct place in client Moved script to correct place in client Commit: a114a8c70f7032929b6e9d142911161cb9731ca2 https://github.com/galaxyproject/galaxy/commit/a114a8c70f7032929b6e9d142911… Author: Daniel <danieltos.bouchard(a)gmail.com> Date: 2015-07-17 (Fri, 17 Jul 2015) Changed paths: M client/galaxy/style/less/base.less A client/galaxy/style/less/reports.less M client/grunt-tasks/style.js M static/style/blue/base.css A static/style/blue/reports.css M templates/webapps/reports/base_panels.mako Log Message: ----------- Merge pull request #1 from jmchilton/reports_newpage_2 Refactor reports styling out into its own less file. 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Message: ----------- Merge pull request #2 from jmchilton/Reports_homepage Merge Reports_homepage against latest dev. Commit: 2a04abe7eac0272776ff81afa121603fedcbdf3d https://github.com/galaxyproject/galaxy/commit/2a04abe7eac0272776ff81afa121… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-07-17 (Fri, 17 Jul 2015) Changed paths: M client/galaxy/scripts/reports_webapp/run_stats.js M static/maps/reports_webapp/run_stats.js.map M static/scripts/reports_webapp/run_stats.js Log Message: ----------- Removed remnant of failed update Commit: 753b5a49830d450824a6669067b75ad6f23c2fbc https://github.com/galaxyproject/galaxy/commit/753b5a49830d450824a6669067b7… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-07-17 (Fri, 17 Jul 2015) Changed paths: M .ci/flake8_wrapper.sh M .ci/pep8_sources.txt M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M 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test/unit/managers/test_UserManager.py M test/unit/test_galaxy_mapping.py M test/unit/test_objectstore.py M test/unit/test_routes.py M test/unit/test_sockets.py M test/unit/tool_shed_unit_tests/test_fabric_util.py M test/unit/tool_shed_unit_tests/test_td_common_util.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/workflows/test_extract_summary.py M tool_list.py M tools/data_source/data_source.py M tools/phenotype_association/pagetag.py M tools/phenotype_association/senatag.py M tools/stats/grouping.py Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into Reports_newpage Conflicts: lib/galaxy/webapps/reports/controllers/jobs.py lib/galaxy/webapps/reports/controllers/workflows.py Commit: 7e6198a8f7f3794167a30526a2123b3045ce2056 https://github.com/galaxyproject/galaxy/commit/7e6198a8f7f3794167a30526a212… Author: Airistotal <danieltos.bouchard(a)gmail.com> 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test/unit/tools/test_evaluation.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_tool_dependency_description.py M test/unit/tools/test_tool_deps.py M test/unit/tools/test_tool_loader.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/workflows/test_extract_summary.py M tool_list.py M tools/data_source/data_source.py M tools/data_source/upload.py M tools/evolution/codingSnps_filter.py M tools/phenotype_association/pagetag.py M tools/phenotype_association/senatag.py M tools/stats/grouping.py Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into Reports_Paginate Conflicts: lib/galaxy/webapps/reports/controllers/jobs.py Commit: e7eb7686ac2a2ce5605e9d440b0a5e595a2f91ff https://github.com/galaxyproject/galaxy/commit/e7eb7686ac2a2ce5605e9d440b0a… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-07-17 (Fri, 17 Jul 2015) Changed paths: M lib/galaxy/webapps/reports/controllers/jobs.py Log Message: ----------- Fix imports Commit: 1ac9e5f05492e16a0cdd1409875efb6aec94d9cd https://github.com/galaxyproject/galaxy/commit/1ac9e5f05492e16a0cdd1409875e… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-07-17 (Fri, 17 Jul 2015) Changed paths: M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/reports/controllers/workflows.py Log Message: ----------- Fixed import clash Commit: 6f4eeb28e3ea8bba34e80b6543b837f2ee834a5b https://github.com/galaxyproject/galaxy/commit/6f4eeb28e3ea8bba34e80b6543b8… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-07-17 (Fri, 17 Jul 2015) Changed paths: M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/reports/controllers/workflows.py Log Message: ----------- Removed duplicate import Commit: 3811c43eb9786c5df596102b74a09ce523071845 https://github.com/galaxyproject/galaxy/commit/3811c43eb9786c5df596102b74a0… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-07-17 (Fri, 17 Jul 2015) Changed paths: M lib/galaxy/webapps/reports/controllers/jobs.py Log Message: ----------- Fixed duplicate imports Commit: f42981810af88c46da482cba940b3c580ee3b193 https://github.com/galaxyproject/galaxy/commit/f42981810af88c46da482cba940b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-07-17 (Fri, 17 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/upload/upload-view-default.js M client/galaxy/scripts/mvc/upload/upload-view.js M static/maps/mvc/ui/ui-misc.js.map M static/maps/mvc/upload/upload-view-default.js.map M static/maps/mvc/upload/upload-view.js.map M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/upload/upload-view-default.js M static/scripts/mvc/upload/upload-view.js Log Message: ----------- [WIP] Fix button states Commit: 5710ee145872fedb6fd267349c09bb66805e4b5a https://github.com/galaxyproject/galaxy/commit/5710ee145872fedb6fd267349c09… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-07-17 (Fri, 17 Jul 2015) Changed paths: M lib/galaxy/webapps/reports/controllers/jobs.py Log Message: ----------- Removed unused import Commit: f36f7854568462bc9615fa7edd45425c49708410 https://github.com/galaxyproject/galaxy/commit/f36f7854568462bc9615fa7edd45… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-07-17 (Fri, 17 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/mvc/upload/upload-view-default.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/style/less/upload.less M static/maps/mvc/upload/upload-view-default.js.map M static/scripts/mvc/upload/upload-view-default.js M static/scripts/mvc/upload/upload-view.js M static/style/blue/base.css Log Message: ----------- [WIP] Adjust styles Commit: ad661147e82e72641e5709dd3a131017d0227e13 https://github.com/galaxyproject/galaxy/commit/ad661147e82e72641e5709dd3a13… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-07-17 (Fri, 17 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/style/less/upload.less M static/maps/mvc/upload/upload-view.js.map M static/scripts/mvc/upload/upload-view.js M static/style/blue/base.css Log Message: ----------- [WIP] Style adjustments Commit: 209ff0f6e62eeb89709dd37c37e6eb5c709cf764 https://github.com/galaxyproject/galaxy/commit/209ff0f6e62eeb89709dd37c37e6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-18 (Sat, 18 Jul 2015) Changed paths: M lib/galaxy/eggs/dist.py Log Message: ----------- Fix for egg building broken in flake8'ing Commit: 428705e7ec0cf9eb06160f00535587a55c202e81 https://github.com/galaxyproject/galaxy/commit/428705e7ec0cf9eb06160f005355… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-07-18 (Sat, 18 Jul 2015) Changed paths: M lib/galaxy/eggs/dist.py Log Message: ----------- Merge pull request #478 from dannon/fix_flake8_breakage Fix for egg building broken by flake8'ing Commit: 3678c111a6547cbcebc48101a39afa42601a481d https://github.com/galaxyproject/galaxy/commit/3678c111a6547cbcebc48101a39a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-07-18 (Sat, 18 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/style/less/upload.less M static/maps/mvc/upload/upload-view.js.map M static/scripts/mvc/upload/upload-view.js M static/style/blue/base.css Log Message: ----------- Prepare composite tab Commit: 04eadf4bfcec7b1848ad4c2e6d84607b40c4eb16 https://github.com/galaxyproject/galaxy/commit/04eadf4bfcec7b1848ad4c2e6d84… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-07-18 (Sat, 18 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/utils/uploadbox.js M static/maps/utils/uploadbox.js.map M static/scripts/mvc/upload/upload-view.js M static/scripts/utils/uploadbox.js Log Message: ----------- Fix uploadbox trigger for local upload Commit: dbc1bd50b425522cfc4cb22369e9efa59c5d3357 https://github.com/galaxyproject/galaxy/commit/dbc1bd50b425522cfc4cb22369e9… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-07-18 (Sat, 18 Jul 2015) Changed paths: M client/galaxy/scripts/utils/uploadbox.js M static/maps/utils/uploadbox.js.map M static/scripts/utils/uploadbox.js Log Message: ----------- Code style adjustments for uploadbox code Commit: 6d9ac6368139d71aeb1105bc9ca4d406cae3d8d9 https://github.com/galaxyproject/galaxy/commit/6d9ac6368139d71aeb1105bc9ca4… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-07-20 (Mon, 20 Jul 2015) Changed paths: M lib/galaxy/webapps/reports/controllers/jobs.py A templates/page_base.mako M templates/sorting_base.mako M templates/webapps/reports/jobs_specified_month_all.mako Log Message: ----------- Merge pull request #370 from Airistotal/Reports_Paginate Reports pagination Commit: 48931a6309b592e81e0033c853affc934e78d492 https://github.com/galaxyproject/galaxy/commit/48931a6309b592e81e0033c853af… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-07-20 (Mon, 20 Jul 2015) Changed paths: M lib/galaxy/eggs/dist.py M lib/galaxy/webapps/reports/controllers/jobs.py A templates/page_base.mako M templates/sorting_base.mako M templates/webapps/reports/jobs_specified_month_all.mako Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into Reports_newpage Conflicts: lib/galaxy/webapps/reports/controllers/jobs.py templates/webapps/reports/jobs_specified_month_all.mako Commit: b0c6512c5b61e9e948d9d8304973b03d07b8d1c7 https://github.com/galaxyproject/galaxy/commit/b0c6512c5b61e9e948d9d8304973… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-20 (Mon, 20 Jul 2015) Changed paths: M lib/galaxy/jobs/handler.py Log Message: ----------- Fix more sqlalchemy comparisons broken during flake8'ing. Commit: fed3bddc30de17332bc31cc9f4f94d372626cd54 https://github.com/galaxyproject/galaxy/commit/fed3bddc30de17332bc31cc9f4f9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-20 (Mon, 20 Jul 2015) Changed paths: M lib/galaxy/jobs/handler.py Log Message: ----------- Import null, oops. Commit: 0a9a2f8ba5203d598910f88947c0e284745ab5c9 https://github.com/galaxyproject/galaxy/commit/0a9a2f8ba5203d598910f88947c0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-07-20 (Mon, 20 Jul 2015) Changed paths: M lib/galaxy/jobs/handler.py Log Message: ----------- Merge pull request #479 from dannon/more_sqla_flake8_fixes More sqla flake8 fixes Commit: 4ba3cf2a13645ecaed119c070b0cd7add1471707 https://github.com/galaxyproject/galaxy/commit/4ba3cf2a13645ecaed119c070b0c… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-07-21 (Tue, 21 Jul 2015) Changed paths: M lib/galaxy/jobs/handler.py Log Message: ----------- Fix last SQLAlchemy comparison broken in 9805294f9773968b2a9707a814fc41dbf596a8a0 . Commit: 54368b185cd2ff5b8e392ba36e896a70c24b586d https://github.com/galaxyproject/galaxy/commit/54368b185cd2ff5b8e392ba36e89… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-21 (Tue, 21 Jul 2015) Changed paths: M lib/galaxy/jobs/handler.py Log Message: ----------- Merge pull request #480 from nsoranzo/dev Fix last SQLAlchemy comparison broken during flake8'ing. Commit: 01010d3a69d6da2983264894e3732bdab9af1938 https://github.com/galaxyproject/galaxy/commit/01010d3a69d6da2983264894e373… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-21 (Tue, 21 Jul 2015) Changed paths: M lib/galaxy/jobs/handler.py Log Message: ----------- Another job handler comparison fix. Commit: ed616f5575176de19751d70e99ef1d0b86c5124f https://github.com/galaxyproject/galaxy/commit/ed616f5575176de19751d70e99ef… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-21 (Tue, 21 Jul 2015) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/repository.py Log Message: ----------- sqlalchemy fixes in toolshed repository controller Commit: e7d3cceb5e695296aed6b88f21750ce0cc39ec96 https://github.com/galaxyproject/galaxy/commit/e7d3cceb5e695296aed6b88f2175… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-21 (Tue, 21 Jul 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Another sqla comparison in the user controller. Commit: b8096640493bced72daaf929bcc65e7a314a7f00 https://github.com/galaxyproject/galaxy/commit/b8096640493bced72daaf929bcc6… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-07-21 (Tue, 21 Jul 2015) Changed paths: M lib/galaxy/eggs/dist.py M lib/galaxy/jobs/handler.py M lib/galaxy/webapps/reports/controllers/jobs.py A templates/page_base.mako M templates/sorting_base.mako M templates/webapps/reports/jobs_specified_month_all.mako Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into Reports_homepage Commit: bbac9c473aa4582ca7bb25475a32c178c00ac45e https://github.com/galaxyproject/galaxy/commit/bbac9c473aa4582ca7bb25475a32… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-07-21 (Tue, 21 Jul 2015) Changed paths: M lib/galaxy/jobs/handler.py Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into Reports_newpage Commit: e9e34c9c5fffc1d408a496297240142b5267c38e https://github.com/galaxyproject/galaxy/commit/e9e34c9c5fffc1d408a496297240… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-07-21 (Tue, 21 Jul 2015) Changed paths: M lib/galaxy/jobs/handler.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/tool_shed/controllers/repository.py Log Message: ----------- Merge pull request #481 from dannon/flake8_contd Even more sqlalchemy/flake8 fixes. Commit: 51dca28794f68ec07647854373d94b33aed19e6e https://github.com/galaxyproject/galaxy/commit/51dca28794f68ec07647854373d9… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-07-21 (Tue, 21 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/upload/upload-view.js M lib/galaxy/webapps/galaxy/api/datatypes.py M static/maps/mvc/upload/upload-view.js.map M static/scripts/mvc/upload/upload-view.js Log Message: ----------- [WIP] Continue API integration Commit: c46be96f21e0cef8b2f8e596f1ae08ff302de894 https://github.com/galaxyproject/galaxy/commit/c46be96f21e0cef8b2f8e596f1ae… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-07-21 (Tue, 21 Jul 2015) Changed paths: M lib/galaxy/managers/annotatable.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/taggable.py M lib/galaxy/webapps/galaxy/api/history_contents.py M test/unit/managers/test_HDAManager.py Log Message: ----------- API, HDAs: use manager copy when copying hdas between histories, preserve tags and annotations when copying Commit: c91cabf2a48160277887174b92f87e6e6672eeda https://github.com/galaxyproject/galaxy/commit/c91cabf2a48160277887174b92f8… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-07-21 (Tue, 21 Jul 2015) Changed paths: A client/grunt-tasks/templates.js M client/package.json Log Message: ----------- Client build: add template task Commit: 04d5b634b9e27c3423ab14523fe761ce2625d5e3 https://github.com/galaxyproject/galaxy/commit/04d5b634b9e27c3423ab14523fe7… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-07-21 (Tue, 21 Jul 2015) Changed paths: M client/bower.json M client/galaxy/scripts/libs/handlebars.runtime.js M client/grunt-tasks/templates.js M static/scripts/templates/compiled/panel_section.js M static/scripts/templates/compiled/tool_form.js M static/scripts/templates/compiled/tool_link.js M static/scripts/templates/compiled/tool_search.js Log Message: ----------- Client build: update handlebars and complete template compilation task Commit: e649ff2e5e2771d76236fc3abfdf63dda0d34833 https://github.com/galaxyproject/galaxy/commit/e649ff2e5e2771d76236fc3abfdf… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-07-21 (Tue, 21 Jul 2015) Changed paths: M client/GruntFile.js M client/README.md R client/galaxy/scripts/templates/compile_templates.py M client/galaxy/scripts/templates/compiled/panel_section.js M client/galaxy/scripts/templates/compiled/tool_form.js M client/galaxy/scripts/templates/compiled/tool_link.js M client/galaxy/scripts/templates/compiled/tool_search.js M client/grunt-tasks/templates.js M static/maps/libs/handlebars.runtime.js.map M static/maps/templates/compiled/panel_section.js.map M static/maps/templates/compiled/tool_form.js.map M static/maps/templates/compiled/tool_link.js.map M static/maps/templates/compiled/tool_search.js.map M static/scripts/libs/handlebars.runtime.js R static/scripts/templates/compile_templates.py M static/scripts/templates/compiled/panel_section.js M static/scripts/templates/compiled/tool_form.js M static/scripts/templates/compiled/tool_link.js M static/scripts/templates/compiled/tool_search.js R static/scripts/templates/panel_section.handlebars R static/scripts/templates/tool_form.handlebars R static/scripts/templates/tool_link.handlebars R static/scripts/templates/tool_search.handlebars Log Message: ----------- Client build: transition to grunt based handlebars compilation and minify/map them to static/scripts; cleanup: remove py script, remove uncompiled from minified Commit: e618782ff7b9c1a5d05fa7ffb60ffcd17766acee https://github.com/galaxyproject/galaxy/commit/e618782ff7b9c1a5d05fa7ffb60f… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-07-21 (Tue, 21 Jul 2015) Changed paths: M test/casperjs/api-history-permission-tests.js M test/casperjs/hda-state-tests.js M test/casperjs/modules/historypanel.js Log Message: ----------- Testing, casperjs: small fixes to selectors and api assertions Commit: cc664ff8a279ef8c4fc32b473f43b14bbc7c205c https://github.com/galaxyproject/galaxy/commit/cc664ff8a279ef8c4fc32b473f43… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-21 (Tue, 21 Jul 2015) Changed paths: M client/GruntFile.js M client/README.md M client/bower.json M client/galaxy/scripts/libs/handlebars.runtime.js R client/galaxy/scripts/templates/compile_templates.py M client/galaxy/scripts/templates/compiled/panel_section.js M client/galaxy/scripts/templates/compiled/tool_form.js M client/galaxy/scripts/templates/compiled/tool_link.js M client/galaxy/scripts/templates/compiled/tool_search.js A client/grunt-tasks/templates.js M client/package.json M static/maps/libs/handlebars.runtime.js.map M static/maps/templates/compiled/panel_section.js.map M static/maps/templates/compiled/tool_form.js.map M static/maps/templates/compiled/tool_link.js.map M static/maps/templates/compiled/tool_search.js.map M static/scripts/libs/handlebars.runtime.js R static/scripts/templates/compile_templates.py M static/scripts/templates/compiled/panel_section.js M static/scripts/templates/compiled/tool_form.js M static/scripts/templates/compiled/tool_link.js M static/scripts/templates/compiled/tool_search.js R static/scripts/templates/panel_section.handlebars R static/scripts/templates/tool_form.handlebars R static/scripts/templates/tool_link.handlebars R static/scripts/templates/tool_search.handlebars Log Message: ----------- Merge pull request #484 from carlfeberhard/client-build.grunt-handlebars Client build: grunt-based handlebars compilation Commit: 6cf4b1b1364f7ed09e219b1b65093b010b6c34e6 https://github.com/galaxyproject/galaxy/commit/6cf4b1b1364f7ed09e219b1b6509… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-07-21 (Tue, 21 Jul 2015) Changed paths: M client/galaxy/scripts/reports_webapp/run_stats.js M lib/galaxy/webapps/reports/controllers/home.py M static/maps/reports_webapp/run_stats.js.map M static/scripts/reports_webapp/run_stats.js Log Message: ----------- Polished the appearance of the graphs Added functionality to ETA graphs Commit: fc09e47a98c8229b9f73bd96a9100c6bc126ed50 https://github.com/galaxyproject/galaxy/commit/fc09e47a98c8229b9f73bd96a910… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-07-21 (Tue, 21 Jul 2015) Changed paths: M client/galaxy/scripts/reports_webapp/run_stats.js M static/maps/reports_webapp/run_stats.js.map M static/scripts/reports_webapp/run_stats.js Log Message: ----------- Small appearance fix Commit: 90ddc23714766c9605b09ca8eb9ff88e6f17091c https://github.com/galaxyproject/galaxy/commit/90ddc23714766c9605b09ca8eb9f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-21 (Tue, 21 Jul 2015) Changed paths: M test/casperjs/api-history-permission-tests.js M test/casperjs/hda-state-tests.js M test/casperjs/modules/historypanel.js Log Message: ----------- Merge pull request #485 from carlfeberhard/testing Testing, casperjs: small fixes to selectors and api assertions Commit: d28f1c70737c58da2dd12fe8c80adc8f81344db8 https://github.com/galaxyproject/galaxy/commit/d28f1c70737c58da2dd12fe8c80a… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-07-22 (Wed, 22 Jul 2015) Changed paths: M test/casperjs/api-anon-history-permission-tests.js Log Message: ----------- Testing, casperjs: fix the hda api show assertion in the anon tests Commit: f751314e61c52c31b2fed8e3bef4cc5357b825fd https://github.com/galaxyproject/galaxy/commit/f751314e61c52c31b2fed8e3bef4… Author: Jeremy Goecks <jgoecks(a)gwu.edu> Date: 2015-07-22 (Wed, 22 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/tools.js M client/galaxy/scripts/viz/sweepster.js M static/maps/mvc/tools.js.map M static/maps/viz/sweepster.js.map M static/scripts/mvc/tools.js M static/scripts/viz/sweepster.js Log Message: ----------- Fixes to make Sweepster work again: (a) update template syntax to match changes made in underscore v1.7 and (b) update tool rerun to account for API changes. Commit: 14f966ec44464f593474232f5fece731a10a8ff2 https://github.com/galaxyproject/galaxy/commit/14f966ec44464f593474232f5fec… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-22 (Wed, 22 Jul 2015) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Improve shortcut logic (in boolean ANDs, lookup first, calculate second...), cleanup flake8'ing that made this significantly LESS readable. Commit: 95a46d162afe864101407103d8471eede196f295 https://github.com/galaxyproject/galaxy/commit/95a46d162afe864101407103d847… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-07-22 (Wed, 22 Jul 2015) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Merge pull request #488 from dannon/tweaks Improve shortcut logic Commit: 96efac89eb61a0e134b0faf2b6250bcf840ec646 https://github.com/galaxyproject/galaxy/commit/96efac89eb61a0e134b0faf2b625… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-07-22 (Wed, 22 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/tools.js M client/galaxy/scripts/viz/sweepster.js M static/maps/mvc/tools.js.map M static/maps/viz/sweepster.js.map M static/scripts/mvc/tools.js M static/scripts/viz/sweepster.js Log Message: ----------- Merge pull request #486 from jgoecks/sweepster-fixes Fixes to make Sweepster work again: (a) update template syntax to mat… Commit: 95f63e7fd3b3034a9d34140bf716526eed843324 https://github.com/galaxyproject/galaxy/commit/95f63e7fd3b3034a9d34140bf716… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-22 (Wed, 22 Jul 2015) Changed paths: M test/casperjs/api-anon-history-permission-tests.js Log Message: ----------- Merge pull request #487 from carlfeberhard/testing Testing, casperjs: fix the hda api show assertion in the anon tests Commit: ba7963da5e98e0dccaff930ac5e4d0d6fd22cd8d https://github.com/galaxyproject/galaxy/commit/ba7963da5e98e0dccaff930ac5e4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-22 (Wed, 22 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/datatypes/metadata.py M lib/galaxy/datatypes/registry.py M lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/scripts/mvc/collection/list-of-pairs-collection-creator.js Log Message: ----------- Merge release_15.07 into dev Commit: a2c50db1fb90a06d98c91bcab3e13316b9162217 https://github.com/galaxyproject/galaxy/commit/a2c50db1fb90a06d98c91bcab3e1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-22 (Wed, 22 Jul 2015) Changed paths: M lib/galaxy/managers/annotatable.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/taggable.py M lib/galaxy/webapps/galaxy/api/history_contents.py M test/unit/managers/test_HDAManager.py Log Message: ----------- Merge pull request #482 from carlfeberhard/copy-tags-annos API, HDAs: use manager copy when copying hdas between histories, pres… Commit: c77bff0b3caa3070dd765dd17f14ac957ec2ca00 https://github.com/galaxyproject/galaxy/commit/c77bff0b3caa3070dd765dd17f14… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-22 (Wed, 22 Jul 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Merge 15.07 into dev Commit: 27692c434ef7544a4cce8b6b6c8b2b1d9180d877 https://github.com/galaxyproject/galaxy/commit/27692c434ef7544a4cce8b6b6c8b… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-07-22 (Wed, 22 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/history/history-panel.js M client/galaxy/scripts/mvc/list/list-panel.js M static/maps/mvc/history/history-panel.js.map M static/maps/mvc/list/list-panel.js.map M static/scripts/mvc/history/history-panel.js M static/scripts/mvc/list/list-panel.js Log Message: ----------- History UI: do not render selector when there are no datasets to select Commit: 15b325673ca0ad43039795f1db03268607e303e1 https://github.com/galaxyproject/galaxy/commit/15b325673ca0ad43039795f1db03… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-07-22 (Wed, 22 Jul 2015) Changed paths: M lib/galaxy/managers/containers.py M lib/galaxy/managers/histories.py M test/unit/managers/base.py M test/unit/managers/test_CollectionManager.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HistoryManager.py Log Message: ----------- History manager: incorporate container interface; add tests Commit: 5a0aa6165a84916cd1cd17fbaebcafb00cb54cde https://github.com/galaxyproject/galaxy/commit/5a0aa6165a84916cd1cd17fbaebc… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-07-22 (Wed, 22 Jul 2015) Changed paths: M lib/galaxy/managers/containers.py M lib/galaxy/managers/histories.py M test/unit/managers/base.py M test/unit/managers/test_CollectionManager.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HistoryManager.py Log Message: ----------- Merge branch 'managers.containers' into managers Commit: 19b2b7d7cc063560a6ee27a1aab4dd7d06c7614e https://github.com/galaxyproject/galaxy/commit/19b2b7d7cc063560a6ee27a1aab4… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-07-22 (Wed, 22 Jul 2015) Changed paths: M lib/galaxy/model/mapping.py Log Message: ----------- Clean up the formatting on mapping.py Commit: a9c0baae29a18559c76d994cee8dd9dd71226f5e https://github.com/galaxyproject/galaxy/commit/a9c0baae29a18559c76d994cee8d… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-07-23 (Thu, 23 Jul 2015) Changed paths: M test/unit/managers/test_HDAManager.py Log Message: ----------- Testing: set order of tags in hda manager tests Commit: 07a0341ab6d00d407fb3364081150fdc621954c4 https://github.com/galaxyproject/galaxy/commit/07a0341ab6d00d407fb336408115… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-23 (Thu, 23 Jul 2015) Changed paths: M test/unit/managers/test_HDAManager.py Log Message: ----------- Merge pull request #493 from carlfeberhard/fix.tests Testing: set order of tags in hda manager tests Commit: df952cb541d7aa41a1aba20bdfbfecb452c8a29a https://github.com/galaxyproject/galaxy/commit/df952cb541d7aa41a1aba20bdfbf… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-07-23 (Thu, 23 Jul 2015) Changed paths: M lib/galaxy/model/mapping.py Log Message: ----------- Fix to 19b2b7d for flubbed text attribute name Commit: b22e1d13298be964e7bd6fed0773150bf1b459ec https://github.com/galaxyproject/galaxy/commit/b22e1d13298be964e7bd6fed0773… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-23 (Thu, 23 Jul 2015) Changed paths: M lib/galaxy/model/mapping.py Log Message: ----------- Merge branch 'pephate' of https://github.com/carlfeberhard/galaxy into carlfeberhard-pephate Commit: 84474c8a94297ad7f444c3c8213dc77199e02ecb https://github.com/galaxyproject/galaxy/commit/84474c8a94297ad7f444c3c8213d… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-07-23 (Thu, 23 Jul 2015) Changed paths: M lib/galaxy/model/mapping.py Log Message: ----------- hulk smash. Commit: ef520569d507a7a70cbfc65583c14f93d1b06ce2 https://github.com/galaxyproject/galaxy/commit/ef520569d507a7a70cbfc65583c1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-23 (Thu, 23 Jul 2015) Changed paths: M lib/galaxy/model/mapping.py Log Message: ----------- Slight bracket adjustment Commit: 5edbdea1fd0092167860116e2e96d23f76e4553e https://github.com/galaxyproject/galaxy/commit/5edbdea1fd0092167860116e2e96… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-23 (Thu, 23 Jul 2015) Changed paths: M .ci/flake8_wrapper.sh Log Message: ----------- Add client/node_modules to ignore so that tox locally doesn't try to lint them. This has not been a problem for the CI server, since these never exist. Commit: 30d7d9a056dacb25152c891442873a980ad3f157 https://github.com/galaxyproject/galaxy/commit/30d7d9a056dacb25152c89144287… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-23 (Thu, 23 Jul 2015) Changed paths: M .ci/flake8_wrapper.sh Log Message: ----------- Ignore the whole client dir instead. Commit: 134e2b40ffbcc1287d9a32fe9c40d4e2b0efe159 https://github.com/galaxyproject/galaxy/commit/134e2b40ffbcc1287d9a32fe9c40… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-23 (Thu, 23 Jul 2015) Changed paths: M .ci/flake8_wrapper.sh M .ci/pep8_sources.txt Log Message: ----------- Move all sources to blacklist instead of inline. Commit: e1ade4ea6de5ba532fc314f4be58ccc12de1f9ff https://github.com/galaxyproject/galaxy/commit/e1ade4ea6de5ba532fc314f4be58… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-23 (Thu, 23 Jul 2015) Changed paths: A .ci/flake8_blacklist.txt M .ci/flake8_wrapper.sh R .ci/pep8_sources.txt Log Message: ----------- Change pep8_sources.txt to flake8_blacklist.txt to be more descriptive about it Commit: cd918f633ccf01b31ab79b8ec5ee4ca71f8252a1 https://github.com/galaxyproject/galaxy/commit/cd918f633ccf01b31ab79b8ec5ee… Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com> Date: 2015-07-23 (Thu, 23 Jul 2015) Changed paths: A .ci/flake8_blacklist.txt M .ci/flake8_wrapper.sh R .ci/pep8_sources.txt Log Message: ----------- Merge pull request #494 from dannon/toxfix Add client to ignore so that tox locally doesn't try to … Commit: 3ccc76555aab8d4f757ae1db75205f2cda89a81f https://github.com/galaxyproject/galaxy/commit/3ccc76555aab8d4f757ae1db7520… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-07-23 (Thu, 23 Jul 2015) Changed paths: M client/galaxy/scripts/reports_webapp/run_stats.js M client/galaxy/style/less/base.less M lib/galaxy/webapps/reports/controllers/home.py M static/maps/reports_webapp/run_stats.js.map M static/scripts/reports_webapp/run_stats.js M static/style/blue/base.css Log Message: ----------- Fixed x axis moving around *hopefully* Commit: 39c7209c9df7b54d58df6e801e974df7c9bf6792 https://github.com/galaxyproject/galaxy/commit/39c7209c9df7b54d58df6e801e97… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-07-23 (Thu, 23 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/tools.js M client/galaxy/scripts/viz/sweepster.js M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/datatypes/metadata.py M lib/galaxy/datatypes/registry.py M lib/galaxy/jobs/__init__.py M lib/galaxy/managers/annotatable.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/taggable.py M lib/galaxy/model/mapping.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/user.py M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/tools.js.map M static/maps/viz/sweepster.js.map M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/tools.js M static/scripts/viz/sweepster.js M test/casperjs/api-anon-history-permission-tests.js M test/unit/managers/test_HDAManager.py Log Message: ----------- Fix conflicts Commit: c253eee479f7dd086d2db31f464d91994b9778ce https://github.com/galaxyproject/galaxy/commit/c253eee479f7dd086d2db31f464d… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-07-23 (Thu, 23 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/tools.js M client/galaxy/scripts/viz/sweepster.js M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/datatypes/metadata.py M lib/galaxy/datatypes/registry.py M lib/galaxy/jobs/__init__.py M lib/galaxy/managers/annotatable.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/taggable.py M lib/galaxy/model/mapping.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/user.py M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/tools.js.map M static/maps/viz/sweepster.js.map M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/tools.js M static/scripts/viz/sweepster.js M test/casperjs/api-anon-history-permission-tests.js M test/unit/managers/test_HDAManager.py Log Message: ----------- Merge branch 'dannon-carlfeberhard-pephate' into pephate Commit: 64a7b9e197d1c029a8846a5cbd1485972ddcab6f https://github.com/galaxyproject/galaxy/commit/64a7b9e197d1c029a8846a5cbd14… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-07-23 (Thu, 23 Jul 2015) Changed paths: M lib/galaxy/util/bunch.py M lib/galaxy/webapps/galaxy/api/datatypes.py Log Message: ----------- Add composite datatype details to datatypes api response Commit: cf6cbd434dea309037c1325de2937d143206d84d https://github.com/galaxyproject/galaxy/commit/cf6cbd434dea309037c1325de293… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-07-23 (Thu, 23 Jul 2015) Changed paths: M lib/tool_shed/metadata/metadata_generator.py Log Message: ----------- Fix for server error when installing some repos. Examples: IUC's gatk2 repository, devteam's samtools_rmdup. When attempting to install either of those, or another repository that has tool tests with an input parameter that does not have a value attribute, the repository would be stuck in state 'Cloning' and show a debug link in the log. This commit resolves that error. Commit: 0c29dd44a430479d4d3c6928fb8ba84c6a479809 https://github.com/galaxyproject/galaxy/commit/0c29dd44a430479d4d3c6928fb8b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-23 (Thu, 23 Jul 2015) Changed paths: M lib/galaxy/model/mapping.py Log Message: ----------- Tweak a few indentations to avoid kicking toplevel parameters into secondary indentation (so they don't get lost), taking logical (as in block) indentation into consideration over line length Commit: a022738cf2f70555f1f8dc67026e87200e5e87a3 https://github.com/galaxyproject/galaxy/commit/a022738cf2f70555f1f8dc67026e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-07-23 (Thu, 23 Jul 2015) Changed paths: M client/galaxy/scripts/utils/uploadbox.js M static/maps/utils/uploadbox.js.map M static/scripts/utils/uploadbox.js Log Message: ----------- Move uploadbox variables to local scope Commit: 05a15c8f7f02a2d5cb255d1ce9e889ba372a681f https://github.com/galaxyproject/galaxy/commit/05a15c8f7f02a2d5cb255d1ce9e8… Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com> Date: 2015-07-23 (Thu, 23 Jul 2015) Changed paths: M lib/galaxy/model/mapping.py Log Message: ----------- Merge pull request #2 from dannon/pephate Tweak a few indentations to avoid kicking toplevel parameters into se… Commit: 3c6a43148ab571a950b0009c1cdb43c6186841f0 https://github.com/galaxyproject/galaxy/commit/3c6a43148ab571a950b0009c1cdb… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-07-23 (Thu, 23 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/upload/upload-view-default.js M client/galaxy/scripts/mvc/upload/upload-view.js M static/maps/mvc/upload/upload-view-default.js.map M static/maps/mvc/upload/upload-view.js.map M static/scripts/mvc/upload/upload-view-default.js M static/scripts/mvc/upload/upload-view.js Log Message: ----------- Parse composite file details to front-end, hide in regular upload view Commit: b8dac9f22f02fc3df6a6468e0a02c92e8c14ff30 https://github.com/galaxyproject/galaxy/commit/b8dac9f22f02fc3df6a6468e0a02… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-07-23 (Thu, 23 Jul 2015) Changed paths: M lib/galaxy/managers/datasets.py Log Message: ----------- HDA API: return role ids associated with each hda permission if the user asking has manage permissions Commit: 137b21283bfe6a12f8cd2e7f9f4ac763ca049f53 https://github.com/galaxyproject/galaxy/commit/137b21283bfe6a12f8cd2e7f9f4a… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-07-23 (Thu, 23 Jul 2015) Changed paths: M lib/galaxy/managers/containers.py M lib/galaxy/managers/histories.py Log Message: ----------- Clean up on 5a0aa61 Commit: 898ff31dd5e6a8fadba8363dca1bea23de69f7c3 https://github.com/galaxyproject/galaxy/commit/898ff31dd5e6a8fadba8363dca1b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-23 (Thu, 23 Jul 2015) Changed paths: M lib/galaxy/model/mapping.py Log Message: ----------- Merge pull request #492 from carlfeberhard/pephate Clean up the formatting on mapping.py Commit: 504b9a263bcd2af033e22fad221f49551ff60714 https://github.com/galaxyproject/galaxy/commit/504b9a263bcd2af033e22fad221f… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-07-23 (Thu, 23 Jul 2015) Changed paths: M lib/galaxy/managers/rbac_secured.py M test/unit/managers/test_DatasetManager.py Log Message: ----------- Fix to 5a0aa61: use file_name and not permissions in testing additional keys via the serializer Commit: 7f22635d040e143f99bf1ff0f5e9bd23f25efe04 https://github.com/galaxyproject/galaxy/commit/7f22635d040e143f99bf1ff0f5e9… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-07-23 (Thu, 23 Jul 2015) Changed paths: M test/unit/managers/test_HDAManager.py Log Message: ----------- Testing: Remove permissions from serializer tests Commit: 10638bad6a7c8c0a5efcf1daf48f01d14d429bcc https://github.com/galaxyproject/galaxy/commit/10638bad6a7c8c0a5efcf1daf48f… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-07-23 (Thu, 23 Jul 2015) Changed paths: A .ci/flake8_blacklist.txt M .ci/flake8_wrapper.sh R .ci/pep8_sources.txt M lib/galaxy/model/mapping.py M test/unit/managers/test_HDAManager.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into managers Commit: 31bed7f83eafd9bc2c120cc0f68e98bdce11e947 https://github.com/galaxyproject/galaxy/commit/31bed7f83eafd9bc2c120cc0f68e… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-07-24 (Fri, 24 Jul 2015) Changed paths: M client/galaxy/scripts/reports_webapp/run_stats.js M lib/galaxy/webapps/reports/controllers/home.py M static/maps/reports_webapp/run_stats.js.map M static/scripts/reports_webapp/run_stats.js M templates/webapps/reports/run_stats.mako Log Message: ----------- Changed zoom on graphs Changed graph title Fixed flake errors Commit: 486ba9f23a5bd35dff56503cff6713b3b9696a32 https://github.com/galaxyproject/galaxy/commit/486ba9f23a5bd35dff56503cff67… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-24 (Fri, 24 Jul 2015) Changed paths: M lib/galaxy/web/framework/base.py Log Message: ----------- Merge branch 'release_15.07' into dev Commit: b5e7e1e615741bad14cd0acbe803981fc7a5a92e https://github.com/galaxyproject/galaxy/commit/b5e7e1e615741bad14cd0acbe803… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-24 (Fri, 24 Jul 2015) Log Message: ----------- Merge branch 'master' into dev Commit: d59c846dc3b3bd53ab592c4db5bfec7f0a3ffec1 https://github.com/galaxyproject/galaxy/commit/d59c846dc3b3bd53ab592c4db5bf… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-07-24 (Fri, 24 Jul 2015) Changed paths: M lib/galaxy/managers/base.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/rbac_secured.py M test/unit/managers/test_DatasetManager.py Log Message: ----------- Dataset manager: allow deserializing permissions Commit: 24360176bd007e652351b4531d77ef4dd80d8056 https://github.com/galaxyproject/galaxy/commit/24360176bd007e652351b4531d77… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-24 (Fri, 24 Jul 2015) Changed paths: M lib/galaxy/managers/histories.py Log Message: ----------- Merge. Commit: e36d1c2e0ebbe0664d6402a07191b7957718f94d https://github.com/galaxyproject/galaxy/commit/e36d1c2e0ebbe0664d6402a07191… Author: jgoecks <jgoecks(a)gwu.edu> Date: 2015-07-24 (Fri, 24 Jul 2015) Changed paths: M lib/galaxy/visualization/data_providers/genome.py Log Message: ----------- Fix BBI data provider underflow bug when computing standard deviation Commit: 28a544c50b2a80e261148a6faeb878aa975fc051 https://github.com/galaxyproject/galaxy/commit/28a544c50b2a80e261148a6faeb8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-24 (Fri, 24 Jul 2015) Changed paths: M lib/galaxy/visualization/data_providers/genome.py Log Message: ----------- Adjust comment for flake8 Commit: 59a3804f099de38c43a4cfba57d6ae61ffa62af7 https://github.com/galaxyproject/galaxy/commit/59a3804f099de38c43a4cfba57d6… Author: Jeremy Goecks <jgoecks(a)users.noreply.github.com> Date: 2015-07-24 (Fri, 24 Jul 2015) Changed paths: M lib/galaxy/visualization/data_providers/genome.py Log Message: ----------- Merge pull request #1 from dannon/bbi-sd-underflow-bug Adjust comment for flake8 Commit: 54a1de77585e0d0f3450428a88dbd6526b185417 https://github.com/galaxyproject/galaxy/commit/54a1de77585e0d0f3450428a88db… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-24 (Fri, 24 Jul 2015) Changed paths: M lib/galaxy/visualization/data_providers/genome.py Log Message: ----------- Merge pull request #499 from jgoecks/bbi-sd-underflow-bug Fix BBI data provider underflow bug when computing standard deviation Commit: 18b058a4968844a5f00c3a779b0f5055f7827fad https://github.com/galaxyproject/galaxy/commit/18b058a4968844a5f00c3a779b0f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-24 (Fri, 24 Jul 2015) Log Message: ----------- Merge branch 'release_15.07' into dev Commit: 486bbb0bf5d7a866a7205aab03d8b63279f3b3de https://github.com/galaxyproject/galaxy/commit/486bbb0bf5d7a866a7205aab03d8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-07-27 (Mon, 27 Jul 2015) Changed paths: R client/galaxy/scripts/mvc/upload/upload-row.js R client/galaxy/scripts/mvc/upload/upload-view-default.js M client/galaxy/scripts/mvc/upload/upload-view.js R static/maps/mvc/upload/upload-row.js.map R static/maps/mvc/upload/upload-view-default.js.map M static/maps/mvc/upload/upload-view.js.map R static/scripts/mvc/upload/upload-row.js R static/scripts/mvc/upload/upload-view-default.js M static/scripts/mvc/upload/upload-view.js Log Message: ----------- Separate regular and composite upload elements into directories Commit: a390f071cc453d7d2895ba6e30ffd025414d63b3 https://github.com/galaxyproject/galaxy/commit/a390f071cc453d7d2895ba6e30ff… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-07-27 (Mon, 27 Jul 2015) Changed paths: A client/galaxy/scripts/mvc/upload/composite/composite-row.js A client/galaxy/scripts/mvc/upload/composite/composite-view.js A client/galaxy/scripts/mvc/upload/default/default-row.js A client/galaxy/scripts/mvc/upload/default/default-view.js A static/maps/mvc/upload/composite/composite-row.js.map A static/maps/mvc/upload/composite/composite-view.js.map A static/maps/mvc/upload/default/default-row.js.map A static/maps/mvc/upload/default/default-view.js.map A static/scripts/mvc/upload/composite/composite-row.js A static/scripts/mvc/upload/composite/composite-view.js A static/scripts/mvc/upload/default/default-row.js A static/scripts/mvc/upload/default/default-view.js Log Message: ----------- Add separated files, repack Commit: 4afc756c6122a71248924f1f6a4bd093a7fc95b6 https://github.com/galaxyproject/galaxy/commit/4afc756c6122a71248924f1f6a4b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-27 (Mon, 27 Jul 2015) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/datatypes/data.py Log Message: ----------- Simplest possible tool whitelist implementation Commit: 1b2fbad49f06983b86b80c40d38a158d48907601 https://github.com/galaxyproject/galaxy/commit/1b2fbad49f06983b86b80c40d38a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-07-27 (Mon, 27 Jul 2015) Changed paths: M lib/galaxy/managers/containers.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/rbac_secured.py M test/unit/managers/base.py M test/unit/managers/test_CollectionManager.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HistoryManager.py Log Message: ----------- Merge pull request #496 from carlfeberhard/managers Managers: containers and hda permissions Commit: a0fc6e3acb58999f25d17f2372c090b3a43ceda6 https://github.com/galaxyproject/galaxy/commit/a0fc6e3acb58999f25d17f2372c0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-07-27 (Mon, 27 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/history/history-panel.js M client/galaxy/scripts/mvc/list/list-panel.js M static/maps/mvc/history/history-panel.js.map M static/maps/mvc/list/list-panel.js.map M static/scripts/mvc/history/history-panel.js M static/scripts/mvc/list/list-panel.js Log Message: ----------- Merge pull request #491 from carlfeberhard/ui.remove-select-button History UI: do not render selector when there are no datasets to select Commit: 29ce33ef34fdd45cc643ec7473443ead554e7755 https://github.com/galaxyproject/galaxy/commit/29ce33ef34fdd45cc643ec747344… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-27 (Mon, 27 Jul 2015) Changed paths: M lib/galaxy/config.py M lib/galaxy/web/base/controllers/admin.py M templates/webapps/galaxy/admin/index.mako Log Message: ----------- Swap from list in universe to a separate config file, add simple UI for managing Commit: e3bbae0e2a222a3b4f1bc0f25fcdb15a6a81b0e9 https://github.com/galaxyproject/galaxy/commit/e3bbae0e2a222a3b4f1bc0f25fcd… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-27 (Mon, 27 Jul 2015) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Update galaxy.ini.sample for the swap from list in galaxy.ini to a separate file. Commit: 674fb8c48b6aa30276e08402794ed1bbdf5f10a9 https://github.com/galaxyproject/galaxy/commit/674fb8c48b6aa30276e08402794e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-27 (Mon, 27 Jul 2015) Changed paths: A templates/webapps/galaxy/admin/sanitize_whitelist.mako Log Message: ----------- Forgot the template... Commit: aa8643014a725bcec016e288f5b434d44586bd2f https://github.com/galaxyproject/galaxy/commit/aa8643014a725bcec016e288f5b4… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-07-27 (Mon, 27 Jul 2015) Changed paths: M lib/galaxy/config.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/web/base/pluginframework.py Log Message: ----------- Interactive environments: move static base url from 'visualizations' to 'interactive_environments' for int env plugins Commit: 58766abe64b65f45251d284bff51c508a454ed41 https://github.com/galaxyproject/galaxy/commit/58766abe64b65f45251d284bff51… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-27 (Mon, 27 Jul 2015) Changed paths: M lib/galaxy/web/base/controllers/admin.py Log Message: ----------- Use config-specified file instead of old hardcoded one Commit: 8d47c0b273a0fff772102b403b4b79d3902e4811 https://github.com/galaxyproject/galaxy/commit/8d47c0b273a0fff772102b403b4b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-27 (Mon, 27 Jul 2015) Changed paths: M lib/galaxy/web/base/controllers/admin.py Log Message: ----------- Coerce incoming param(s) to a list (otherwise python will iterate over string and not actually add any tools to the list, obviously) Commit: 054b4d58c53744d0c6426d9a1d5ea0d5a4ff7042 https://github.com/galaxyproject/galaxy/commit/054b4d58c53744d0c6426d9a1d5e… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-07-27 (Mon, 27 Jul 2015) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Interactive environments: correct app_root Commit: c35a5f57dc0fcb02cbe12225979afd29c5936ee5 https://github.com/galaxyproject/galaxy/commit/c35a5f57dc0fcb02cbe12225979a… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-07-27 (Mon, 27 Jul 2015) Changed paths: M lib/galaxy/config.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/base/pluginframework.py Log Message: ----------- Merge pull request #500 from carlfeberhard/int_envs.seperate Interactive environments: allow their own static base url Commit: 15618d6d224e6320c340e754faec44088e1f8e9d https://github.com/galaxyproject/galaxy/commit/15618d6d224e6320c340e754faec… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-27 (Mon, 27 Jul 2015) Changed paths: M lib/galaxy/web/base/controllers/admin.py M templates/webapps/galaxy/admin/sanitize_whitelist.mako Log Message: ----------- Add some help text, hopefully *just* scary enough. Commit: 5280393708fcef8b95ae5a33f0ed8a166efa7267 https://github.com/galaxyproject/galaxy/commit/5280393708fcef8b95ae5a33f0ed… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-27 (Mon, 27 Jul 2015) Changed paths: M templates/webapps/galaxy/admin/sanitize_whitelist.mako Log Message: ----------- Slight tweak to message to bold sanitize_all_html Commit: abe5571d431bd2dda5d84e642463e81cfd4ed16f https://github.com/galaxyproject/galaxy/commit/abe5571d431bd2dda5d84e642463… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-27 (Mon, 27 Jul 2015) Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/web/base/controllers/admin.py Log Message: ----------- Kick message to control queue to reload sanitize whitelist in multiprocess mode. Commit: 3c372fce95c90ee1f1d5599155471f8bc16983b2 https://github.com/galaxyproject/galaxy/commit/3c372fce95c90ee1f1d559915547… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-07-27 (Mon, 27 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/style/less/upload.less M static/maps/mvc/upload/composite/composite-view.js.map M static/scripts/mvc/upload/composite/composite-view.js M static/style/blue/base.css Log Message: ----------- Fix and adjust styles for composite upload view Commit: 638ef77b3c2cde48b7277e07baec50be19efada2 https://github.com/galaxyproject/galaxy/commit/638ef77b3c2cde48b7277e07baec… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-07-27 (Mon, 27 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-slider.js M static/maps/mvc/ui/ui-slider.js.map M static/scripts/mvc/ui/ui-slider.js Log Message: ----------- Add numpad key codes to ui-slider element Commit: e8b267b93136e2b6551f8b55979dbec52e2fca92 https://github.com/galaxyproject/galaxy/commit/e8b267b93136e2b6551f8b55979d… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-07-27 (Mon, 27 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-slider.js M static/maps/mvc/ui/ui-slider.js.map M static/scripts/mvc/ui/ui-slider.js Log Message: ----------- Merge pull request #509 from guerler/fix_numpad_000 Add numpad support to integer inputs Commit: 0de044dc09d17869c9b2f6a6f5f49ec19b80a25b https://github.com/galaxyproject/galaxy/commit/0de044dc09d17869c9b2f6a6f5f4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-27 (Mon, 27 Jul 2015) Changed paths: M lib/galaxy/datatypes/data.py M templates/webapps/galaxy/admin/sanitize_whitelist.mako Log Message: ----------- Force sanitization even when whitelisted for imported datasets, since we can't necessarily trust the archive contents. Commit: e55c5e5d9d4d5bf878570ebe9d8b1803f3404204 https://github.com/galaxyproject/galaxy/commit/e55c5e5d9d4d5bf878570ebe9d8b… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2015-07-28 (Tue, 28 Jul 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Fix the ChangeDirectory.execute_step() method and enhance the "directory" recipe step classes to perform within the temporary working directory created by the InstallEnvironment.make_tmp_dir() method (via the use of a new TMP_WORK_DIR reserved word in recipes) in addition to the $INSTALL_DIR reserved word (which has always been supported in recipes). This commit grew out of a fix for the following code in the ChangeDirectory.execute_step() method, which does not perform as the comment describes: ================= # Change directory to a directory above the current working directory, but within the defined work_dir. dir = target_directory.replace( os.path.realpath( work_dir ), '' ).lstrip( '/' ) ================== The resulting directory is always within the current working directory rather than "above" it. The new TMP_WORK_DIR reserved word points to the actual temporary working directory, so recipes now have a way to do perform actions within that directory during the compilation and installation process. Commit: e382378140c37a79dae75b929fe11e71ac509f65 https://github.com/galaxyproject/galaxy/commit/e382378140c37a79dae75b929fe1… Author: nitesh1989 <nitesh.turaga(a)gmail.com> Date: 2015-07-28 (Tue, 28 Jul 2015) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Fix: rdata extension type Commit: 484099d41feedb27f780f4214576682a94c5e1cf https://github.com/galaxyproject/galaxy/commit/484099d41feedb27f780f4214576… Author: nitesh1989 <nitesh.turaga(a)gmail.com> Date: 2015-07-28 (Tue, 28 Jul 2015) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py Log Message: ----------- Fix: Typo the other way. Supposed to be "RData" Ref: https://stat.ethz.ch/R-manual/R-devel/library/base/html/save.html Commit: 0ff497cdb9ceb71385fff328b5de62f4aaa1247d https://github.com/galaxyproject/galaxy/commit/0ff497cdb9ceb71385fff328b5de… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-07-28 (Tue, 28 Jul 2015) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Merge pull request #512 from nitesh1989/dev Fix: rdata extension type Commit: 6849970cec76a0726a840311f5932ab1bb0c8f7a https://github.com/galaxyproject/galaxy/commit/6849970cec76a0726a840311f593… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-07-28 (Tue, 28 Jul 2015) Changed paths: M client/galaxy/scripts/reports_webapp/run_stats.js M client/galaxy/style/less/base.less M lib/galaxy/webapps/reports/controllers/home.py M static/maps/reports_webapp/run_stats.js.map M static/scripts/reports_webapp/run_stats.js M static/style/blue/base.css Log Message: ----------- Automatic x axis creation was inconsistent, changed to manual x axis creation Commit: 3d335f810c2f4ff8ece43a692b79de483ba68164 https://github.com/galaxyproject/galaxy/commit/3d335f810c2f4ff8ece43a692b79… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-07-28 (Tue, 28 Jul 2015) Changed paths: M lib/galaxy/webapps/reports/controllers/home.py Log Message: ----------- Fix for annoying flake error #226 Commit: c1fb3604371a8f5d1c1681e23abcd2f20786bfda https://github.com/galaxyproject/galaxy/commit/c1fb3604371a8f5d1c1681e23abc… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-07-28 (Tue, 28 Jul 2015) Changed paths: M client/galaxy/scripts/reports_webapp/run_stats.js M templates/webapps/reports/run_stats.mako Log Message: ----------- Refactored out dead code Commit: 1afe5b7ba7e827554a99dbf760292b8a3c52cb17 https://github.com/galaxyproject/galaxy/commit/1afe5b7ba7e827554a99dbf76029… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-07-28 (Tue, 28 Jul 2015) Changed paths: M lib/tool_shed/util/web_util.py Log Message: ----------- Fix for toolshed escape method, where an error/log message contains non-ASCII characters. Commit: adaf150c0f749c4a143fddb1db8c3d913896a7a3 https://github.com/galaxyproject/galaxy/commit/adaf150c0f749c4a143fddb1db8c… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-07-28 (Tue, 28 Jul 2015) Changed paths: M lib/galaxy/datatypes/genetics.py Log Message: ----------- Restore line wrongly removed in fa7c5c531e07056cbf194b514ea9ccee5c214e18 and again in 9805294f9773968b2a9707a814fc41dbf596a8a0 . Reorder imports. Commit: 48a2566305bcbaedf573a40dd98af47b98d282a8 https://github.com/galaxyproject/galaxy/commit/48a2566305bcbaedf573a40dd98a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-28 (Tue, 28 Jul 2015) Changed paths: M lib/galaxy/web/base/controllers/admin.py Log Message: ----------- Update commentary per @nsoranzo's suggestion, thanks Commit: 1c727a4b6becd3aed6a69fa5866c6d01340d63c3 https://github.com/galaxyproject/galaxy/commit/1c727a4b6becd3aed6a69fa5866c… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-07-28 (Tue, 28 Jul 2015) Changed paths: M lib/galaxy/managers/taggable.py Log Message: ----------- Managers, taggable: make anon set_tags fail silently Commit: 16928704e675ed8217dc9b4ca7d01c4a01a4d817 https://github.com/galaxyproject/galaxy/commit/16928704e675ed8217dc9b4ca7d0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-28 (Tue, 28 Jul 2015) Changed paths: M lib/galaxy/datatypes/genetics.py Log Message: ----------- Merge pull request #515 from nsoranzo/dev Restore line wrongly removed in fa7c5c5 and again in 9805294 . Commit: 1e6c49b2771f4f1861a015da56ef25ab97c38638 https://github.com/galaxyproject/galaxy/commit/1e6c49b2771f4f1861a015da56ef… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-07-28 (Tue, 28 Jul 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M lib/tool_shed/util/repository_util.py M templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako Log Message: ----------- Allow uninstalling multiple toolshed repositories at a time within the Galaxy UI, using checkboxes with grid multi-actions. Commit: 2ddb97091ddfc38b57cfacd8daa102b09202db68 https://github.com/galaxyproject/galaxy/commit/2ddb97091ddfc38b57cfacd8daa1… Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com> Date: 2015-07-28 (Tue, 28 Jul 2015) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/datatypes/data.py M lib/galaxy/queue_worker.py M lib/galaxy/web/base/controllers/admin.py M templates/webapps/galaxy/admin/index.mako A templates/webapps/galaxy/admin/sanitize_whitelist.mako Log Message: ----------- Merge pull request #510 from dannon/whitelist_tools Whitelist for tools Commit: 95ed2a2921110686a55afff909b466aa7bb7022b https://github.com/galaxyproject/galaxy/commit/95ed2a2921110686a55afff909b4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-07-29 (Wed, 29 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-model.js M client/galaxy/scripts/mvc/upload/upload-settings.js M client/galaxy/style/less/upload.less M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/composite/composite-view.js.map M static/maps/mvc/upload/default/default-row.js.map M static/maps/mvc/upload/default/default-view.js.map M static/maps/mvc/upload/upload-model.js.map M static/maps/mvc/upload/upload-settings.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/composite/composite-view.js M static/scripts/mvc/upload/default/default-row.js M static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/upload-model.js M static/scripts/mvc/upload/upload-settings.js M static/style/blue/base.css Log Message: ----------- [WIP] Further customizations and adjustments of the upload ui Commit: e5d61f3766588a4b9624a085035d20282bcd67a6 https://github.com/galaxyproject/galaxy/commit/e5d61f3766588a4b9624a085035d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-07-29 (Wed, 29 Jul 2015) Changed paths: A .ci/flake8_blacklist.txt M .ci/flake8_wrapper.sh R .ci/pep8_sources.txt M client/GruntFile.js M client/README.md M client/bower.json M client/galaxy/scripts/libs/handlebars.runtime.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/history/history-panel.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/list/list-panel.js M client/galaxy/scripts/mvc/tools.js M client/galaxy/scripts/mvc/ui/ui-slider.js R client/galaxy/scripts/templates/compile_templates.py M client/galaxy/scripts/templates/compiled/panel_section.js M client/galaxy/scripts/templates/compiled/tool_form.js M client/galaxy/scripts/templates/compiled/tool_link.js M client/galaxy/scripts/templates/compiled/tool_search.js M client/galaxy/scripts/utils/config.js M client/galaxy/scripts/viz/sweepster.js M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/style/less/base.less M client/galaxy/style/less/galaxy_bootstrap/variables.less M client/galaxy/style/less/history.less M client/galaxy/style/less/trackster.less M client/galaxy/style/source_material/circle.py M client/grunt-tasks/style.js A client/grunt-tasks/templates.js M client/package.json M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M contrib/nagios/check_galaxy.py M cron/add_manual_builds.py M cron/build_chrom_db.py M cron/parse_builds_3_sites.py M doc/patch.py M lib/galaxy/__init__.py A lib/galaxy/auth/providers/pam_auth.py M lib/galaxy/config.py M lib/galaxy/dataset_collections/subcollections.py M 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scripts/cleanup_datasets/update_dataset_size.py M scripts/cleanup_datasets/update_metadata.py M scripts/db_shell.py M scripts/dist-scramble.py M scripts/drmaa_external_killer.py M scripts/drmaa_external_runner.py M scripts/edam_mapping.py M scripts/egg_packager_template.py M scripts/external_chown_script.py M scripts/extract_dataset_part.py M scripts/extract_toolbox_sections.py M scripts/fetch_eggs.py M scripts/functional_tests.py M scripts/get_platforms.py M scripts/helper.py M scripts/make_egg_packager.py M scripts/metagenomics/convert_title.py M scripts/microbes/BeautifulSoup.py M scripts/microbes/create_bacteria_table.py M scripts/migrate_tools/migrate_tools.py M scripts/nosetests.py M scripts/paster.py M scripts/runtime_stats.py M scripts/scramble.py M scripts/scramble/lib/scramble_lib.py M scripts/scramble/scripts/DRMAA_python-macosx.py M scripts/scramble/scripts/DRMAA_python-solaris.py M scripts/scramble/scripts/DRMAA_python.py M scripts/scramble/scripts/MySQL_python-solaris.py M scripts/scramble/scripts/MySQL_python.py M scripts/scramble/scripts/PyRods.py M scripts/scramble/scripts/bx_python-solaris.py M scripts/scramble/scripts/generic.py M scripts/scramble/scripts/pbs_python.py M scripts/scramble/scripts/psycopg2-linux.py M scripts/scramble/scripts/psycopg2-macosx.py M scripts/scramble/scripts/psycopg2-solaris.py M scripts/scramble/scripts/psycopg2.py M scripts/scramble/scripts/pysam-solaris.py M scripts/scramble/scripts/pysqlite.py M scripts/set_dataset_sizes.py M scripts/set_metadata.py M scripts/set_user_disk_usage.py M scripts/summarize_timings.py M scripts/sync_reports_config.py M scripts/test_dist_egg.py M scripts/transfer.py M scripts/update_shed_config_path.py M setup.cfg M static/maps/libs/handlebars.runtime.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/history/history-panel.js.map M static/maps/mvc/library/library-folderlist-view.js.map M 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static/scripts/mvc/list/list-panel.js M static/scripts/mvc/tools.js M static/scripts/mvc/ui/ui-slider.js R static/scripts/templates/compile_templates.py M static/scripts/templates/compiled/panel_section.js M static/scripts/templates/compiled/tool_form.js M static/scripts/templates/compiled/tool_link.js M static/scripts/templates/compiled/tool_search.js R static/scripts/templates/panel_section.handlebars R static/scripts/templates/tool_form.handlebars R static/scripts/templates/tool_link.handlebars R static/scripts/templates/tool_search.handlebars M static/scripts/utils/config.js M static/scripts/viz/sweepster.js M static/scripts/viz/trackster/painters.js M static/scripts/viz/trackster/tracks.js M static/style/blue/autocomplete_tagging.css M static/style/blue/base.css M static/style/blue/circster.css M static/style/blue/embed_item.css M static/style/blue/iphone.css M static/style/blue/library.css M static/style/blue/masthead.css M static/style/blue/sprite-fugue.png M static/style/blue/sprite-history-buttons.png M static/style/blue/sprite-history-states.png M static/style/blue/trackster.css A templates/page_base.mako M templates/show_params.mako M templates/sorting_base.mako M templates/webapps/galaxy/admin/index.mako A templates/webapps/galaxy/admin/sanitize_whitelist.mako M templates/webapps/reports/jobs_specified_month_all.mako M test/api/test_dataset_collections.py M test/api/test_datasets.py M test/api/test_histories.py M test/api/test_workflow_extraction.py M test/api/test_workflows.py M test/api/yaml_to_workflow.py M test/base/test_db_util.py M test/base/twilltestcase.py M test/casperjs/api-anon-history-permission-tests.js M test/casperjs/api-history-permission-tests.js M test/casperjs/hda-state-tests.js M test/casperjs/modules/historypanel.js M test/functional/test_admin_features.py M test/functional/test_data_managers.py M test/functional/test_data_security.py M test/functional/test_get_data.py M test/functional/test_library_features.py M test/functional/test_library_security.py M test/functional/test_library_templates.py M test/functional/test_metadata_editing.py M test/functional/test_sample_tracking.py M test/functional/test_toolbox.py M test/functional/test_ucsc_table_browser.py M test/functional/test_user_info.py A test/functional/tools/output_collection_filter.xml M test/functional/tools/samples_tool_conf.xml M test/functional/workflow.py M test/install_and_test_tool_shed_repositories/base/test_db_util.py M test/tool_shed/base/test_db_util.py M test/unit/jobs/test_job_output_checker.py M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_rules/20_instance.py M test/unit/managers/base.py M test/unit/managers/test_CollectionManager.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HistoryManager.py M test/unit/managers/test_UserManager.py M test/unit/test_galaxy_mapping.py M test/unit/test_objectstore.py M test/unit/test_routes.py M test/unit/test_sockets.py M test/unit/tool_shed_unit_tests/test_fabric_util.py M test/unit/tool_shed_unit_tests/test_td_common_util.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/workflows/test_extract_summary.py M tool_list.py M tools/data_source/data_source.py M tools/phenotype_association/pagetag.py M tools/phenotype_association/senatag.py M tools/stats/grouping.py Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into upload_000 Conflicts: static/style/blue/base.css Commit: fb190f622f7a53d42e3244f47d3911043e9a6eb8 https://github.com/galaxyproject/galaxy/commit/fb190f622f7a53d42e3244f47d39… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-07-29 (Wed, 29 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M static/maps/mvc/upload/composite/composite-row.js.map M static/scripts/mvc/upload/composite/composite-row.js Log Message: ----------- Remove mode icon from row Commit: 6de2953c98cfc4ea32b8f6ae6bb6dc096c747d38 https://github.com/galaxyproject/galaxy/commit/6de2953c98cfc4ea32b8f6ae6bb6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-07-29 (Wed, 29 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/mvc/upload/upload-settings.js M client/galaxy/scripts/mvc/upload/upload-view.js M static/maps/mvc/ui/ui-modal.js.map M static/maps/mvc/upload/upload-settings.js.map M static/maps/mvc/upload/upload-view.js.map M static/scripts/mvc/ui/ui-modal.js M static/scripts/mvc/upload/upload-view.js Log Message: ----------- Add 'hide_separator' attribute to modals Commit: e5503824d1c6f691b58e9d790c1c596151285a5c https://github.com/galaxyproject/galaxy/commit/e5503824d1c6f691b58e9d790c1c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-07-29 (Wed, 29 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/mvc/upload/upload-view.js M static/maps/mvc/ui/ui-modal.js.map M static/maps/mvc/upload/upload-view.js.map M static/scripts/mvc/ui/ui-modal.js M static/scripts/mvc/upload/upload-view.js Log Message: ----------- Rename property to 'title_separator' Commit: c62db518734a776abe9761c65fef3bd66b51f879 https://github.com/galaxyproject/galaxy/commit/c62db518734a776abe9761c65fef… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-07-29 (Wed, 29 Jul 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M lib/tool_shed/util/repository_util.py M templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako Log Message: ----------- Merge pull request #517 from blankenberg/multi-uninstall Allow uninstalling multiple toolshed repositories at a time … Commit: 2c2f49bf8e980ff7879452f0073ec755906f5591 https://github.com/galaxyproject/galaxy/commit/2c2f49bf8e980ff7879452f0073e… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-07-29 (Wed, 29 Jul 2015) Changed paths: A client/galaxy/scripts/utils/query-string-parsing.js M client/galaxy/scripts/viz/trackster.js M config/plugins/visualizations/trackster/config/trackster.xml A static/maps/utils/query-string-parsing.js.map M static/maps/viz/trackster.js.map A static/scripts/utils/query-string-parsing.js M static/scripts/viz/trackster.js Log Message: ----------- Visualizations, trackster: allow the user to add the dataset launched from as a new track in an existing trackster visualization; add utils/query-string-parsing.js for pulling query params from the query string Commit: 96836156fe530c6dacf625507a8bea01cb544f2e https://github.com/galaxyproject/galaxy/commit/96836156fe530c6dacf625507a8b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-29 (Wed, 29 Jul 2015) Changed paths: M lib/galaxy/managers/taggable.py Log Message: ----------- Merge pull request #516 from carlfeberhard/fix.taggable-anon Managers, taggable: make anon set_tags fail silently Commit: cf011d652b5503067e0ad75488466244b854ac99 https://github.com/galaxyproject/galaxy/commit/cf011d652b5503067e0ad7548846… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-29 (Wed, 29 Jul 2015) Changed paths: M lib/tool_shed/util/web_util.py Log Message: ----------- Merge pull request #514 from blankenberg/toolshed-fix Fix for toolshed escape method, where an error/log message contains non-ASCII characters. Commit: bb7f9a8a51b9de8b48b15078de498f3f46515442 https://github.com/galaxyproject/galaxy/commit/bb7f9a8a51b9de8b48b15078de49… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-07-29 (Wed, 29 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/style/less/upload.less M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/composite/composite-view.js.map M static/maps/mvc/upload/default/default-row.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/composite/composite-view.js M static/scripts/mvc/upload/default/default-row.js M static/style/blue/base.css Log Message: ----------- [WIP] Further adjustments to styles and colors Commit: 9c3be3efb41b44ac2f8a15f511292d2d9db85886 https://github.com/galaxyproject/galaxy/commit/9c3be3efb41b44ac2f8a15f51129… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-29 (Wed, 29 Jul 2015) Changed paths: A client/galaxy/scripts/reports_webapp/run_stats.js M client/galaxy/style/less/base.less A lib/galaxy/webapps/reports/controllers/home.py A static/images/reports_webapp/bases/home-icon-active.png A static/images/reports_webapp/bases/home-icon-hov.png A static/images/reports_webapp/bases/home-icon.png A static/images/reports_webapp/home-icon-active.png A static/images/reports_webapp/home-icon-hov.png A static/images/reports_webapp/home-icon.png A static/maps/reports_webapp/run_stats.js.map A static/scripts/reports_webapp/run_stats.js M static/style/blue/base.css M templates/base.mako M templates/webapps/reports/index.mako A templates/webapps/reports/run_stats.mako Log Message: ----------- Merge branch 'Reports_homepage' of https://github.com/Airistotal/galaxy into Airistotal-Reports_homepage Commit: 09f0aaf37151011aa928db8d7f8e3a0903764c51 https://github.com/galaxyproject/galaxy/commit/09f0aaf37151011aa928db8d7f8e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-29 (Wed, 29 Jul 2015) Changed paths: M static/maps/reports_webapp/run_stats.js.map M static/scripts/reports_webapp/run_stats.js Log Message: ----------- Run grunt. Commit: 8ae3406f414e55d3e8dd21cbaa212b4f7ba097f0 https://github.com/galaxyproject/galaxy/commit/8ae3406f414e55d3e8dd21cbaa21… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-29 (Wed, 29 Jul 2015) Changed paths: M templates/webapps/reports/run_stats.mako Log Message: ----------- Fix inclusion of new reports charts javascript file to not use a static path. Commit: 29d7f8be7a9648afeea3ac40f8b146153334d323 https://github.com/galaxyproject/galaxy/commit/29d7f8be7a9648afeea3ac40f8b1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-29 (Wed, 29 Jul 2015) Changed paths: M templates/webapps/reports/run_stats.mako Log Message: ----------- trim whitespace Commit: a9274619afcbf2d114ef07ab7759e457411d8a46 https://github.com/galaxyproject/galaxy/commit/a9274619afcbf2d114ef07ab7759… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-07-29 (Wed, 29 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/style/less/upload.less M static/maps/mvc/upload/composite/composite-row.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/style/blue/base.css Log Message: ----------- Adjust icon styles Commit: 951ac2d3d8192237338ffccd8e3b5cbecb945b20 https://github.com/galaxyproject/galaxy/commit/951ac2d3d8192237338ffccd8e3b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-29 (Wed, 29 Jul 2015) Changed paths: M client/galaxy/style/less/base.less M static/style/blue/base.css Log Message: ----------- Fix incorrect absolute paths in reports styles. Commit: 5fd4daf2dd0a8c7c7a12d1c5ab690e71780e5719 https://github.com/galaxyproject/galaxy/commit/5fd4daf2dd0a8c7c7a12d1c5ab69… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-07-29 (Wed, 29 Jul 2015) Changed paths: M client/galaxy/style/less/galaxy_bootstrap/variables.less M static/style/blue/base.css M static/style/blue/iphone.css M static/style/blue/library.css Log Message: ----------- Fix to 9e2e909: revert saturate/lighten changes, use backwards compat 'luminance' function instead of newly w3c-spec'd 'luma' function Commit: 6a8fed5feed54263bac775dda908a046d9244c41 https://github.com/galaxyproject/galaxy/commit/6a8fed5feed54263bac775dda908… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-07-29 (Wed, 29 Jul 2015) Changed paths: M client/galaxy/style/less/upload.less M static/style/blue/base.css Log Message: ----------- Fix ftp row label style Commit: 8d5ef14d4f40b20cb6450f4417d74dc4a54b65dc https://github.com/galaxyproject/galaxy/commit/8d5ef14d4f40b20cb6450f4417d7… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-07-29 (Wed, 29 Jul 2015) Changed paths: M client/galaxy/scripts/reports_webapp/run_stats.js M static/maps/reports_webapp/run_stats.js.map M static/scripts/reports_webapp/run_stats.js Log Message: ----------- Changed spacing Commit: e3b1302606861ecec9901162719918017b3046a5 https://github.com/galaxyproject/galaxy/commit/e3b1302606861ecec99011627199… Author: Daniel <danieltos.bouchard(a)gmail.com> Date: 2015-07-29 (Wed, 29 Jul 2015) Changed paths: A .ci/flake8_blacklist.txt M .ci/flake8_wrapper.sh R .ci/pep8_sources.txt M client/GruntFile.js M client/README.md M client/bower.json M client/galaxy/scripts/libs/handlebars.runtime.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/history/history-panel.js M client/galaxy/scripts/mvc/list/list-panel.js M client/galaxy/scripts/mvc/tools.js M client/galaxy/scripts/mvc/ui/ui-slider.js A client/galaxy/scripts/reports_webapp/run_stats.js R client/galaxy/scripts/templates/compile_templates.py M client/galaxy/scripts/templates/compiled/panel_section.js M client/galaxy/scripts/templates/compiled/tool_form.js M client/galaxy/scripts/templates/compiled/tool_link.js M client/galaxy/scripts/templates/compiled/tool_search.js M client/galaxy/scripts/viz/sweepster.js M client/galaxy/style/less/base.less A client/grunt-tasks/templates.js M client/package.json M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/metadata.py M lib/galaxy/datatypes/registry.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/handler.py M lib/galaxy/managers/annotatable.py M lib/galaxy/managers/containers.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/rbac_secured.py M lib/galaxy/managers/taggable.py M lib/galaxy/model/mapping.py M lib/galaxy/queue_worker.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/base/pluginframework.py M lib/galaxy/web/framework/base.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/user.py A lib/galaxy/webapps/reports/controllers/home.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M lib/tool_shed/util/repository_util.py A static/images/reports_webapp/bases/home-icon-active.png A static/images/reports_webapp/bases/home-icon-hov.png A static/images/reports_webapp/bases/home-icon.png A static/images/reports_webapp/home-icon-active.png A static/images/reports_webapp/home-icon-hov.png A static/images/reports_webapp/home-icon.png M static/maps/libs/handlebars.runtime.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/history/history-panel.js.map M static/maps/mvc/list/list-panel.js.map M static/maps/mvc/tools.js.map M static/maps/mvc/ui/ui-slider.js.map A static/maps/reports_webapp/run_stats.js.map M static/maps/templates/compiled/panel_section.js.map M static/maps/templates/compiled/tool_form.js.map M static/maps/templates/compiled/tool_link.js.map M static/maps/templates/compiled/tool_search.js.map M static/maps/viz/sweepster.js.map M static/scripts/libs/handlebars.runtime.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/history/history-panel.js M static/scripts/mvc/list/list-panel.js M static/scripts/mvc/tools.js M static/scripts/mvc/ui/ui-slider.js A static/scripts/reports_webapp/run_stats.js R static/scripts/templates/compile_templates.py M static/scripts/templates/compiled/panel_section.js M static/scripts/templates/compiled/tool_form.js M static/scripts/templates/compiled/tool_link.js M static/scripts/templates/compiled/tool_search.js R static/scripts/templates/panel_section.handlebars R static/scripts/templates/tool_form.handlebars R static/scripts/templates/tool_link.handlebars R static/scripts/templates/tool_search.handlebars M static/scripts/viz/sweepster.js M static/style/blue/base.css M templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako M templates/base.mako M templates/webapps/galaxy/admin/index.mako A templates/webapps/galaxy/admin/sanitize_whitelist.mako M templates/webapps/reports/index.mako A templates/webapps/reports/run_stats.mako M test/casperjs/api-anon-history-permission-tests.js M test/casperjs/api-history-permission-tests.js M test/casperjs/hda-state-tests.js M test/casperjs/modules/historypanel.js M test/unit/managers/base.py M test/unit/managers/test_CollectionManager.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HistoryManager.py Log Message: ----------- Merge pull request #3 from dannon/Airistotal-Reports_homepage Several fixes necessary for merging. Commit: cc2cd0fb01ff1da8f0abc61641a1bbbdac022ea0 https://github.com/galaxyproject/galaxy/commit/cc2cd0fb01ff1da8f0abc61641a1… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-07-29 (Wed, 29 Jul 2015) Changed paths: A .ci/flake8_blacklist.txt M .ci/flake8_wrapper.sh R .ci/pep8_sources.txt M client/GruntFile.js M client/README.md M client/bower.json M client/galaxy/scripts/libs/handlebars.runtime.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/history/history-panel.js M client/galaxy/scripts/mvc/list/list-panel.js M client/galaxy/scripts/mvc/tools.js M client/galaxy/scripts/mvc/ui/ui-slider.js R client/galaxy/scripts/templates/compile_templates.py M client/galaxy/scripts/templates/compiled/panel_section.js M client/galaxy/scripts/templates/compiled/tool_form.js M client/galaxy/scripts/templates/compiled/tool_link.js M client/galaxy/scripts/templates/compiled/tool_search.js M client/galaxy/scripts/viz/sweepster.js M client/galaxy/style/less/base.less A client/grunt-tasks/templates.js M client/package.json M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/metadata.py M lib/galaxy/datatypes/registry.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/handler.py M lib/galaxy/managers/annotatable.py M lib/galaxy/managers/containers.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/rbac_secured.py M lib/galaxy/managers/taggable.py M lib/galaxy/model/mapping.py M lib/galaxy/queue_worker.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/base/pluginframework.py M lib/galaxy/web/framework/base.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M lib/tool_shed/util/repository_util.py M static/maps/libs/handlebars.runtime.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/history/history-panel.js.map M static/maps/mvc/list/list-panel.js.map M static/maps/mvc/tools.js.map M static/maps/mvc/ui/ui-slider.js.map M static/maps/templates/compiled/panel_section.js.map M static/maps/templates/compiled/tool_form.js.map M static/maps/templates/compiled/tool_link.js.map M static/maps/templates/compiled/tool_search.js.map M static/maps/viz/sweepster.js.map M static/scripts/libs/handlebars.runtime.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/history/history-panel.js M static/scripts/mvc/list/list-panel.js M static/scripts/mvc/tools.js M static/scripts/mvc/ui/ui-slider.js R static/scripts/templates/compile_templates.py M static/scripts/templates/compiled/panel_section.js M static/scripts/templates/compiled/tool_form.js M static/scripts/templates/compiled/tool_link.js M static/scripts/templates/compiled/tool_search.js R static/scripts/templates/panel_section.handlebars R static/scripts/templates/tool_form.handlebars R static/scripts/templates/tool_link.handlebars R static/scripts/templates/tool_search.handlebars M static/scripts/viz/sweepster.js M static/style/blue/base.css M templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako M templates/webapps/galaxy/admin/index.mako A templates/webapps/galaxy/admin/sanitize_whitelist.mako M templates/webapps/reports/run_stats.mako M test/casperjs/api-anon-history-permission-tests.js M test/casperjs/api-history-permission-tests.js M test/casperjs/hda-state-tests.js M test/casperjs/modules/historypanel.js M test/unit/managers/base.py M test/unit/managers/test_CollectionManager.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HistoryManager.py Log Message: ----------- Merge branch 'dev' of https://github.com/Airistotal/galaxy into Reports_homepage Conflicts: static/scripts/reports_webapp/run_stats.js Commit: 13522af7d1a185c416ba87f447a80bc980254441 https://github.com/galaxyproject/galaxy/commit/13522af7d1a185c416ba87f447a8… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-07-29 (Wed, 29 Jul 2015) Changed paths: A .ci/flake8_blacklist.txt M .ci/flake8_wrapper.sh R .ci/pep8_sources.txt M client/GruntFile.js M client/README.md M client/bower.json M client/galaxy/scripts/libs/handlebars.runtime.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/history/history-panel.js M client/galaxy/scripts/mvc/list/list-panel.js M client/galaxy/scripts/mvc/tools.js M client/galaxy/scripts/mvc/ui/ui-slider.js R client/galaxy/scripts/templates/compile_templates.py M client/galaxy/scripts/templates/compiled/panel_section.js M client/galaxy/scripts/templates/compiled/tool_form.js M client/galaxy/scripts/templates/compiled/tool_link.js M client/galaxy/scripts/templates/compiled/tool_search.js M client/galaxy/scripts/viz/sweepster.js A client/grunt-tasks/templates.js M client/package.json M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/metadata.py M lib/galaxy/datatypes/registry.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/handler.py M lib/galaxy/managers/annotatable.py M lib/galaxy/managers/containers.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/rbac_secured.py M lib/galaxy/managers/taggable.py M lib/galaxy/model/mapping.py M lib/galaxy/queue_worker.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/base/pluginframework.py M lib/galaxy/web/framework/base.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/web_util.py M static/maps/libs/handlebars.runtime.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/history/history-panel.js.map M static/maps/mvc/list/list-panel.js.map M static/maps/mvc/tools.js.map M static/maps/mvc/ui/ui-slider.js.map M static/maps/templates/compiled/panel_section.js.map M static/maps/templates/compiled/tool_form.js.map M static/maps/templates/compiled/tool_link.js.map M static/maps/templates/compiled/tool_search.js.map M static/maps/viz/sweepster.js.map M static/scripts/libs/handlebars.runtime.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/history/history-panel.js M static/scripts/mvc/list/list-panel.js M static/scripts/mvc/tools.js M static/scripts/mvc/ui/ui-slider.js R static/scripts/templates/compile_templates.py M static/scripts/templates/compiled/panel_section.js M static/scripts/templates/compiled/tool_form.js M static/scripts/templates/compiled/tool_link.js M static/scripts/templates/compiled/tool_search.js R static/scripts/templates/panel_section.handlebars R static/scripts/templates/tool_form.handlebars R static/scripts/templates/tool_link.handlebars R static/scripts/templates/tool_search.handlebars M static/scripts/viz/sweepster.js M templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako M templates/webapps/galaxy/admin/index.mako A templates/webapps/galaxy/admin/sanitize_whitelist.mako M test/casperjs/api-anon-history-permission-tests.js M test/casperjs/api-history-permission-tests.js M test/casperjs/hda-state-tests.js M test/casperjs/modules/historypanel.js M test/unit/managers/base.py M test/unit/managers/test_CollectionManager.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HistoryManager.py Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into Reports_newpage Commit: 91a29d8a6af6f26c556b6655a0697c3524554783 https://github.com/galaxyproject/galaxy/commit/91a29d8a6af6f26c556b6655a069… Author: y.hoogstrate(a)erasmusmc.nl <y.hoogstrate(a)erasmusmc.nl> Date: 2015-07-30 (Thu, 30 Jul 2015) Changed paths: M tools/extract/extract_genomic_dna.py M tools/extract/extract_genomic_dna.xml Log Message: ----------- extract_genomic_dna support for 2bit files from Local data Commit: 6ce94ce7e6b54f50720cc9559477d3b8035527a5 https://github.com/galaxyproject/galaxy/commit/6ce94ce7e6b54f50720cc9559477… Author: y.hoogstrate(a)erasmusmc.nl <y.hoogstrate(a)erasmusmc.nl> Date: 2015-07-30 (Thu, 30 Jul 2015) Changed paths: M tools/extract/extract_genomic_dna.py Log Message: ----------- Fixed comments Commit: 73dc6f69d1d592824ea2947c189039b9f4d49f55 https://github.com/galaxyproject/galaxy/commit/73dc6f69d1d592824ea2947c1890… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2015-07-30 (Thu, 30 Jul 2015) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/managers/taggable.py M lib/galaxy/queue_worker.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/web_util.py M templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako M templates/webapps/galaxy/admin/index.mako A templates/webapps/galaxy/admin/sanitize_whitelist.mako Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into dev Commit: cce64def93f6902d5b7c4da8feb3a2854a094884 https://github.com/galaxyproject/galaxy/commit/cce64def93f6902d5b7c4da8feb3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-30 (Thu, 30 Jul 2015) Changed paths: M client/galaxy/style/less/galaxy_bootstrap/variables.less Log Message: ----------- Retab galaxy_bootstrap/variables.less Commit: 87a58e2d4337c8b73fa75003d28b062e535d221b https://github.com/galaxyproject/galaxy/commit/87a58e2d4337c8b73fa75003d28b… Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com> Date: 2015-07-30 (Thu, 30 Jul 2015) Changed paths: M client/galaxy/style/less/galaxy_bootstrap/variables.less Log Message: ----------- Merge pull request #3 from dannon/style-colors Retab galaxy_bootstrap/variables.less Commit: ed29f74147e6e1f5737b4b2cfd37eb2ea5e2ff2b https://github.com/galaxyproject/galaxy/commit/ed29f74147e6e1f5737b4b2cfd37… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-30 (Thu, 30 Jul 2015) Changed paths: M client/galaxy/style/less/galaxy_bootstrap/variables.less M static/style/blue/base.css M static/style/blue/iphone.css M static/style/blue/library.css Log Message: ----------- Merge pull request #527 from carlfeberhard/style-colors Fix to 9e2e909: revert saturate/lighten changes, use backwards compat… Commit: 699764283c329d7a3af92b3386a7e9f2dacda7b5 https://github.com/galaxyproject/galaxy/commit/699764283c329d7a3af92b3386a7… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-07-30 (Thu, 30 Jul 2015) Changed paths: M lib/tool_shed/util/web_util.py Log Message: ----------- Merge branch 'dev' of https://github.com/Airistotal/galaxy into Reports_homepage Commit: bb4588aaaf268e56baf3e8d35e5f8cbc1979207b https://github.com/galaxyproject/galaxy/commit/bb4588aaaf268e56baf3e8d35e5f… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-07-30 (Thu, 30 Jul 2015) Changed paths: M lib/galaxy/managers/histories.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Managers, history: replace _get_history_data with proper serializers Commit: 8644b21808fd779c062e1fbd475b8912845226d8 https://github.com/galaxyproject/galaxy/commit/8644b21808fd779c062e1fbd475b… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-07-30 (Thu, 30 Jul 2015) Changed paths: M lib/galaxy/managers/histories.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/root.py M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/embed.mako M templates/webapps/galaxy/history/structure.mako M templates/webapps/galaxy/history/view.mako M templates/webapps/galaxy/root/history.mako Log Message: ----------- Managers, history: remove _get_history_data; rename hdas -> contents in altered templates and web methods Commit: 45fb7f8994bbbcc21505379f37a46d8608390c89 https://github.com/galaxyproject/galaxy/commit/45fb7f8994bbbcc21505379f37a4… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-07-30 (Thu, 30 Jul 2015) Changed paths: M client/galaxy/style/less/base.less M client/galaxy/style/less/reports.less M lib/galaxy/webapps/reports/controllers/jobs.py M static/style/blue/base.css M static/style/blue/reports.css M templates/page_base.mako M templates/sorting_base.mako M templates/spark_base.mako M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_all.mako M templates/webapps/reports/jobs_specified_month_in_error.mako M templates/webapps/reports/jobs_tool_per_month.mako M templates/webapps/reports/jobs_user_per_month.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako M templates/webapps/reports/workflows_per_workflow.mako M templates/webapps/reports/workflows_user_per_month.mako Log Message: ----------- Moved styles to reports.less Added import to base.less to include reports.less Commit: 701328cf849c5ae31daf8ad7f1a03a614cb454bf https://github.com/galaxyproject/galaxy/commit/701328cf849c5ae31daf8ad7f1a0… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-07-30 (Thu, 30 Jul 2015) Changed paths: M client/galaxy/style/less/galaxy_bootstrap/variables.less M static/style/blue/base.css M static/style/blue/iphone.css M static/style/blue/library.css Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into Reports_newpage Conflicts: static/style/blue/base.css Commit: 45e31f758e0b131874623fbe8bb10c9d0650769c https://github.com/galaxyproject/galaxy/commit/45e31f758e0b131874623fbe8bb1… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-07-30 (Thu, 30 Jul 2015) Changed paths: M client/galaxy/style/less/reports.less Log Message: ----------- Changed reports.less comment format Commit: bd03135703d4ebb151299f81a950d507a8d5668d https://github.com/galaxyproject/galaxy/commit/bd03135703d4ebb151299f81a950… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-07-30 (Thu, 30 Jul 2015) Changed paths: M client/galaxy/style/less/galaxy_bootstrap/variables.less M static/style/blue/base.css M static/style/blue/iphone.css M static/style/blue/library.css Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into Reports_homepage Conflicts: static/style/blue/base.css Commit: 5cdd511b7a528940090c01d4d306ccf153f2fc1f https://github.com/galaxyproject/galaxy/commit/5cdd511b7a528940090c01d4d306… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-07-30 (Thu, 30 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/style/less/galaxy_bootstrap/variables.less M lib/galaxy/managers/taggable.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/web_util.py M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/composite/composite-view.js.map M static/maps/utils/uploadbox.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/composite/composite-view.js M static/scripts/mvc/upload/default/default-view.js M static/scripts/utils/uploadbox.js M static/style/blue/base.css M static/style/blue/iphone.css M static/style/blue/library.css M templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into upload_000 Conflicts: static/style/blue/base.css Commit: f83eaa8fe7a39f03c522a5b387961ac9154df9d8 https://github.com/galaxyproject/galaxy/commit/f83eaa8fe7a39f03c522a5b38796… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-07-30 (Thu, 30 Jul 2015) Changed paths: M client/galaxy/scripts/utils/uploadbox.js M static/maps/utils/uploadbox.js.map M static/scripts/utils/uploadbox.js Log Message: ----------- Uploadbox plugin touchup Commit: de375004c9b349c1ccd2084f83040ed59ff792f1 https://github.com/galaxyproject/galaxy/commit/de375004c9b349c1ccd2084f8304… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-07-30 (Thu, 30 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-panel-edit.js M client/galaxy/scripts/utils/utils.js M lib/galaxy/managers/histories.py M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-panel-edit.js.map M static/maps/utils/utils.js.map M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-panel-edit.js M static/scripts/utils/utils.js Log Message: ----------- UI, histories: render nice_size on the client Commit: f36fb54beaa9e23fa34f2cc82fdb2cc2ecdd4458 https://github.com/galaxyproject/galaxy/commit/f36fb54beaa9e23fa34f2cc82fdb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-30 (Thu, 30 Jul 2015) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py Log Message: ----------- Swap track_jobs_in_database to be True by default. This removes the current multiprocess detection logic in favor of simplifying the configuration, and fixes a bug where uwsgi + 1 handler will not work. Commit: 237a3d307d808d5be2e6e4d1a093a646f7d791a7 https://github.com/galaxyproject/galaxy/commit/237a3d307d808d5be2e6e4d1a093… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-07-30 (Thu, 30 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/style/less/upload.less M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/default/default-row.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/default/default-row.js M static/style/blue/base.css Log Message: ----------- More touchup/cleanup for upload views Commit: bf8d74da29ba02c08cc1debed38dbf63a13dd686 https://github.com/galaxyproject/galaxy/commit/bf8d74da29ba02c08cc1debed38d… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-07-30 (Thu, 30 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/options-menu.js M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/options-menu.js.map M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/options-menu.js Log Message: ----------- UI, Histories: move unhide_datasets and delete_hidden_datasets to the client, remove them from the web controller Commit: d20add4ff8abe54cbc15704edc0222935631c767 https://github.com/galaxyproject/galaxy/commit/d20add4ff8abe54cbc15704edc02… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-07-30 (Thu, 30 Jul 2015) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/root.py A templates/webapps/galaxy/history/as_xml.mako M templates/webapps/galaxy/history/view.mako R templates/webapps/galaxy/root/history.mako R templates/webapps/galaxy/root/history_as_xml.mako Log Message: ----------- UI, Histories: use /history/view with current to replace /history, move history_as_xml to /history/as_xml Commit: 13ea86753ad778aaaf6e6470a9370190fc2e91a0 https://github.com/galaxyproject/galaxy/commit/13ea86753ad778aaaf6e6470a937… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-07-31 (Fri, 31 Jul 2015) Changed paths: M lib/galaxy/managers/collections.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parser/xml.py M test/functional/test_toolbox.py A test/functional/tools/collection_creates_list_of_pairs.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Allow tools to explicitly create nested collections with static structure. https://bitbucket.org/galaxy/galaxy-central/pull-request/634/allow-tools-to… added the ability for tool to create simple collections (lists and pairs). It also outlined three creation scenarios - fixed collections, pre-determinable collection structures (like output lists based on input lists), and fully dynamic output collections. This pull request allows tool to output nested collections for these first two. Fully dynamic nested collections (using <discover_datasets> tags) is not implemented in this commit. Additionally, the tool test syntax has been extended to allow testing nested collection elements and an example tool is included that demonstrates this functionality - test/functional/tools/collection_creates_list_of_pairs.xml. Commit: d5c5be87105160a6cb5bd17b659c08330d0ed368 https://github.com/galaxyproject/galaxy/commit/d5c5be87105160a6cb5bd17b659c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-07-31 (Fri, 31 Jul 2015) Changed paths: M lib/galaxy/managers/collections.py M lib/galaxy/managers/collections_util.py Log Message: ----------- Slightly improved collection-related exception handling/reporting. Commit: 84e8e3e71f930078ab426b6e428fe5ef7c5da35d https://github.com/galaxyproject/galaxy/commit/84e8e3e71f930078ab426b6e428f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-07-31 (Fri, 31 Jul 2015) Changed paths: M lib/galaxy/dataset_collections/builder.py M lib/galaxy/managers/collections.py M lib/galaxy/tools/parameters/output_collect.py A test/functional/tools/collection_creates_dynamic_list_of_pairs.xml A test/functional/tools/collection_creates_dynamic_nested.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Allow tools to create nested collections with dynamic structure. In this context dynamic structure means the number of elements and identifiers in lists (at some or any level) are not known ahead of time. In these cases, tool authors must resort to using <discover_dataset> tags. The generic example tool demonstrating this is test/functional/tools/collection_creates_dynamic_nested.xml - which demonstrates building a list of lists from a tool. A common use case will probably be building a list of pairs, a tool demonstrating this can be found at test/functional/tools/collection_creates_dynamic_list_of_pairs.xml. The <discover_datasets> tag infers dynamic information from the filename - so this tool demonstrates mass renaming of a common file name pattern for pairs (_1/_2 suffixes) into a format more readily consumed by <discover_datasets> in a portable shell fashion. Previously, these <discover_dataset> tags would just use the "designation" concept as the element identifier when building collections. This was insufficient for nested collections because an identifier must be specified at each level of the collection. Now <discover_dataset> tags may define multiple identifier_N patterns - e.g. identifier_0, identifier_1, etc.... If these are specified, a desigination no longer must be specified and will just be interpreted as <value_0>:<value_1>:.... This scheme is completely backward compatible and when there is only a single identifier - desigination and identifier_0 can be used interchangeably. Testing: The simple list of lists tool test case can be executed using: ``` ./run_tests.sh -framework -id collection_creates_dynamic_list_of_pairs ``` This verifies the nested datasets are setup properly. The list of pairs example tool test case can be executed using: ``` ./run_tests.sh -framework -id collection_creates_dynamic_list_of_pairs ``` This additionally verifies paired dataset collections can be created this way and that the shell commands in the example work properly for renaming the files for easy discovery. Finally, the following existing test case verifies that designation can be used in lieu of identifier_0 for flat collections (i.e. this generalization is backward compatible): ``` ./run_tests.sh -framework -id collection_split_on_column ``` Commit: 3945c5ed6cf6dc58a3f61ab40c50c05e6af219b8 https://github.com/galaxyproject/galaxy/commit/3945c5ed6cf6dc58a3f61ab40c50… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-07-31 (Fri, 31 Jul 2015) Changed paths: M test/functional/tools/collection_creates_dynamic_list_of_pairs.xml M test/functional/tools/collection_creates_dynamic_nested.xml Log Message: ----------- Add some docs to more complicated nested collection creation examples. As suggested by @bgruening in https://github.com/galaxyproject/galaxy/pull/538#discussion_r36004578. Commit: f753a6159e980df064d794c43b1440dd54a241dd https://github.com/galaxyproject/galaxy/commit/f753a6159e980df064d794c43b14… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-07-31 (Fri, 31 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-model.js M client/galaxy/scripts/mvc/upload/upload-settings.js M client/galaxy/scripts/utils/uploadbox.js M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/default/default-row.js.map M static/maps/mvc/upload/default/default-view.js.map M static/maps/mvc/upload/upload-ftp.js.map M static/maps/mvc/upload/upload-model.js.map M static/maps/mvc/upload/upload-settings.js.map M static/maps/utils/uploadbox.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/default/default-row.js M static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/upload-ftp.js M static/scripts/mvc/upload/upload-model.js M static/scripts/mvc/upload/upload-settings.js M static/scripts/utils/uploadbox.js Log Message: ----------- Fix for settings popup and more code cleanup Commit: e3f831f1dba47e28f500566bf7c5967edd3be2b2 https://github.com/galaxyproject/galaxy/commit/e3f831f1dba47e28f500566bf7c5… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-07-31 (Fri, 31 Jul 2015) Changed paths: M client/bower.json M client/galaxy/scripts/libs/d3.js M client/galaxy/scripts/libs/raven.js M client/galaxy/scripts/libs/require.js M client/galaxy/scripts/libs/tracekit.js Log Message: ----------- Client, libs: fix tracekit bower location, switch bib2json location to our fork, minor bumps to d3, raven, require, and tracekit Commit: 8078d7225fe4e531c180d3a506ea8ee7770166f5 https://github.com/galaxyproject/galaxy/commit/8078d7225fe4e531c180d3a506ea… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-07-31 (Fri, 31 Jul 2015) Changed paths: M client/grunt-tasks/install-libs.js Log Message: ----------- Client, libs: add bib2json in the copied scripts Commit: ba4aabc1869cfa31c0ff0d82ee9ca85d580149c1 https://github.com/galaxyproject/galaxy/commit/ba4aabc1869cfa31c0ff0d82ee9c… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-07-31 (Fri, 31 Jul 2015) Changed paths: M client/galaxy/scripts/libs/farbtastic.js M client/galaxy/scripts/libs/jquery/jqtouch.js M client/grunt-tasks/install-libs.js M static/maps/libs/d3.js.map M static/maps/libs/farbtastic.js.map M static/maps/libs/jquery/jqtouch.js.map M static/maps/libs/raven.js.map M static/maps/libs/require.js.map M static/maps/libs/tracekit.js.map M static/scripts/libs/d3.js M static/scripts/libs/farbtastic.js M static/scripts/libs/jquery/jqtouch.js M static/scripts/libs/raven.js M static/scripts/libs/require.js M static/scripts/libs/tracekit.js Log Message: ----------- Client, libs: update and track farbtastic and jqtouch; compress scripts Commit: 6f93df1f48796e664f048a30a34b1747e8e56f63 https://github.com/galaxyproject/galaxy/commit/6f93df1f48796e664f048a30a34b… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-07-31 (Fri, 31 Jul 2015) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/text.py M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Standardize nice_size() import. Commit: 78d0edf9e0199377c1f2e5b0e838e15e65faaffd https://github.com/galaxyproject/galaxy/commit/78d0edf9e0199377c1f2e5b0e838… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-07-31 (Fri, 31 Jul 2015) Changed paths: M client/galaxy/style/less/history.less M static/style/blue/base.css M templates/display_base.mako M templates/search/index.mako M templates/webapps/galaxy/library/common/ldda_info.mako M templates/webapps/galaxy/library/common/ldda_permissions.mako M templates/webapps/galaxy/root/history.mako M templates/webapps/galaxy/workflow/build_from_current_history.mako Log Message: ----------- UI, history: Remove older history style rules ('historyItem*', etc.) from less and mako files that used them Commit: 71a5b0d30f34dd691b79fb8f268200bab07d51cd https://github.com/galaxyproject/galaxy/commit/71a5b0d30f34dd691b79fb8f2682… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-07-31 (Fri, 31 Jul 2015) Changed paths: M templates/search/index.mako Log Message: ----------- Fix to 78d0edf9: remove less variable Commit: 4db7db29779da8835fa33850bf2916128a4cd3ac https://github.com/galaxyproject/galaxy/commit/4db7db29779da8835fa33850bf29… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-31 (Fri, 31 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-panel-edit.js M client/galaxy/scripts/utils/utils.js M lib/galaxy/managers/histories.py M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-panel-edit.js.map M static/maps/utils/utils.js.map M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-panel-edit.js M static/scripts/utils/utils.js Log Message: ----------- Merge pull request #532 from carlfeberhard/history.nice_size UI, histories: render nice_size on the client Commit: f046c5187160629e2cf48d1bfdcf2f31e0ff08a0 https://github.com/galaxyproject/galaxy/commit/f046c5187160629e2cf48d1bfdcf… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-07-31 (Fri, 31 Jul 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/histories.py Log Message: ----------- API, histories: allow ordering of the index list using an 'order' query param Commit: 13728e7fe73cf2ab2c0cc9bec69d5e5ceba80b27 https://github.com/galaxyproject/galaxy/commit/13728e7fe73cf2ab2c0cc9bec69d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-31 (Fri, 31 Jul 2015) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/text.py M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Merge pull request #537 from nsoranzo/dev Standardize nice_size() import. Commit: 4b5d0a82592502f2ceef45ace1d029759f5218de https://github.com/galaxyproject/galaxy/commit/4b5d0a82592502f2ceef45ace1d0… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-07-31 (Fri, 31 Jul 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/histories.py Log Message: ----------- Fix to f046c51: remove TODO and fix docstring Commit: cf516c569838c5eade1a8ad71978b2101a80f268 https://github.com/galaxyproject/galaxy/commit/cf516c569838c5eade1a8ad71978… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-08-01 (Sat, 01 Aug 2015) Changed paths: M client/bower.json M client/galaxy/scripts/libs/d3.js M client/galaxy/scripts/libs/farbtastic.js M client/galaxy/scripts/libs/jquery/jqtouch.js M client/galaxy/scripts/libs/raven.js M client/galaxy/scripts/libs/require.js M client/galaxy/scripts/libs/tracekit.js M client/grunt-tasks/install-libs.js M static/maps/libs/d3.js.map M static/maps/libs/farbtastic.js.map M static/maps/libs/jquery/jqtouch.js.map M static/maps/libs/raven.js.map M static/maps/libs/require.js.map M static/maps/libs/tracekit.js.map M static/scripts/libs/d3.js M static/scripts/libs/farbtastic.js M static/scripts/libs/jquery/jqtouch.js M static/scripts/libs/raven.js M static/scripts/libs/require.js M static/scripts/libs/tracekit.js Log Message: ----------- Merge pull request #536 from carlfeberhard/client.update-libs Update client libs: farbtastic, jqtouch, bib2json Commit: d6cc36e5ac79cf3076f38cab6745148880d27d75 https://github.com/galaxyproject/galaxy/commit/d6cc36e5ac79cf3076f38cab6745… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-08-01 (Sat, 01 Aug 2015) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py Log Message: ----------- Merge pull request #533 from dannon/track_jobs_tweak Swap track_jobs_in_database to be True by default. This removes the … Commit: f379de18b6e359bb05bf30ae9fb8d077aa6935ff https://github.com/galaxyproject/galaxy/commit/f379de18b6e359bb05bf30ae9fb8… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-08-01 (Sat, 01 Aug 2015) Changed paths: M tools/extract/extract_genomic_dna.py M tools/extract/extract_genomic_dna.xml Log Message: ----------- Merge pull request #529 from yhoogstrate/extract_genomic_dna_2bit_from_ref extract_genomic_dna support for 2bit files from Local data Commit: 7c299faed3859735f1794316076d8902946ec537 https://github.com/galaxyproject/galaxy/commit/7c299faed3859735f1794316076d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-01 (Sat, 01 Aug 2015) Changed paths: M lib/galaxy/tools/parameters/dynamic_options.py M lib/tool_shed/galaxy_install/install_manager.py M test/functional/test_toolbox.py A test/functional/tool-data/fasta_indexes.loc M test/functional/tool-data/sample_tool_data_tables.xml A test/functional/tools/dbkey_filter_input.xml A test/functional/tools/dbkey_filter_multi_input.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge branch 'release_15.07' into dev Commit: ecd38ef6dba00cfdb94365616210690091825651 https://github.com/galaxyproject/galaxy/commit/ecd38ef6dba00cfdb94365616210… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-02 (Sun, 02 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-button-menu.js M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/style/less/ui.less M client/galaxy/style/less/upload.less M static/maps/mvc/ui/ui-button-menu.js.map M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/composite/composite-view.js.map M static/maps/mvc/upload/default/default-view.js.map M static/maps/utils/uploadbox.js.map M static/scripts/mvc/ui/ui-button-menu.js M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/composite/composite-view.js M static/scripts/mvc/upload/default/default-view.js M static/scripts/utils/uploadbox.js M static/style/blue/base.css Log Message: ----------- Enable drag-and-drop, use dropdown instead of select, style fix uploadbox.js Commit: 1f9d5443fb5700fe47e3d57a0687f68db6508952 https://github.com/galaxyproject/galaxy/commit/1f9d5443fb5700fe47e3d57a0687… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-02 (Sun, 02 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/upload-settings.js M client/galaxy/style/less/ui.less M static/scripts/mvc/upload/upload-settings.js M static/style/blue/base.css Log Message: ----------- Style margin fixes Commit: c244c7c819515d7650509b5091b38a54ddabee2d https://github.com/galaxyproject/galaxy/commit/c244c7c819515d7650509b5091b3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-08-03 (Mon, 03 Aug 2015) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Improve job config error when no handler elements are defined. NoneValue has not attribute 'get' isn't super helpful in tracking that problem down. Commit: 1dd4694fb9279098daea456d3029fbab6d1cdcda https://github.com/galaxyproject/galaxy/commit/1dd4694fb9279098daea456d3029… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-08-03 (Mon, 03 Aug 2015) Changed paths: M lib/galaxy/tools/parameters/output.py Log Message: ----------- Update output actions code for some collection operations. Required to fix bowtie2 wrapper for specifying that unmapped reads will be collected when using paired collections. See galaxyproject/tools-devteam#97 and galaxyproject/tools-devteam#201. Commit: 2b87e650ae56feebf6ea554e8b7788e6158873f1 https://github.com/galaxyproject/galaxy/commit/2b87e650ae56feebf6ea554e8b77… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2015-08-03 (Mon, 03 Aug 2015) Changed paths: M client/bower.json M client/galaxy/scripts/libs/d3.js M client/galaxy/scripts/libs/farbtastic.js M client/galaxy/scripts/libs/jquery/jqtouch.js M client/galaxy/scripts/libs/raven.js M client/galaxy/scripts/libs/require.js M client/galaxy/scripts/libs/tracekit.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-panel-edit.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/galaxy_bootstrap/variables.less M client/grunt-tasks/install-libs.js M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/text.py M lib/galaxy/managers/histories.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/tool_shed/galaxy_install/install_manager.py M static/maps/libs/d3.js.map M static/maps/libs/farbtastic.js.map M static/maps/libs/jquery/jqtouch.js.map M static/maps/libs/raven.js.map M static/maps/libs/require.js.map M static/maps/libs/tracekit.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-panel-edit.js.map M static/maps/utils/utils.js.map M static/scripts/libs/d3.js M static/scripts/libs/farbtastic.js M static/scripts/libs/jquery/jqtouch.js M static/scripts/libs/raven.js M static/scripts/libs/require.js M static/scripts/libs/tracekit.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-panel-edit.js M static/scripts/utils/utils.js M static/style/blue/base.css M static/style/blue/iphone.css M static/style/blue/library.css M test/functional/test_toolbox.py A test/functional/tool-data/fasta_indexes.loc M test/functional/tool-data/sample_tool_data_tables.xml A test/functional/tools/dbkey_filter_input.xml A test/functional/tools/dbkey_filter_multi_input.xml M test/functional/tools/samples_tool_conf.xml M tools/extract/extract_genomic_dna.py M tools/extract/extract_genomic_dna.xml Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into dev Commit: 8d12ff2169cd0176a6f197820e86300d406088bd https://github.com/galaxyproject/galaxy/commit/8d12ff2169cd0176a6f197820e86… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-03 (Mon, 03 Aug 2015) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Merge pull request #543 from jmchilton/job_config_exception Improve job config error when no handler elements are defined. Commit: 7401aa0c300341afab2fa08ae4150c85584632e4 https://github.com/galaxyproject/galaxy/commit/7401aa0c300341afab2fa08ae415… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-08-03 (Mon, 03 Aug 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Ensure file exists before attempting chmod. Commit: 261a637cc028e6f9b23a920e96de16db4408a907 https://github.com/galaxyproject/galaxy/commit/261a637cc028e6f9b23a920e96de… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-08-03 (Mon, 03 Aug 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge pull request #545 from davebx/bugfix Ensure file exists before attempting chmod. Commit: ea26355761cd04512d4e392f821e7d63fbfc1b53 https://github.com/galaxyproject/galaxy/commit/ea26355761cd04512d4e392f821e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-03 (Mon, 03 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/composite/composite-view.js M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/composite/composite-view.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/composite/composite-view.js Log Message: ----------- More cleanup, fix model creation Commit: efcfc897d66dba32c70d1ab4eb6f31151f66f9fb https://github.com/galaxyproject/galaxy/commit/efcfc897d66dba32c70d1ab4eb6f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-03 (Mon, 03 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-library.js M static/maps/mvc/ui/ui-select-library.js.map M static/scripts/mvc/ui/ui-select-library.js Log Message: ----------- Filter deleted library datasets Commit: a0639b8f1218b9070b997f2f547d553c84c95eff https://github.com/galaxyproject/galaxy/commit/a0639b8f1218b9070b997f2f547d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-08-04 (Tue, 04 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/histories.py Log Message: ----------- Merge pull request #540 from carlfeberhard/api.histories-order API, histories: allow ordering of the index list using an 'order' que… Commit: 7f9df48aac0dbf91b54063e8d97c61d120bac196 https://github.com/galaxyproject/galaxy/commit/7f9df48aac0dbf91b54063e8d97c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-04 (Tue, 04 Aug 2015) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Merge branch 'release_15.07' into dev Commit: e5bacc090a2a410f637f11990b640f145c8b8c1f https://github.com/galaxyproject/galaxy/commit/e5bacc090a2a410f637f11990b64… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-08-04 (Tue, 04 Aug 2015) Changed paths: M client/galaxy/style/less/history.less M static/style/blue/base.css M templates/display_base.mako M templates/search/index.mako M templates/webapps/galaxy/library/common/ldda_info.mako M templates/webapps/galaxy/library/common/ldda_permissions.mako M templates/webapps/galaxy/root/history.mako M templates/webapps/galaxy/workflow/build_from_current_history.mako Log Message: ----------- Merge pull request #539 from carlfeberhard/css.s-n-d Remove older history style rules ('historyItem*', etc.) Commit: cdf764bba616ca9eafe03c9ea182ec59a51e1207 https://github.com/galaxyproject/galaxy/commit/cdf764bba616ca9eafe03c9ea182… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-04 (Tue, 04 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-library.js M static/maps/mvc/ui/ui-select-library.js.map M static/scripts/mvc/ui/ui-select-library.js Log Message: ----------- Merge pull request #546 from guerler/fix_library_select_001 Filter deleted library datasets Commit: 253ce7b8e3ddad7693da034374bed1a751173839 https://github.com/galaxyproject/galaxy/commit/253ce7b8e3ddad7693da034374be… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-08-04 (Tue, 04 Aug 2015) Changed paths: M lib/galaxy/managers/histories.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/root.py M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/embed.mako M templates/webapps/galaxy/history/structure.mako M templates/webapps/galaxy/history/view.mako M templates/webapps/galaxy/root/history.mako Log Message: ----------- Merge pull request #530 from carlfeberhard/managers.remove-history-data Remove history+contents serializer _get_history_data Commit: 8574f7207ba5edd518392d6b6a59dd05d78a6b61 https://github.com/galaxyproject/galaxy/commit/8574f7207ba5edd518392d6b6a59… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-08-04 (Tue, 04 Aug 2015) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Core, histories: use sqlalchemy hybrid_property to allow use of History.disk_size as a column (order, query, filter, etc.) and history.disk_size as an instance property Commit: 326175cabf8c1a0566a22c74f3d9915e3765ac3d https://github.com/galaxyproject/galaxy/commit/326175cabf8c1a0566a22c74f3d9… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-08-04 (Tue, 04 Aug 2015) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Fix to 8574f72: remove unused import Commit: 7eb075e711fed2f796e276d1d53925c496bc34ca https://github.com/galaxyproject/galaxy/commit/7eb075e711fed2f796e276d1d539… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-08-04 (Tue, 04 Aug 2015) Changed paths: M client/galaxy/scripts/reports_webapp/run_stats.js M client/galaxy/style/less/base.less M static/maps/reports_webapp/run_stats.js.map M static/scripts/reports_webapp/run_stats.js M static/style/blue/base.css Log Message: ----------- Added cursor change to indicate that you can zoom Added comments to script to make it easier to find Organized script to make it easier to understand Commit: 711166c4817f214f3f13d6dab751ea30b0539723 https://github.com/galaxyproject/galaxy/commit/711166c4817f214f3f13d6dab751… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-08-04 (Tue, 04 Aug 2015) Changed paths: M lib/galaxy/webapps/reports/controllers/jobs.py Log Message: ----------- Added checking for anonymous user jobs Commit: 5df41184d44ae4053b1190c956611cdb09335184 https://github.com/galaxyproject/galaxy/commit/5df41184d44ae4053b1190c95661… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-08-04 (Tue, 04 Aug 2015) Changed paths: M client/bower.json M client/galaxy/scripts/libs/d3.js M client/galaxy/scripts/libs/farbtastic.js M client/galaxy/scripts/libs/jquery/jqtouch.js M client/galaxy/scripts/libs/raven.js M client/galaxy/scripts/libs/require.js M client/galaxy/scripts/libs/tracekit.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-panel-edit.js M client/galaxy/scripts/mvc/ui/ui-select-library.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/history.less M client/grunt-tasks/install-libs.js M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/text.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/managers/histories.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M static/maps/libs/d3.js.map M static/maps/libs/farbtastic.js.map M static/maps/libs/jquery/jqtouch.js.map M static/maps/libs/raven.js.map M static/maps/libs/require.js.map M static/maps/libs/tracekit.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-panel-edit.js.map M static/maps/mvc/ui/ui-select-library.js.map M static/maps/utils/utils.js.map M static/scripts/libs/d3.js M static/scripts/libs/farbtastic.js M static/scripts/libs/jquery/jqtouch.js M static/scripts/libs/raven.js M static/scripts/libs/require.js M static/scripts/libs/tracekit.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-panel-edit.js M static/scripts/mvc/ui/ui-select-library.js M static/scripts/utils/utils.js M static/style/blue/base.css M templates/display_base.mako M templates/search/index.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/embed.mako M templates/webapps/galaxy/history/structure.mako M templates/webapps/galaxy/history/view.mako M templates/webapps/galaxy/library/common/ldda_info.mako M templates/webapps/galaxy/library/common/ldda_permissions.mako M templates/webapps/galaxy/root/history.mako M templates/webapps/galaxy/workflow/build_from_current_history.mako M test/functional/test_toolbox.py A test/functional/tool-data/fasta_indexes.loc M test/functional/tool-data/sample_tool_data_tables.xml A test/functional/tools/dbkey_filter_input.xml A test/functional/tools/dbkey_filter_multi_input.xml M test/functional/tools/samples_tool_conf.xml M tools/extract/extract_genomic_dna.py M tools/extract/extract_genomic_dna.xml Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into Reports_newpage Conflicts: static/style/blue/base.css Commit: 8395244a38bf1d3c58467a9577de228cd8012894 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lib/galaxy/datatypes/text.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/managers/histories.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M static/maps/libs/d3.js.map M static/maps/libs/farbtastic.js.map M static/maps/libs/jquery/jqtouch.js.map M static/maps/libs/raven.js.map M static/maps/libs/require.js.map M static/maps/libs/tracekit.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-panel-edit.js.map M static/maps/mvc/ui/ui-select-library.js.map M static/maps/utils/utils.js.map M static/scripts/libs/d3.js M static/scripts/libs/farbtastic.js M static/scripts/libs/jquery/jqtouch.js M static/scripts/libs/raven.js M static/scripts/libs/require.js M static/scripts/libs/tracekit.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-panel-edit.js M static/scripts/mvc/ui/ui-select-library.js M static/scripts/utils/utils.js M static/style/blue/base.css M templates/display_base.mako M templates/search/index.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/embed.mako M templates/webapps/galaxy/history/structure.mako M templates/webapps/galaxy/history/view.mako M templates/webapps/galaxy/library/common/ldda_info.mako M templates/webapps/galaxy/library/common/ldda_permissions.mako M templates/webapps/galaxy/root/history.mako M templates/webapps/galaxy/workflow/build_from_current_history.mako M test/functional/test_toolbox.py A test/functional/tool-data/fasta_indexes.loc M test/functional/tool-data/sample_tool_data_tables.xml A test/functional/tools/dbkey_filter_input.xml A test/functional/tools/dbkey_filter_multi_input.xml M test/functional/tools/samples_tool_conf.xml M tools/extract/extract_genomic_dna.py M tools/extract/extract_genomic_dna.xml Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into Reports_homepage Conflicts: static/style/blue/base.css Commit: 0b7b0b484e2fa94f65d10cbf0348ef39411acae0 https://github.com/galaxyproject/galaxy/commit/0b7b0b484e2fa94f65d10cbf0348… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-08-04 (Tue, 04 Aug 2015) Changed paths: M lib/galaxy/managers/datasets.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- API, datasets: create a way to get or create a converted datasets for a particular format: api/datasets/:id/converted/:format_ext, and a way to return all existing conversions in a dictionary: api/datasets/:id/converted Commit: 13389042883fe657c6b289ba6fb2db7630ffd86e https://github.com/galaxyproject/galaxy/commit/13389042883fe657c6b289ba6fb2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-05 (Wed, 05 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/utils/uploadbox.js M static/maps/mvc/upload/composite/composite-view.js.map M static/maps/mvc/upload/default/default-view.js.map M static/maps/utils/uploadbox.js.map M static/scripts/mvc/upload/composite/composite-view.js M static/scripts/mvc/upload/default/default-view.js M static/scripts/utils/uploadbox.js Log Message: ----------- Separate file submission from upload queue, augment and generalize send function Commit: cc46b65d16275e8f73cfceb4c1546e795146bf35 https://github.com/galaxyproject/galaxy/commit/cc46b65d16275e8f73cfceb4c154… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-05 (Wed, 05 Aug 2015) Changed paths: M 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lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M static/maps/libs/d3.js.map M static/maps/libs/farbtastic.js.map M static/maps/libs/jquery/jqtouch.js.map M static/maps/libs/raven.js.map M static/maps/libs/require.js.map M static/maps/libs/tracekit.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-panel-edit.js.map M static/maps/mvc/ui/ui-select-library.js.map M static/maps/utils/utils.js.map M static/scripts/libs/d3.js M static/scripts/libs/farbtastic.js M static/scripts/libs/jquery/jqtouch.js M static/scripts/libs/raven.js M static/scripts/libs/require.js M static/scripts/libs/tracekit.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-panel-edit.js M static/scripts/mvc/ui/ui-select-library.js M static/scripts/utils/utils.js M static/style/blue/base.css M templates/display_base.mako M templates/search/index.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/embed.mako M templates/webapps/galaxy/history/structure.mako M templates/webapps/galaxy/history/view.mako M templates/webapps/galaxy/library/common/ldda_info.mako M templates/webapps/galaxy/library/common/ldda_permissions.mako M templates/webapps/galaxy/root/history.mako M templates/webapps/galaxy/workflow/build_from_current_history.mako M test/functional/test_toolbox.py A test/functional/tool-data/fasta_indexes.loc M test/functional/tool-data/sample_tool_data_tables.xml A test/functional/tools/dbkey_filter_input.xml A test/functional/tools/dbkey_filter_multi_input.xml M test/functional/tools/samples_tool_conf.xml M tools/extract/extract_genomic_dna.py M tools/extract/extract_genomic_dna.xml Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into upload_000 Conflicts: static/style/blue/base.css Commit: 42c61535d6abdf5b30a4ad10396a42b4e22eb514 https://github.com/galaxyproject/galaxy/commit/42c61535d6abdf5b30a4ad10396a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-05 (Wed, 05 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/utils/uploadbox.js M static/maps/mvc/upload/composite/composite-view.js.map M static/maps/utils/uploadbox.js.map M static/scripts/mvc/upload/composite/composite-view.js M static/scripts/utils/uploadbox.js Log Message: ----------- Separate upload post function, remove some unnecessary functions Commit: d85342d5097e66756900592bda86eb0bf4e5c363 https://github.com/galaxyproject/galaxy/commit/d85342d5097e66756900592bda86… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-05 (Wed, 05 Aug 2015) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Fix comment Commit: 8e093847f9a718de63c7ac698adadebdffc076e7 https://github.com/galaxyproject/galaxy/commit/8e093847f9a718de63c7ac698ada… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-05 (Wed, 05 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/utils/uploadbox.js M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/composite/composite-view.js.map M static/maps/mvc/upload/default/default-view.js.map M static/maps/mvc/upload/upload-view.js.map M static/maps/utils/uploadbox.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/composite/composite-view.js M static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/upload-view.js M static/scripts/utils/uploadbox.js Log Message: ----------- Enable composite data submission Commit: 8eca23e4b473824d1b75635e057d018d0825d767 https://github.com/galaxyproject/galaxy/commit/8eca23e4b473824d1b75635e057d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-05 (Wed, 05 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/utils/uploadbox.js M static/maps/mvc/upload/composite/composite-view.js.map M static/maps/mvc/upload/default/default-view.js.map M static/maps/mvc/upload/upload-view.js.map M static/maps/utils/uploadbox.js.map M static/scripts/mvc/upload/composite/composite-view.js M static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/upload-view.js M static/scripts/utils/uploadbox.js Log Message: ----------- Attach success, error handlers for composite uploads, fixes Commit: e3f2255a09ac4a4827aa9a38908ac21285f7c482 https://github.com/galaxyproject/galaxy/commit/e3f2255a09ac4a4827aa9a38908a… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-08-05 (Wed, 05 Aug 2015) Changed paths: M CONTRIBUTING.md M doc/source/project/organization.rst Log Message: ----------- This commit implements #382 in response to the lack of explicit language on how reversions are to be handled. This is in response to the events transpiring in #433 and #449. Additionally this PR corrects the misspelling of the pluralization of the word veto. This is a direct follow up, per procedures with a single squashed commit, of #450. Commit: aa3080ff38e2a9d676b650ead86c99c781ed91b5 https://github.com/galaxyproject/galaxy/commit/aa3080ff38e2a9d676b650ead86c… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-08-05 (Wed, 05 Aug 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Correct typo Commit: 9ad5c6c1874d8c969632d0516fb0ce5420acd20b https://github.com/galaxyproject/galaxy/commit/9ad5c6c1874d8c969632d0516fb0… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-05 (Wed, 05 Aug 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge pull request #561 from erasche/rerl-typo Correct typo Commit: 45b4a4ef333ffc40f99d28fdf48618927fa4c4d3 https://github.com/galaxyproject/galaxy/commit/45b4a4ef333ffc40f99d28fdf486… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2015-08-05 (Wed, 05 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-library.js M client/galaxy/style/less/history.less M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/managers/histories.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M static/maps/mvc/ui/ui-select-library.js.map M static/scripts/mvc/ui/ui-select-library.js M static/style/blue/base.css M templates/display_base.mako M templates/search/index.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/embed.mako M templates/webapps/galaxy/history/structure.mako M templates/webapps/galaxy/history/view.mako M templates/webapps/galaxy/library/common/ldda_info.mako M templates/webapps/galaxy/library/common/ldda_permissions.mako M templates/webapps/galaxy/root/history.mako M templates/webapps/galaxy/workflow/build_from_current_history.mako Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into dev Commit: d6a854006f5cd6ffde2bd08df7eb70864f3c9591 https://github.com/galaxyproject/galaxy/commit/d6a854006f5cd6ffde2bd08df7eb… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2015-08-05 (Wed, 05 Aug 2015) Changed paths: M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/util/basic_util.py Log Message: ----------- Reworked fix for the change_directory action, and enhancements for directory actions to now make use of $TMP_WORK_DIR in recipes. Commit: 668e650f52c434d428ad13544d8425f5cbed521f https://github.com/galaxyproject/galaxy/commit/668e650f52c434d428ad13544d84… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-08-05 (Wed, 05 Aug 2015) Changed paths: A client/galaxy/scripts/utils/query-string-parsing.js M client/galaxy/scripts/viz/trackster.js M config/plugins/visualizations/trackster/config/trackster.xml A static/maps/utils/query-string-parsing.js.map M static/maps/viz/trackster.js.map A static/scripts/utils/query-string-parsing.js M static/scripts/viz/trackster.js Log Message: ----------- Merge pull request #526 from carlfeberhard/trackster.existing-browser Visualizations, trackster: allow the user to add the dataset launched… Commit: 871e25301598edc8ed698ac6ce893a5b9f399216 https://github.com/galaxyproject/galaxy/commit/871e25301598edc8ed698ac6ce89… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-06 (Thu, 06 Aug 2015) Changed paths: M lib/galaxy/webapps/tool_shed/search/tool_search.py M scripts/tool_shed/build_ts_whoosh_index.py M templates/webapps/galaxy/cloud/index.mako Log Message: ----------- merge 15.07 into dev Commit: 9d22cd678e462a4dd8d32b30cb080869dca7eb77 https://github.com/galaxyproject/galaxy/commit/9d22cd678e462a4dd8d32b30cb08… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-06 (Thu, 06 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Correct examples in workflow invocations. Commit: 8a683848ee98c3b5f8a674dda037263a5016b4ad https://github.com/galaxyproject/galaxy/commit/8a683848ee98c3b5f8a674dda037… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-08-06 (Thu, 06 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Merge pull request #565 from dannon/dev Correct examples in workflow invocations. Commit: 7a3986793364c6534b484d0ff6d5d7dcbaa6a720 https://github.com/galaxyproject/galaxy/commit/7a3986793364c6534b484d0ff6d5… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-06 (Thu, 06 Aug 2015) Changed paths: M scripts/tool_shed/build_ts_whoosh_index.py Log Message: ----------- Merge branch 'release_15.07' into dev Commit: 9838d938a2b0f619029db904ecfe499b99a653a5 https://github.com/galaxyproject/galaxy/commit/9838d938a2b0f619029db904ecfe… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-06 (Thu, 06 Aug 2015) Changed paths: M lib/galaxy/datatypes/registry.py Log Message: ----------- Merge branch 'release_15.07' into dev Commit: a781f0abb9cd3ffed9b01c4b3c6bd037f9bab700 https://github.com/galaxyproject/galaxy/commit/a781f0abb9cd3ffed9b01c4b3c6b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-06 (Thu, 06 Aug 2015) Changed paths: A doc/source/api/guidelines.rst M doc/source/api_doc.rst M doc/source/index.rst A doc/source/ts_api_doc.rst Log Message: ----------- initial commit to include TS API documentation on readthedocs Commit: 6d620438b5a977f575dd98e97c9abb68721a53a8 https://github.com/galaxyproject/galaxy/commit/6d620438b5a977f575dd98e97c9a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-06 (Thu, 06 Aug 2015) Changed paths: M doc/source/releases/_header.rst Log Message: ----------- fix the url for galaxy logo that has changed on the wiki Commit: 4441fb4732465ab90c1591621f6b053ec8f230c8 https://github.com/galaxyproject/galaxy/commit/4441fb4732465ab90c1591621f6b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-08-06 (Thu, 06 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/form/form-select-content.js M static/maps/mvc/form/form-select-content.js.map M static/scripts/mvc/form/form-select-content.js Log Message: ----------- Merge pull request #568 from ericenns/new-tool-form-batch-collection [15.05] Fix batch mode input in new tool form ui Commit: 0e48775f91e930cb32e72808ea18623f42dd9b34 https://github.com/galaxyproject/galaxy/commit/0e48775f91e930cb32e72808ea18… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-06 (Thu, 06 Aug 2015) Changed paths: A doc/source/api/guidelines.rst M doc/source/api_doc.rst M doc/source/index.rst M doc/source/releases/_header.rst A doc/source/ts_api_doc.rst Log Message: ----------- Merge pull request #569 from martenson/doc-include-ts-api Include TS API docs in readthedocs Commit: 8f8d9ff55cd25c9634384bb8d93b04362891ff5e https://github.com/galaxyproject/galaxy/commit/8f8d9ff55cd25c9634384bb8d93b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-08-06 (Thu, 06 Aug 2015) Changed paths: M lib/galaxy/managers/datasets.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Merge pull request #553 from carlfeberhard/api.implicit-conversion API, datasets: create a way to get or create a converted datasets for… Commit: b8332caa4d1c19af79341e067b67fd7b0bd8b38d 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templates/page_base.mako M templates/sorting_base.mako A templates/spark_base.mako M templates/webapps/reports/base_panels.mako M templates/webapps/reports/index.mako M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_all.mako M templates/webapps/reports/jobs_specified_month_in_error.mako M templates/webapps/reports/jobs_tool_per_month.mako M templates/webapps/reports/jobs_user_per_month.mako M templates/webapps/reports/registered_users_per_month.mako M templates/webapps/reports/registered_users_specified_month.mako M templates/webapps/reports/requests_per_month_all.mako M templates/webapps/reports/requests_per_user.mako M templates/webapps/reports/requests_user_per_month.mako M templates/webapps/reports/users_last_access_date.mako M templates/webapps/reports/users_user_disk_usage.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako A templates/webapps/reports/workflows_per_workflow.mako M templates/webapps/reports/workflows_user_per_month.mako Log Message: ----------- Merge pull request #410 from Airistotal/Reports_newpage Reports newpage Commit: c7b9ee3c1330dd86dffac51e9d9ff23f6fbf99ce https://github.com/galaxyproject/galaxy/commit/c7b9ee3c1330dd86dffac51e9d9f… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-08-06 (Thu, 06 Aug 2015) Changed paths: A client/galaxy/scripts/libs/jquery.sparklines.js M client/galaxy/scripts/mvc/form/form-select-content.js A client/galaxy/scripts/utils/query-string-parsing.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/style/less/base.less A client/galaxy/style/less/reports.less M client/grunt-tasks/style.js M config/plugins/visualizations/trackster/config/trackster.xml A doc/source/api/guidelines.rst M doc/source/api_doc.rst M doc/source/index.rst M doc/source/releases/_header.rst A doc/source/ts_api_doc.rst M lib/galaxy/datatypes/registry.py M lib/galaxy/managers/datasets.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/reports/controllers/workflows.py M lib/galaxy/webapps/tool_shed/search/tool_search.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M scripts/tool_shed/build_ts_whoosh_index.py A static/maps/libs/jquery.sparklines.js.map M static/maps/mvc/form/form-select-content.js.map A static/maps/utils/query-string-parsing.js.map M static/maps/viz/trackster.js.map A static/scripts/libs/jquery.sparklines.js M static/scripts/mvc/form/form-select-content.js A static/scripts/utils/query-string-parsing.js M static/scripts/viz/trackster.js M static/style/blue/base.css A static/style/blue/reports.css M templates/base.mako M templates/page_base.mako M templates/sorting_base.mako A templates/spark_base.mako M templates/webapps/galaxy/cloud/index.mako M templates/webapps/reports/base_panels.mako M templates/webapps/reports/index.mako M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_all.mako M templates/webapps/reports/jobs_specified_month_in_error.mako M templates/webapps/reports/jobs_tool_per_month.mako M templates/webapps/reports/jobs_user_per_month.mako M templates/webapps/reports/registered_users_per_month.mako M templates/webapps/reports/registered_users_specified_month.mako M templates/webapps/reports/requests_per_month_all.mako M templates/webapps/reports/requests_per_user.mako M templates/webapps/reports/requests_user_per_month.mako M templates/webapps/reports/users_last_access_date.mako M templates/webapps/reports/users_user_disk_usage.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako A templates/webapps/reports/workflows_per_workflow.mako M templates/webapps/reports/workflows_user_per_month.mako Log Message: ----------- Merge branch 'dev' of https://github.com/Airistotal/galaxy into Reports_homepage Conflicts: client/galaxy/style/less/base.less static/style/blue/base.css Commit: 2a8aea00e5a369b5ac826064c1235c4611b2355a https://github.com/galaxyproject/galaxy/commit/2a8aea00e5a369b5ac826064c123… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-08-07 (Fri, 07 Aug 2015) Changed paths: M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/util/basic_util.py Log Message: ----------- Merge pull request #511 from gregvonkuster/dev Fix the ChangeDirectory.execute_step() method and enhance the Commit: d9d86ee8a749550d052ef4f7dc3ff4be51e00734 https://github.com/galaxyproject/galaxy/commit/d9d86ee8a749550d052ef4f7dc3f… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-07 (Fri, 07 Aug 2015) Changed paths: M CONTRIBUTING.md Log Message: ----------- Update contact email address for security issues. Commit: 55e0f109fcebbee3da19e0d5a568ff5b4cedcddb https://github.com/galaxyproject/galaxy/commit/55e0f109fcebbee3da19e0d5a568… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-07 (Fri, 07 Aug 2015) Changed paths: M CONTRIBUTING.md Log Message: ----------- Mention GitHub issues. Commit: 86aa07d87e61a980b98cf6fa6e6360e7d649f5e5 https://github.com/galaxyproject/galaxy/commit/86aa07d87e61a980b98cf6fa6e63… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-07 (Fri, 07 Aug 2015) Changed paths: M CONTRIBUTING.md Log Message: ----------- Require PRs to pass the CI tests. Commit: 3df58181cdf13f6a8e7e41fb813c49de4c5a6dd6 https://github.com/galaxyproject/galaxy/commit/3df58181cdf13f6a8e7e41fb813c… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-07 (Fri, 07 Aug 2015) Changed paths: M CONTRIBUTING.md Log Message: ----------- Small fixes for CONTRIBUTING.md . Commit: f49fc1c72465d71c774194b7c0d6b5ee808cc0f8 https://github.com/galaxyproject/galaxy/commit/f49fc1c72465d71c774194b7c0d6… Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com> Date: 2015-08-07 (Fri, 07 Aug 2015) Changed paths: M lib/galaxy/tools/parameters/output.py Log Message: ----------- Merge pull request #544 from jmchilton/collection_actions Update output actions code for some collection operations. Commit: 725261e35e47bb0a9dd64d36ef2546959883401e https://github.com/galaxyproject/galaxy/commit/725261e35e47bb0a9dd64d36ef25… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-07 (Fri, 07 Aug 2015) Changed paths: M lib/galaxy/dataset_collections/builder.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/collections_util.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parser/xml.py M test/functional/test_toolbox.py A test/functional/tools/collection_creates_dynamic_list_of_pairs.xml A test/functional/tools/collection_creates_dynamic_nested.xml A test/functional/tools/collection_creates_list_of_pairs.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #538 from jmchilton/dynamic_nested_collections Allow tools to explicitly produce nested collections. Commit: 48da7d6207ad82a5b01dc4cfa69eba6cef7979ef https://github.com/galaxyproject/galaxy/commit/48da7d6207ad82a5b01dc4cfa69e… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-08-07 (Fri, 07 Aug 2015) Changed paths: R templates/webapps/tool_shed/message.mako Log Message: ----------- Stop creating database/message.mako.py Commit: d6ef0458309a9cfea12cb33b9d0931fd75eeb04a https://github.com/galaxyproject/galaxy/commit/d6ef0458309a9cfea12cb33b9d09… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-08-07 (Fri, 07 Aug 2015) Changed paths: M lib/galaxy/webapps/reports/controllers/jobs.py M templates/page_base.mako M templates/spark_base.mako M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_in_error.mako Log Message: ----------- Applied paging to all pages Commit: 3feaedbf17ed6f1e6542dfaa07985f89fbff7c97 https://github.com/galaxyproject/galaxy/commit/3feaedbf17ed6f1e6542dfaa0798… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-07 (Fri, 07 Aug 2015) Changed paths: R templates/webapps/tool_shed/message.mako Log Message: ----------- Merge pull request #575 from davebx/database_message Stop creating database/message.mako.py Commit: ff13fb85cc46cdf8399e3477ba8808dfc6078ed5 https://github.com/galaxyproject/galaxy/commit/ff13fb85cc46cdf8399e3477ba88… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-08-07 (Fri, 07 Aug 2015) Changed paths: M client/bower.json M client/galaxy/scripts/libs/d3.js M client/galaxy/scripts/libs/farbtastic.js A client/galaxy/scripts/libs/jquery.sparklines.js M client/galaxy/scripts/libs/jquery/jqtouch.js M client/galaxy/scripts/libs/raven.js M client/galaxy/scripts/libs/require.js M client/galaxy/scripts/libs/tracekit.js M client/galaxy/scripts/mvc/form/form-select-content.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-panel-edit.js M client/galaxy/scripts/mvc/ui/ui-select-library.js A client/galaxy/scripts/utils/query-string-parsing.js M client/galaxy/scripts/utils/utils.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/style/less/base.less M client/galaxy/style/less/history.less A client/galaxy/style/less/reports.less M client/grunt-tasks/install-libs.js M client/grunt-tasks/style.js M config/galaxy.ini.sample M config/plugins/visualizations/trackster/config/trackster.xml A doc/source/api/guidelines.rst M doc/source/api_doc.rst M doc/source/index.rst M doc/source/releases/_header.rst A doc/source/ts_api_doc.rst M lib/galaxy/config.py M lib/galaxy/dataset_collections/builder.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/text.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/collections_util.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/histories.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parameters/output.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/reports/controllers/workflows.py M lib/galaxy/webapps/tool_shed/search/tool_search.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/util/basic_util.py M scripts/tool_shed/build_ts_whoosh_index.py M static/maps/libs/d3.js.map M static/maps/libs/farbtastic.js.map A static/maps/libs/jquery.sparklines.js.map M static/maps/libs/jquery/jqtouch.js.map M static/maps/libs/raven.js.map M static/maps/libs/require.js.map M static/maps/libs/tracekit.js.map M static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-panel-edit.js.map M static/maps/mvc/ui/ui-select-library.js.map A static/maps/utils/query-string-parsing.js.map M static/maps/utils/utils.js.map M static/maps/viz/trackster.js.map M static/scripts/libs/d3.js M static/scripts/libs/farbtastic.js A static/scripts/libs/jquery.sparklines.js M static/scripts/libs/jquery/jqtouch.js M static/scripts/libs/raven.js M static/scripts/libs/require.js M static/scripts/libs/tracekit.js M static/scripts/mvc/form/form-select-content.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-panel-edit.js M static/scripts/mvc/ui/ui-select-library.js A static/scripts/utils/query-string-parsing.js M static/scripts/utils/utils.js M static/scripts/viz/trackster.js M static/style/blue/base.css A static/style/blue/reports.css M templates/base.mako M templates/display_base.mako M templates/page_base.mako M templates/search/index.mako M templates/sorting_base.mako A templates/spark_base.mako M templates/webapps/galaxy/cloud/index.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/embed.mako M templates/webapps/galaxy/history/structure.mako M templates/webapps/galaxy/history/view.mako M templates/webapps/galaxy/library/common/ldda_info.mako M templates/webapps/galaxy/library/common/ldda_permissions.mako M templates/webapps/galaxy/workflow/build_from_current_history.mako M templates/webapps/reports/base_panels.mako M templates/webapps/reports/index.mako M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_all.mako M templates/webapps/reports/jobs_specified_month_in_error.mako M templates/webapps/reports/jobs_tool_per_month.mako M templates/webapps/reports/jobs_user_per_month.mako M templates/webapps/reports/registered_users_per_month.mako M templates/webapps/reports/registered_users_specified_month.mako M templates/webapps/reports/requests_per_month_all.mako M templates/webapps/reports/requests_per_user.mako M templates/webapps/reports/requests_user_per_month.mako M templates/webapps/reports/users_last_access_date.mako M templates/webapps/reports/users_user_disk_usage.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako A templates/webapps/reports/workflows_per_workflow.mako M templates/webapps/reports/workflows_user_per_month.mako R templates/webapps/tool_shed/message.mako M test/functional/test_toolbox.py A test/functional/tool-data/fasta_indexes.loc M test/functional/tool-data/sample_tool_data_tables.xml A test/functional/tools/collection_creates_dynamic_list_of_pairs.xml A test/functional/tools/collection_creates_dynamic_nested.xml A test/functional/tools/collection_creates_list_of_pairs.xml A test/functional/tools/dbkey_filter_input.xml A test/functional/tools/dbkey_filter_multi_input.xml M test/functional/tools/samples_tool_conf.xml M tools/extract/extract_genomic_dna.py M tools/extract/extract_genomic_dna.xml Log Message: ----------- Merge conflicts Commit: b88760661621910f3165dd3f1d978b3a1a434ca0 https://github.com/galaxyproject/galaxy/commit/b88760661621910f3165dd3f1d97… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-07 (Fri, 07 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/upload-view.js M static/maps/mvc/upload/upload-view.js.map M static/scripts/mvc/upload/upload-view.js Log Message: ----------- make the 'Start' button green when enabled I have seen numerous times how people struggle to find the correct button when uploading. This should help them. Commit: 960d9e5634826ea6ef1734f9adba25c3bb72a76b https://github.com/galaxyproject/galaxy/commit/960d9e5634826ea6ef1734f9adba… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-07 (Fri, 07 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/style/less/ui.less M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/composite/composite-view.js.map M static/maps/mvc/upload/default/default-view.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/composite/composite-view.js M static/style/blue/base.css Log Message: ----------- Fix ui behavior for restart, progress and result states Commit: d6d8604d5315ce7268d361afc10307535b735b58 https://github.com/galaxyproject/galaxy/commit/d6d8604d5315ce7268d361afc103… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-07 (Fri, 07 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/upload-view.js M static/maps/mvc/upload/upload-view.js.map M static/scripts/mvc/upload/upload-view.js Log Message: ----------- update with @jxtx suggesting of using existing classes Commit: 2d332e9b71b4ff28d228ef57c8bd46b6c8b1d2c4 https://github.com/galaxyproject/galaxy/commit/2d332e9b71b4ff28d228ef57c8bd… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-07 (Fri, 07 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-view.js M static/maps/mvc/upload/composite/composite-view.js.map M static/scripts/mvc/upload/composite/composite-view.js Log Message: ----------- Disable restart button if upload completed Commit: 868087c78b5b95f0d2c0a8456c0d8c82a4f7533c https://github.com/galaxyproject/galaxy/commit/868087c78b5b95f0d2c0a8456c0d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-07 (Fri, 07 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/upload-view.js M static/maps/mvc/upload/upload-view.js.map M static/scripts/mvc/upload/upload-view.js Log Message: ----------- Merge pull request #577 from martenson/upload-green-button make the upload 'Start' button green when enabled Commit: d76efc57523daa5cbb05200a2c6868e2eb9db228 https://github.com/galaxyproject/galaxy/commit/d76efc57523daa5cbb05200a2c68… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-07 (Fri, 07 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/composite/composite-view.js M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/composite/composite-view.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/composite/composite-view.js Log Message: ----------- Activate paste/fetch feature, improve behavior Commit: b0c7b736d450121528c4518880a2c6f128a4ee7c https://github.com/galaxyproject/galaxy/commit/b0c7b736d450121528c4518880a2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-07 (Fri, 07 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-view.js M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/composite/composite-view.js.map M static/maps/mvc/upload/default/default-view.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/composite/composite-view.js M static/scripts/mvc/upload/default/default-view.js Log Message: ----------- Add green start button, fix text field Commit: 1f3ee5f64806d41bc4166248370aab443c60c49e https://github.com/galaxyproject/galaxy/commit/1f3ee5f64806d41bc4166248370a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-07 (Fri, 07 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/default/default-view.js M static/maps/mvc/upload/default/default-view.js.map M static/scripts/mvc/upload/default/default-view.js Log Message: ----------- Adjust start button location Commit: 3fae23368b85682c99b82a855c8ddf0d28238e7b https://github.com/galaxyproject/galaxy/commit/3fae23368b85682c99b82a855c8d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-07 (Fri, 07 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/composite/composite-view.js M static/scripts/mvc/upload/default/default-view.js Log Message: ----------- Fix color to primary/blue Commit: 94676038ec6a6f4396e331e7c374fc40087b1c0e https://github.com/galaxyproject/galaxy/commit/94676038ec6a6f4396e331e7c374… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-08 (Sat, 08 Aug 2015) Changed paths: M lib/tool_shed/metadata/metadata_generator.py Log Message: ----------- Merge pull request #495 from davebx/empty_test_values Fix for server error when installing certain repositories. Commit: f55b70e2d395c3aaa7745c46e35a79913f3a1374 https://github.com/galaxyproject/galaxy/commit/f55b70e2d395c3aaa7745c46e35a… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-08-09 (Sun, 09 Aug 2015) Changed paths: M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge pull request #462 from scholtalbers/dev Some minor changes to get ipython running on my instance Commit: c51b5c9b8de0019030542b040ce824866a85c435 https://github.com/galaxyproject/galaxy/commit/c51b5c9b8de0019030542b040ce8… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-09 (Sun, 09 Aug 2015) Changed paths: A client/galaxy/scripts/reports_webapp/run_stats.js M client/galaxy/style/less/reports.less A lib/galaxy/webapps/reports/controllers/home.py A static/images/reports_webapp/bases/home-icon-active.png A static/images/reports_webapp/bases/home-icon-hov.png A static/images/reports_webapp/bases/home-icon.png A static/images/reports_webapp/home-icon-active.png A static/images/reports_webapp/home-icon-hov.png A static/images/reports_webapp/home-icon.png A static/maps/reports_webapp/run_stats.js.map A static/scripts/reports_webapp/run_stats.js M static/style/blue/base.css M static/style/blue/reports.css M templates/base.mako M templates/webapps/reports/index.mako A templates/webapps/reports/run_stats.mako Log Message: ----------- Merge pull request #472 from Airistotal/Reports_homepage Reports homepage Commit: 17b84cb7b4bd67e4b0d9941b77cbed3c60201b43 https://github.com/galaxyproject/galaxy/commit/17b84cb7b4bd67e4b0d9941b77cb… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-10 (Mon, 10 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/style/less/upload.less M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/default/default-row.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/default/default-row.js M static/style/blue/base.css Log Message: ----------- Fix paste/fetch field style Commit: 5e4c0bcf64666b4c30fe4519479d0d7e1aee9000 https://github.com/galaxyproject/galaxy/commit/5e4c0bcf64666b4c30fe4519479d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-10 (Mon, 10 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-view.js M static/maps/mvc/upload/composite/composite-view.js.map M static/maps/mvc/upload/default/default-view.js.map M static/scripts/mvc/upload/composite/composite-view.js M static/scripts/mvc/upload/default/default-view.js Log Message: ----------- Fix start button style Commit: 971b96ddd6855e0e2fd61b89499a15d9e6fb3b93 https://github.com/galaxyproject/galaxy/commit/971b96ddd6855e0e2fd61b89499a… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-08-10 (Mon, 10 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js M static/maps/mvc/history/options-menu.js.map M static/scripts/mvc/history/options-menu.js Log Message: ----------- UI, Histories: when calling 'Delete hidden', both delete *and* unhide the datasets (preventing them from being both deleted and hidden) Commit: 3e212507defb88e91799883754d4a1d1ae8c0876 https://github.com/galaxyproject/galaxy/commit/3e212507defb88e91799883754d4… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-08-10 (Mon, 10 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py M templates/webapps/galaxy/history/view.mako Log Message: ----------- UI, Histories: fix view.mako json ref, remove unused import in root Commit: b0a8c6f52bfda10244e12b08ff3143c1f4ef0d45 https://github.com/galaxyproject/galaxy/commit/b0a8c6f52bfda10244e12b08ff31… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-08-10 (Mon, 10 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js M static/maps/mvc/history/options-menu.js.map M static/scripts/mvc/history/options-menu.js Log Message: ----------- UI, Histories: use renderItems for batched changes in options menu Commit: f658e1577d36a66fa3f6ca7f8d09a44bf2051658 https://github.com/galaxyproject/galaxy/commit/f658e1577d36a66fa3f6ca7f8d09… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-08-10 (Mon, 10 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- UI, Histories: page Saved Histories at 10 histories Commit: 4395c7f89d6618b9649b8af919cd3f4ec87b072b https://github.com/galaxyproject/galaxy/commit/4395c7f89d6618b9649b8af919cd… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-10 (Mon, 10 Aug 2015) Changed paths: M config/datatypes_conf.xml.sample M templates/webapps/tool_shed/repository/manage_repository.mako Log Message: ----------- Merge branch 'release_15.07' into dev Commit: 92526c834049a4b8e16f479521400542eeb503c8 https://github.com/galaxyproject/galaxy/commit/92526c834049a4b8e16f47952140… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-10 (Mon, 10 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/default/default-view.js M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/default/default-view.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/default/default-view.js Log Message: ----------- Fix update screen calls Commit: eaff25b6eb89bf1cd563b6a350f119e3a8371bc3 https://github.com/galaxyproject/galaxy/commit/eaff25b6eb89bf1cd563b6a350f1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-10 (Mon, 10 Aug 2015) Changed paths: A client/galaxy/scripts/libs/jquery.sparklines.js M client/galaxy/scripts/mvc/form/form-select-content.js M client/galaxy/scripts/mvc/upload/upload-view.js A client/galaxy/scripts/reports_webapp/run_stats.js A client/galaxy/scripts/utils/query-string-parsing.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/style/less/base.less A client/galaxy/style/less/reports.less M client/grunt-tasks/style.js M config/datatypes_conf.xml.sample M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/visualizations/trackster/config/trackster.xml A doc/source/api/guidelines.rst M doc/source/api_doc.rst M doc/source/index.rst M doc/source/releases/_header.rst A doc/source/ts_api_doc.rst M lib/galaxy/dataset_collections/builder.py M lib/galaxy/datatypes/registry.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/collections_util.py M lib/galaxy/managers/datasets.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parameters/output.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py A lib/galaxy/webapps/reports/controllers/home.py M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/reports/controllers/workflows.py M lib/galaxy/webapps/tool_shed/search/tool_search.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/basic_util.py M scripts/tool_shed/build_ts_whoosh_index.py A static/images/reports_webapp/bases/home-icon-active.png A static/images/reports_webapp/bases/home-icon-hov.png A static/images/reports_webapp/bases/home-icon.png A static/images/reports_webapp/home-icon-active.png A static/images/reports_webapp/home-icon-hov.png A static/images/reports_webapp/home-icon.png A static/maps/libs/jquery.sparklines.js.map M static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/upload/upload-view.js.map A static/maps/reports_webapp/run_stats.js.map A static/maps/utils/query-string-parsing.js.map M static/maps/viz/trackster.js.map A static/scripts/libs/jquery.sparklines.js M static/scripts/mvc/form/form-select-content.js A static/scripts/reports_webapp/run_stats.js A static/scripts/utils/query-string-parsing.js M static/scripts/viz/trackster.js M static/style/blue/base.css A static/style/blue/reports.css M templates/base.mako M templates/page_base.mako M templates/sorting_base.mako A templates/spark_base.mako M templates/webapps/galaxy/cloud/index.mako M templates/webapps/reports/base_panels.mako M templates/webapps/reports/index.mako M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_all.mako M templates/webapps/reports/jobs_specified_month_in_error.mako M templates/webapps/reports/jobs_tool_per_month.mako M templates/webapps/reports/jobs_user_per_month.mako M templates/webapps/reports/registered_users_per_month.mako M templates/webapps/reports/registered_users_specified_month.mako M templates/webapps/reports/requests_per_month_all.mako M templates/webapps/reports/requests_per_user.mako M templates/webapps/reports/requests_user_per_month.mako A templates/webapps/reports/run_stats.mako M templates/webapps/reports/users_last_access_date.mako M templates/webapps/reports/users_user_disk_usage.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako A templates/webapps/reports/workflows_per_workflow.mako M templates/webapps/reports/workflows_user_per_month.mako R templates/webapps/tool_shed/message.mako M templates/webapps/tool_shed/repository/manage_repository.mako M test/functional/test_toolbox.py A test/functional/tools/collection_creates_dynamic_list_of_pairs.xml A test/functional/tools/collection_creates_dynamic_nested.xml A test/functional/tools/collection_creates_list_of_pairs.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into upload_000 Conflicts: client/galaxy/scripts/mvc/upload/upload-view.js static/maps/mvc/upload/upload-view.js.map static/scripts/mvc/upload/upload-view.js static/style/blue/base.css Commit: dcf1e9910b310a68770a87542adcbfb3160e35d6 https://github.com/galaxyproject/galaxy/commit/dcf1e9910b310a68770a87542adc… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-08-10 (Mon, 10 Aug 2015) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Core, history: coalesce empty histories to size Decimal(0) Commit: 4beeeecf4c3dda5ee18c4dc928fb416a7b56de79 https://github.com/galaxyproject/galaxy/commit/4beeeecf4c3dda5ee18c4dc928fb… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-10 (Mon, 10 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/upload-model.js M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/composite/composite-view.js.map M static/maps/mvc/upload/upload-model.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/composite/composite-view.js M static/scripts/mvc/upload/upload-model.js Log Message: ----------- Fix file names and description Commit: 87d571120972a50dc5d25967a1f10e627c0dff91 https://github.com/galaxyproject/galaxy/commit/87d571120972a50dc5d25967a1f1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-10 (Mon, 10 Aug 2015) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Merge pull request #550 from carlfeberhard/history.size Core, histories: use sqlalchemy hybrid_property to allow use of Histo… Commit: 11f03d363c55f16a6b7f02975405391809098ce0 https://github.com/galaxyproject/galaxy/commit/11f03d363c55f16a6b7f02975405… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-10 (Mon, 10 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Merge pull request #581 from carlfeberhard/history.page-at-10 UI, Histories: page Saved Histories at 10 histories Commit: 67e1ad3716b7047f9d51149014cbadff472c3cf0 https://github.com/galaxyproject/galaxy/commit/67e1ad3716b7047f9d51149014cb… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-08-10 (Mon, 10 Aug 2015) Changed paths: M lib/galaxy/managers/histories.py M lib/galaxy/model/__init__.py M lib/galaxy/quota/__init__.py M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Core, histories: remove older references to get_disk_size and associated Commit: 524fd95ca6764dfde58b1d047474b2d3afad1e9b https://github.com/galaxyproject/galaxy/commit/524fd95ca6764dfde58b1d047474… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-10 (Mon, 10 Aug 2015) Changed paths: R static/help.css R static/help.html R static/help.rst R static/images/SetAttr.png R static/images/SetGenome.png R static/images/brochure.pdf R static/images/galaxy.png R static/images/galaxyLogo_small.png R static/images/lock.jpg R static/images/qk/quickie1_small.png R static/images/qk/quickie2_small.png R static/images/qk/quickie3_small.png R static/images/qk/quickie4_small.png R static/images/qk/quickie5_small.png R static/images/qk/quickie6_small.png R static/images/qk/quickie7_small.png R static/images/screencast.png R static/images/sequencer.png R static/images/tools.gif R static/images/toolsExpandingMenu.gif R static/images/welcomePhoto.jpg R static/welcome.rst Log Message: ----------- remove undused files Commit: 19e97d6dea150acb9cb678ee9779e8225dcd8d70 https://github.com/galaxyproject/galaxy/commit/19e97d6dea150acb9cb678ee9779… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-10 (Mon, 10 Aug 2015) Changed paths: M client/galaxy/style/less/reports.less R static/images/reports_webapp/bases/home-icon-active.png R static/images/reports_webapp/bases/home-icon-hov.png R static/images/reports_webapp/bases/home-icon.png R static/images/reports_webapp/home-icon-active.png R static/images/reports_webapp/home-icon-hov.png R static/images/reports_webapp/home-icon.png M static/style/blue/base.css M static/style/blue/reports.css M templates/webapps/reports/index.mako Log Message: ----------- use fontawesome instead of custom home icon Commit: 98861824e2f1ab3cd7f4085c31db4f1ed4b79ca3 https://github.com/galaxyproject/galaxy/commit/98861824e2f1ab3cd7f4085c31db… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-10 (Mon, 10 Aug 2015) Changed paths: M templates/webapps/reports/base_panels.mako Log Message: ----------- fix the class for reports brand so it is actually shown and not black text on dark background Commit: 1b64bea779eab01a5a190d1f44707148b18e2d21 https://github.com/galaxyproject/galaxy/commit/1b64bea779eab01a5a190d1f4470… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-08-10 (Mon, 10 Aug 2015) Changed paths: M lib/galaxy/managers/histories.py M lib/galaxy/webapps/galaxy/api/histories.py Log Message: ----------- API, histories: allow sorting by disk_size, move order parsing into manager Commit: a2c2f09211ca9af6d7867732681822dc37321aed https://github.com/galaxyproject/galaxy/commit/a2c2f09211ca9af6d78677326818… Author: Nitesh Turaga <nitesh.turaga(a)gmail.com> Date: 2015-08-10 (Mon, 10 Aug 2015) Changed paths: M templates/webapps/reports/base_panels.mako Log Message: ----------- Merge pull request #585 from martenson/reports-navbar-brand fix the class for reports brand so it is actually shown Commit: fc6b965bba06d0bb718ce68456c01d8bbbda2c5b https://github.com/galaxyproject/galaxy/commit/fc6b965bba06d0bb718ce68456c0… Author: Nitesh Turaga <nitesh.turaga(a)gmail.com> Date: 2015-08-10 (Mon, 10 Aug 2015) Changed paths: M client/galaxy/style/less/reports.less R static/images/reports_webapp/bases/home-icon-active.png R static/images/reports_webapp/bases/home-icon-hov.png R static/images/reports_webapp/bases/home-icon.png R static/images/reports_webapp/home-icon-active.png R static/images/reports_webapp/home-icon-hov.png R static/images/reports_webapp/home-icon.png M static/style/blue/base.css M static/style/blue/reports.css M templates/webapps/reports/index.mako Log Message: ----------- Merge pull request #584 from martenson/reports-fa-icon reports: use fontawesome instead of custom home icon Commit: 0f2e2152ee17532488a8231cf1220ed9ddddb3aa https://github.com/galaxyproject/galaxy/commit/0f2e2152ee17532488a8231cf122… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-08-10 (Mon, 10 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/galaxy_install/dependency_display.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/galaxy_install/update_repository_manager.py M lib/tool_shed/scripts/api/common.py M lib/tool_shed/scripts/deprecate_repositories_without_metadata.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Cleanup of the toolshed's url handling methods. Commit: 9f975e85067c1c5f695979f13d26ae4d132cb36f https://github.com/galaxyproject/galaxy/commit/9f975e85067c1c5f695979f13d26… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-08-10 (Mon, 10 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Make travis happier. Commit: 7baab04081cbc6a280443ff967a1f69e8ec721d8 https://github.com/galaxyproject/galaxy/commit/7baab04081cbc6a280443ff967a1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-10 (Mon, 10 Aug 2015) Changed paths: R static/help.css R static/help.html R static/help.rst R static/images/SetAttr.png R static/images/SetGenome.png R static/images/brochure.pdf R static/images/galaxy.png R static/images/galaxyLogo_small.png R static/images/lock.jpg R static/images/qk/quickie1_small.png R static/images/qk/quickie2_small.png R static/images/qk/quickie3_small.png R static/images/qk/quickie4_small.png R static/images/qk/quickie5_small.png R static/images/qk/quickie6_small.png R static/images/qk/quickie7_small.png R static/images/screencast.png R static/images/sequencer.png R static/images/tools.gif R static/images/toolsExpandingMenu.gif R static/images/welcomePhoto.jpg R static/welcome.rst Log Message: ----------- Merge pull request #583 from martenson/cleanup-static remove unused files in /static Commit: 624cf19ba5bec88dfee58380722720fc47d68eb3 https://github.com/galaxyproject/galaxy/commit/624cf19ba5bec88dfee583807227… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-08-10 (Mon, 10 Aug 2015) Changed paths: M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/util/common_util.py Log Message: ----------- More linting. Commit: ee4f077c526dbda7752baef59d97b671b9effac6 https://github.com/galaxyproject/galaxy/commit/ee4f077c526dbda7752baef59d97… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-10 (Mon, 10 Aug 2015) Changed paths: M tool-data/all_fasta.loc.sample M tool-data/faseq.loc.sample M tool-data/liftOver.loc.sample M tool-data/mosaik_index.loc.sample M tool-data/ngs_sim_fasta.loc.sample M tool-data/perm_base_index.loc.sample M tool-data/perm_color_index.loc.sample M tool-data/picard_index.loc.sample M tool-data/regions.loc.sample M tool-data/srma_index.loc.sample Log Message: ----------- Per @yhoogstrate's suggestion https://github.com/galaxyproject/galaxy/commit/c0c286a9c69dcb23a50a0b9b249c…, retab .loc.samples Commit: a04147dc56cc747c67aeacc1773b5bb747347957 https://github.com/galaxyproject/galaxy/commit/a04147dc56cc747c67aeacc1773b… Author: Nitesh Turaga <nitesh.turaga(a)gmail.com> Date: 2015-08-10 (Mon, 10 Aug 2015) Changed paths: M tool-data/all_fasta.loc.sample M tool-data/faseq.loc.sample M tool-data/liftOver.loc.sample M tool-data/mosaik_index.loc.sample M tool-data/ngs_sim_fasta.loc.sample M tool-data/perm_base_index.loc.sample M tool-data/perm_color_index.loc.sample M tool-data/picard_index.loc.sample M tool-data/regions.loc.sample M tool-data/srma_index.loc.sample Log Message: ----------- Merge pull request #587 from dannon/retab_loc_samples Retab .loc.samples Commit: 83bc5b74ff8c4d45ab4742af7a434c2f7d7869e6 https://github.com/galaxyproject/galaxy/commit/83bc5b74ff8c4d45ab4742af7a43… Author: youri <y.hoogstrate(a)erasmusmc.nl> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M config/tool_data_table_conf.xml.sample M tools/extract/liftOver_wrapper.xml Log Message: ----------- liftOver.loc was not accessible from local data Commit: b3c0725d97a1cf5c4229f60a46a878710c41cab5 https://github.com/galaxyproject/galaxy/commit/b3c0725d97a1cf5c4229f60a46a8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-popover.js M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/style/less/ui.less M client/galaxy/style/less/upload.less M static/maps/mvc/ui/ui-popover.js.map M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/composite/composite-view.js.map M static/maps/mvc/upload/default/default-row.js.map M static/maps/mvc/upload/default/default-view.js.map M static/maps/mvc/upload/upload-ftp.js.map M static/scripts/mvc/ui/ui-popover.js M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/default/default-row.js M static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/upload-ftp.js M static/style/blue/base.css Log Message: ----------- Continue ftp popup integration Commit: d7e6d627d0679a5cc95f30e71f5a9d30cc753802 https://github.com/galaxyproject/galaxy/commit/d7e6d627d0679a5cc95f30e71f5a… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Correct errors found by Nicola. Commit: 84329f8f3d7423106f197fb880fc12aee2d2b71d https://github.com/galaxyproject/galaxy/commit/84329f8f3d7423106f197fb880fc… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M lib/tool_shed/util/common_util.py Log Message: ----------- Remove debug output. Commit: 21ab4d2dbfa8576f89a13018d962cd8dc3738239 https://github.com/galaxyproject/galaxy/commit/21ab4d2dbfa8576f89a13018d962… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/upload-view.js A client/galaxy/scripts/reports_webapp/run_stats.js M client/galaxy/style/less/reports.less M config/datatypes_conf.xml.sample M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M lib/galaxy/dataset_collections/builder.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/collections_util.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parameters/output.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/webapps/galaxy/controllers/history.py A lib/galaxy/webapps/reports/controllers/home.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/basic_util.py R static/help.css R static/help.html R static/help.rst R static/images/SetAttr.png R static/images/SetGenome.png R static/images/brochure.pdf R static/images/galaxy.png R static/images/galaxyLogo_small.png R static/images/lock.jpg R static/images/qk/quickie1_small.png R static/images/qk/quickie2_small.png R static/images/qk/quickie3_small.png R static/images/qk/quickie4_small.png R static/images/qk/quickie5_small.png R static/images/qk/quickie6_small.png R static/images/qk/quickie7_small.png R static/images/screencast.png R static/images/sequencer.png R static/images/tools.gif R static/images/toolsExpandingMenu.gif R static/images/welcomePhoto.jpg M static/maps/mvc/upload/upload-view.js.map A static/maps/reports_webapp/run_stats.js.map M static/scripts/mvc/upload/upload-view.js A static/scripts/reports_webapp/run_stats.js M static/style/blue/base.css M static/style/blue/reports.css R static/welcome.rst M templates/base.mako M templates/webapps/reports/base_panels.mako M templates/webapps/reports/index.mako A templates/webapps/reports/run_stats.mako R templates/webapps/tool_shed/message.mako M templates/webapps/tool_shed/repository/manage_repository.mako M test/functional/test_toolbox.py A test/functional/tools/collection_creates_dynamic_list_of_pairs.xml A test/functional/tools/collection_creates_dynamic_nested.xml A test/functional/tools/collection_creates_list_of_pairs.xml M test/functional/tools/samples_tool_conf.xml M tool-data/all_fasta.loc.sample M tool-data/faseq.loc.sample M tool-data/liftOver.loc.sample M tool-data/mosaik_index.loc.sample M tool-data/ngs_sim_fasta.loc.sample M tool-data/perm_base_index.loc.sample M tool-data/perm_color_index.loc.sample M tool-data/picard_index.loc.sample M tool-data/regions.loc.sample M tool-data/srma_index.loc.sample Log Message: ----------- Merge branch 'dev' of https://github.com/Airistotal/galaxy into Reports_pages Commit: 0efc866a07699067beb930dc0275aab7dfb40cd5 https://github.com/galaxyproject/galaxy/commit/0efc866a07699067beb930dc0275… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Correct additional errors discovered by Nicola. Commit: 5ddd2c92a3caeb75bcb379f297f2967af26afc47 https://github.com/galaxyproject/galaxy/commit/5ddd2c92a3caeb75bcb379f297f2… Author: Dave B. <dave(a)bx.psu.edu> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M lib/tool_shed/galaxy_install/install_manager.py Log Message: ----------- Fix missing parameter. Commit: dd51cfe6e0ae23e8faab7b43673f9f3bc6cc6dcf https://github.com/galaxyproject/galaxy/commit/dd51cfe6e0ae23e8faab7b43673f… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M lib/galaxy/webapps/reports/controllers/workflows.py M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako M templates/webapps/reports/workflows_per_workflow.mako Log Message: ----------- Added Paging to Workflows Commit: a27ff9b2922aff5f863cf7d2e84094e236d8c6bb https://github.com/galaxyproject/galaxy/commit/a27ff9b2922aff5f863cf7d2e840… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M client/galaxy/style/less/reports.less M lib/galaxy/webapps/reports/controllers/workflows.py M static/style/blue/base.css M static/style/blue/reports.css Log Message: ----------- Added limits to queries (bug fix) Changed homepage button location (small style change) Changes for CI Commit: c7ad46099c1118a62936d0f2df4bdb2ff920895e https://github.com/galaxyproject/galaxy/commit/c7ad46099c1118a62936d0f2df4b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-model.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/upload.less M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/default/default-view.js.map M static/maps/mvc/upload/upload-ftp.js.map M static/maps/mvc/upload/upload-model.js.map M static/maps/utils/utils.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/upload-ftp.js M static/scripts/mvc/upload/upload-model.js M static/scripts/utils/utils.js M static/style/blue/base.css Log Message: ----------- Enable ftp file selection for composite uploads Commit: a8def9a910ecae7fe5d3507ce38d235e20810038 https://github.com/galaxyproject/galaxy/commit/a8def9a910ecae7fe5d3507ce38d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/style/less/upload.less M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/upload-ftp.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/upload-ftp.js M static/style/blue/base.css Log Message: ----------- Style fixes, adjustments for ftp popover table Commit: 80e45d230b1ea5a3bf8a77e573ed8a33a4263f4d https://github.com/galaxyproject/galaxy/commit/80e45d230b1ea5a3bf8a77e573ed… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M static/maps/mvc/upload/default/default-view.js.map M static/maps/mvc/upload/upload-ftp.js.map M static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/upload-ftp.js Log Message: ----------- Add icons to buttons in regular view Commit: ab87393897b2948b306c86c692aaabd748abec31 https://github.com/galaxyproject/galaxy/commit/ab87393897b2948b306c86c692aa… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M lib/galaxy/datatypes/genetics.py Log Message: ----------- Place string split in make_html_table call into try block Commit: 7695fec2fa217a056fa34a1cf78fcb41864549f2 https://github.com/galaxyproject/galaxy/commit/7695fec2fa217a056fa34a1cf78f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M client/galaxy/style/less/reports.less M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/controllers/history.py R static/help.css R static/help.html R static/help.rst R static/images/SetAttr.png R static/images/SetGenome.png R static/images/brochure.pdf R static/images/galaxy.png R static/images/galaxyLogo_small.png R static/images/lock.jpg R static/images/qk/quickie1_small.png R static/images/qk/quickie2_small.png R static/images/qk/quickie3_small.png R static/images/qk/quickie4_small.png R static/images/qk/quickie5_small.png R static/images/qk/quickie6_small.png R static/images/qk/quickie7_small.png R static/images/reports_webapp/bases/home-icon-active.png R static/images/reports_webapp/bases/home-icon-hov.png R static/images/reports_webapp/bases/home-icon.png R static/images/reports_webapp/home-icon-active.png R static/images/reports_webapp/home-icon-hov.png R static/images/reports_webapp/home-icon.png R static/images/screencast.png R static/images/sequencer.png R static/images/tools.gif R static/images/toolsExpandingMenu.gif R static/images/welcomePhoto.jpg M static/style/blue/base.css M static/style/blue/reports.css R static/welcome.rst M templates/webapps/reports/base_panels.mako M templates/webapps/reports/index.mako M tool-data/all_fasta.loc.sample M tool-data/faseq.loc.sample M tool-data/liftOver.loc.sample M tool-data/mosaik_index.loc.sample M tool-data/ngs_sim_fasta.loc.sample M tool-data/perm_base_index.loc.sample M tool-data/perm_color_index.loc.sample M tool-data/picard_index.loc.sample M tool-data/regions.loc.sample M tool-data/srma_index.loc.sample Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into upload_000 Conflicts: static/style/blue/base.css Commit: 4da5f1370f8bad346e1a26b913f8fab0bd567f0d https://github.com/galaxyproject/galaxy/commit/4da5f1370f8bad346e1a26b913f8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-view.js M lib/galaxy/webapps/galaxy/api/datatypes.py M static/maps/mvc/upload/composite/composite-view.js.map M static/scripts/mvc/upload/composite/composite-view.js Log Message: ----------- Fix corner cases ie missing datatype details Commit: 82c732752f2c201ed223e46abb533ea262f9fe9e https://github.com/galaxyproject/galaxy/commit/82c732752f2c201ed223e46abb53… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/upload-view.js M static/maps/mvc/upload/upload-view.js.map M static/scripts/mvc/upload/upload-view.js Log Message: ----------- Fix unload message if queue is running/active Commit: 1686109ae8d6ac615ffdb45d1a0a6e7b5f48c786 https://github.com/galaxyproject/galaxy/commit/1686109ae8d6ac615ffdb45d1a0a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/upload-view.js M static/maps/mvc/upload/upload-view.js.map M static/scripts/mvc/upload/upload-view.js Log Message: ----------- Fix sorting for upper case extension Commit: 71bcb8dc9d4b478c098e8ba2adf63e227eb3f658 https://github.com/galaxyproject/galaxy/commit/71bcb8dc9d4b478c098e8ba2adf6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/upload-view.js M static/maps/mvc/upload/upload-view.js.map Log Message: ----------- Remove comments Commit: 2bdbe8036f93409a8a2d5b7a9b75c205201bd448 https://github.com/galaxyproject/galaxy/commit/2bdbe8036f93409a8a2d5b7a9b75… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/upload-view.js M static/maps/mvc/upload/upload-view.js.map Log Message: ----------- Remove comments Commit: b07625b0c03045a4539b5f01a7115324f8905ff0 https://github.com/galaxyproject/galaxy/commit/b07625b0c03045a4539b5f01a711… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/upload-ftp.js M static/maps/mvc/upload/upload-ftp.js.map M static/scripts/mvc/upload/upload-ftp.js Log Message: ----------- Remove unnecessary if condition in ftp uploader Commit: 249d185d88bfdca668ca08775ef8c93bef34557c https://github.com/galaxyproject/galaxy/commit/249d185d88bfdca668ca08775ef8… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/dependencies/tool/tag_attribute_handler.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/grids/repository_grids.py Log Message: ----------- Minor cleanup of some iterators. Commit: 5885ce870e4b42b94be9115180880b7e2a1c96db https://github.com/galaxyproject/galaxy/commit/5885ce870e4b42b94be911518088… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M lib/tool_shed/grids/repository_grids.py Log Message: ----------- Address Nicola's concerns. Commit: 7907136ffd4e3ee293ec96d39bf48357cf433539 https://github.com/galaxyproject/galaxy/commit/7907136ffd4e3ee293ec96d39bf4… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/scripts/api/common.py M lib/tool_shed/utility_containers/__init__.py M lib/tool_shed/utility_containers/utility_container_manager.py Log Message: ----------- Code style cleanup. Commit: db4461177162fae94b2100363d3e617c213d09df https://github.com/galaxyproject/galaxy/commit/db4461177162fae94b2100363d3e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/dependencies/tool/tag_attribute_handler.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/grids/repository_grids.py Log Message: ----------- Merge pull request #589 from davebx/cleanup_ts Minor cleanup of some iterators. Commit: 1d3e304644f0f5b7b3cb828a9016e2b679791f46 https://github.com/galaxyproject/galaxy/commit/1d3e304644f0f5b7b3cb828a9016… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M lib/galaxy/webapps/reports/controllers/jobs.py M templates/webapps/reports/jobs_per_user.mako Log Message: ----------- Timing of the queries on the jobs per user page. Commit: f1fc95e3655950a9f2064c5bc1506fecc936e4d4 https://github.com/galaxyproject/galaxy/commit/f1fc95e3655950a9f2064c5bc150… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M lib/tool_shed/utility_containers/utility_container_manager.py Log Message: ----------- Use correct formatting for multi-line if. Commit: bb6a784f13ff3f91762244d4488437ffef9e5acf https://github.com/galaxyproject/galaxy/commit/bb6a784f13ff3f91762244d44884… Author: Enis Afgan <afgane(a)gmail.com> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py Log Message: ----------- Include valid_tools as part of metadata returned with the repository install info. Otherwise, no linkage exists bwtween tool version and a revision that can be used via the API. Commit: 1d325e217e03e13fbfcfc8c4ed46a00277382ed9 https://github.com/galaxyproject/galaxy/commit/1d325e217e03e13fbfcfc8c4ed46… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/scripts/api/common.py M lib/tool_shed/utility_containers/__init__.py M lib/tool_shed/utility_containers/utility_container_manager.py Log Message: ----------- Merge pull request #591 from davebx/ts_lint Code style cleanup. Commit: 6a38e0bda72ee44dc603b8f996a3c08427d579c1 https://github.com/galaxyproject/galaxy/commit/6a38e0bda72ee44dc603b8f996a3… Author: yhoogstrate <y.hoogstrate(a)erasmusmc.nl> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M tools/extract/liftOver_wrapper.xml Log Message: ----------- Update liftOver_wrapper.xml version++ Commit: 01b69e327b524be014f86b9e98375f3e5d660141 https://github.com/galaxyproject/galaxy/commit/01b69e327b524be014f86b9e9837… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py Log Message: ----------- Merge pull request #592 from afgane/dev Include valid_tools as part of metadata returned with the repository … Commit: 6a25d979e1329aec4366bf6943aa65d9b41ec18f https://github.com/galaxyproject/galaxy/commit/6a25d979e1329aec4366bf6943aa… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/galaxy/managers/sharable.py Log Message: ----------- fix _query method to return a query instead of a list Commit: 40f61610f1133e142de32389aad1a04294cb3164 https://github.com/galaxyproject/galaxy/commit/40f61610f1133e142de32389aad1… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- introduce new API endpoint&method for published histories Commit: dd421d00076660ef368757c7871b5fa7c3ab80c9 https://github.com/galaxyproject/galaxy/commit/dd421d00076660ef368757c7871b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-view.js M static/maps/mvc/upload/upload-view.js.map M static/scripts/mvc/upload/upload-view.js Log Message: ----------- Minor fixes Commit: c72c7e51e15ce11df81657b3ed0001fedd9f8679 https://github.com/galaxyproject/galaxy/commit/c72c7e51e15ce11df81657b3ed00… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/galaxy/managers/histories.py M lib/galaxy/model/__init__.py Log Message: ----------- Histories: make disk_nice_size a property Commit: a4274913e195d0c1d6f558f5f877346a18c1e310 https://github.com/galaxyproject/galaxy/commit/a4274913e195d0c1d6f558f5f877… Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/galaxy/managers/sharable.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Merge pull request #594 from martenson/expose-api-pub-hist new API for published histories Commit: c00196fd2cb4eb7f999bd2176c570b0834c81c2d https://github.com/galaxyproject/galaxy/commit/c00196fd2cb4eb7f999bd2176c57… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/galaxy/tools/toolbox/lineages/stock.py Log Message: ----------- Fix StockLineage.get_versions() when reverse=True . Commit: 4b3a34f1d25cd00c12a5ee3815f609f238f83aa5 https://github.com/galaxyproject/galaxy/commit/4b3a34f1d25cd00c12a5ee3815f6… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/galaxy/model/tool_shed_install/__init__.py Log Message: ----------- Simplify ToolVersion.get_version_ids() . Commit: 9c318ac1f7dac48e25e8b1c315c372e36dc0323e https://github.com/galaxyproject/galaxy/commit/9c318ac1f7dac48e25e8b1c315c3… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Remove existing wrong tool version associations in ToolVersionManager.handle_tool_versions() . Fix #552. To fix a tool with a wrong lineage, click on "Set tool versions" on the "Repository Actions" menu. Commit: 303597e48a8503aac09c33910aa5482a374f06a1 https://github.com/galaxyproject/galaxy/commit/303597e48a8503aac09c33910aa5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M client/galaxy/scripts/galaxy.menu.js M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/managers/configuration.py R lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py M static/maps/galaxy.menu.js.map M static/scripts/galaxy.menu.js R templates/webapps/galaxy/cloud/index.mako Log Message: ----------- Remove old cloudlaunch in favor of https://github.com/galaxyproject/cloudlaunch, at launch.usegalaxy.org Commit: accd5ebc8c4cd4dfe707560f6b00ef21ac0cc521 https://github.com/galaxyproject/galaxy/commit/accd5ebc8c4cd4dfe707560f6b00… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/tools/parser/xml.py Log Message: ----------- Merge branch 'security-20150812-ldap' into dev Commit: 95c80f0b342aa08093a7f271f29d50d3df488d1d https://github.com/galaxyproject/galaxy/commit/95c80f0b342aa08093a7f271f29d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py Log Message: ----------- Merge branch 'security-20150812-shed' into dev Commit: 28f5021766d618c108f17fccc092925c6c5fe3c8 https://github.com/galaxyproject/galaxy/commit/28f5021766d618c108f17fccc092… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Merge branch 'security-20150812-xss' into dev Conflicts: lib/galaxy/webapps/galaxy/controllers/workflow.py Commit: c4a12f61fb6e6da499cdb5aa2e96f556ab031a80 https://github.com/galaxyproject/galaxy/commit/c4a12f61fb6e6da499cdb5aa2e96… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-08-12 (Wed, 12 Aug 2015) Log Message: ----------- Merge branch 'release_15.07' into dev Commit: e218a2c72b1b1c9df8ab80f1e8c62833d813125d https://github.com/galaxyproject/galaxy/commit/e218a2c72b1b1c9df8ab80f1e8c6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/galaxy/version.py Log Message: ----------- Merge branch 'release_15.07' into dev Commit: d554136658e165c84a42b988f39009c185325919 https://github.com/galaxyproject/galaxy/commit/d554136658e165c84a42b988f390… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/galaxy/version.py Log Message: ----------- Bump version to 15.10.dev Commit: 6925bbd85cf79b7117ac1f77b5bd83e6e6964b5a https://github.com/galaxyproject/galaxy/commit/6925bbd85cf79b7117ac1f77b5bd… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-13 (Thu, 13 Aug 2015) Changed paths: M lib/galaxy/managers/histories.py M lib/galaxy/model/__init__.py M lib/galaxy/quota/__init__.py M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Merge pull request #582 from carlfeberhard/history.size Core, histories: remove older references to get_disk_size and associated Commit: 369760aabe2747d64411c7c2dc61c701a9064c3d https://github.com/galaxyproject/galaxy/commit/369760aabe2747d64411c7c2dc61… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-08-13 (Thu, 13 Aug 2015) Changed paths: M CONTRIBUTING.md M doc/source/project/organization.rst Log Message: ----------- Merge pull request #556 from erasche/contributing-wip-revert-v3 [PROCEDURES] Explicit language on reversions and WIP v3 Commit: 635ef189df60e9a1ce6e0e8c177fdc3b136da9a1 https://github.com/galaxyproject/galaxy/commit/635ef189df60e9a1ce6e0e8c177f… Author: Nitesh Turaga <nitesh.turaga(a)gmail.com> Date: 2015-08-13 (Thu, 13 Aug 2015) Changed paths: M client/galaxy/scripts/galaxy.menu.js M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/managers/configuration.py R lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py M static/maps/galaxy.menu.js.map M static/scripts/galaxy.menu.js R templates/webapps/galaxy/cloud/index.mako Log Message: ----------- Merge pull request #597 from dannon/no_more_cloudlaunch Remove old cloudlaunch in favor of … Commit: cafe872bfb20633de770be9b2a8c6111eed75023 https://github.com/galaxyproject/galaxy/commit/cafe872bfb20633de770be9b2a8c… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-13 (Thu, 13 Aug 2015) Changed paths: M lib/tool_shed/metadata/repository_metadata_manager.py Log Message: ----------- Merge branch 'release_15.07' into dev Commit: 64608685393a235bad5c161421861af6c5609048 https://github.com/galaxyproject/galaxy/commit/64608685393a235bad5c16142186… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-13 (Thu, 13 Aug 2015) Changed paths: M client/grunt-tasks/scripts.js Log Message: ----------- Add a --develop flag to grunt that is compatible with both standard build *and* watch to allow for easier debugging instead of requiring the 'decompress' task -- though this still works. This makes it possible to drop in 'debugger' statements, etc., and should help when working on the client. Additionally enable drop_console for the compressor, since it's now much easier to use local development tweaks. Commit: 63d6c37a39a53bae6806e3bb9267a1659313f878 https://github.com/galaxyproject/galaxy/commit/63d6c37a39a53bae6806e3bb9267… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-13 (Thu, 13 Aug 2015) Changed paths: M static/maps/galaxy.interactive_environments.js.map M static/maps/libs/jquery/jqtouch.js.map M static/maps/libs/raven.js.map M static/maps/libs/toastr.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/data.js.map M static/maps/mvc/dataset/dataset-choice.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-repeat.js.map M static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/job/job-model.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/list/list-panel.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/tools/tools-form-workflow.js.map M static/maps/mvc/tools/tools-jobs.js.map M static/maps/mvc/ui/ui-frames.js.map M static/maps/mvc/ui/ui-select.js.map M static/maps/utils/deferred.js.map M static/maps/utils/graph.js.map M static/maps/utils/metrics-logger.js.map M static/maps/utils/utils.js.map M static/maps/viz/trackster.js.map M static/maps/viz/trackster/filters.js.map M static/maps/viz/visualization.js.map M static/scripts/galaxy.interactive_environments.js M static/scripts/libs/jquery/jqtouch.js M static/scripts/libs/raven.js M static/scripts/libs/toastr.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/data.js M static/scripts/mvc/dataset/dataset-choice.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-select-content.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/job/job-model.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/list/list-panel.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/tools/tools-form-workflow.js M static/scripts/mvc/tools/tools-jobs.js M static/scripts/mvc/ui/ui-frames.js M static/scripts/mvc/ui/ui-select.js M static/scripts/utils/deferred.js M static/scripts/utils/graph.js M static/scripts/utils/metrics-logger.js M static/scripts/utils/utils.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/visualization.js Log Message: ----------- Rebuild client w/ new options. Commit: 2666499da649fdbb3524d11ceab90b9af86205da https://github.com/galaxyproject/galaxy/commit/2666499da649fdbb3524d11ceab9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-13 (Thu, 13 Aug 2015) Changed paths: M client/grunt-tasks/scripts.js Log Message: ----------- One minor styling issue Commit: 304e693fd36fe5a84aeef0b1b1a2e3c909e1eb59 https://github.com/galaxyproject/galaxy/commit/304e693fd36fe5a84aeef0b1b1a2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-14 (Fri, 14 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-view.js M static/maps/mvc/upload/default/default-view.js.map M static/maps/mvc/upload/upload-view.js.map M static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/upload-view.js Log Message: ----------- Allow safe switching between histories while queue is running Commit: 704e031f6339f63103e24805369db1c28653fd58 https://github.com/galaxyproject/galaxy/commit/704e031f6339f63103e24805369d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-14 (Fri, 14 Aug 2015) Changed paths: M CONTRIBUTING.md M client/galaxy/scripts/galaxy.menu.js M config/galaxy.ini.sample M doc/source/project/organization.rst M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/config.py M lib/galaxy/managers/configuration.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/sharable.py M lib/galaxy/model/__init__.py M lib/galaxy/quota/__init__.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/version.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/buildapp.py R lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/dependencies/tool/tag_attribute_handler.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/scripts/api/common.py M lib/tool_shed/utility_containers/__init__.py M lib/tool_shed/utility_containers/utility_container_manager.py M static/maps/galaxy.menu.js.map M static/scripts/galaxy.menu.js R templates/webapps/galaxy/cloud/index.mako Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into upload_000 Commit: d0a0536085821e667d39cc30423d7bdcbc8e5115 https://github.com/galaxyproject/galaxy/commit/d0a0536085821e667d39cc30423d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-08-14 (Fri, 14 Aug 2015) Changed paths: M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/tools/toolbox/lineages/stock.py M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Merge pull request #596 from nsoranzo/lineage_fixes Tool lineage fixes. Commit: 266d96bcb0c34365b1f3ea136909abad7180a118 https://github.com/galaxyproject/galaxy/commit/266d96bcb0c34365b1f3ea136909… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-08-14 (Fri, 14 Aug 2015) Changed paths: M lib/galaxy/webapps/reports/controllers/jobs.py M templates/webapps/reports/jobs_per_user.mako Log Message: ----------- Changed for CI, added total time for page load Commit: 4459e9411b610ea106fe2db74d20dfd27363aa23 https://github.com/galaxyproject/galaxy/commit/4459e9411b610ea106fe2db74d20… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-14 (Fri, 14 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/options-menu.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/root.py M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/options-menu.js.map M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/options-menu.js A templates/webapps/galaxy/history/as_xml.mako M templates/webapps/galaxy/history/view.mako R templates/webapps/galaxy/root/history.mako R templates/webapps/galaxy/root/history_as_xml.mako Log Message: ----------- Merge pull request #578 from carlfeberhard/history.s-n-d Remove more history UIController methods. Commit: 1383ced0bdf55d3355a2927db42b584d3b00b15f https://github.com/galaxyproject/galaxy/commit/1383ced0bdf55d3355a2927db42b… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-14 (Fri, 14 Aug 2015) Changed paths: M .ci/flake8_blacklist.txt M lib/galaxy_utils/sequence/fasta.py M lib/galaxy_utils/sequence/fastq.py M lib/galaxy_utils/sequence/sequence.py M lib/galaxy_utils/sequence/transform.py M lib/galaxy_utils/sequence/vcf.py Log Message: ----------- flake8 lib/galaxy_utils/ Commit: cb1538588d8a7632dcb29232bbad1b299173a84c https://github.com/galaxyproject/galaxy/commit/cb1538588d8a7632dcb29232bbad… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-14 (Fri, 14 Aug 2015) Changed paths: M .ci/flake8_blacklist.txt M lib/galaxy_utils/sequence/fasta.py M lib/galaxy_utils/sequence/fastq.py M lib/galaxy_utils/sequence/sequence.py M lib/galaxy_utils/sequence/transform.py M lib/galaxy_utils/sequence/vcf.py Log Message: ----------- Merge pull request #604 from nsoranzo/flake8_fixes flake8 lib/galaxy_utils/ Commit: 5b2e208b775f8284c651f67dad86fd55929456ac https://github.com/galaxyproject/galaxy/commit/5b2e208b775f8284c651f67dad86… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-15 (Sat, 15 Aug 2015) Changed paths: M CONTRIBUTING.md Log Message: ----------- Merge pull request #574 from nsoranzo/dev [PROCEDURES] GitHub issues, security email contact and CI testing Commit: 2da0083cdfdfc268229d730ef2a8f5432da781f1 https://github.com/galaxyproject/galaxy/commit/2da0083cdfdfc268229d730ef2a8… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-15 (Sat, 15 Aug 2015) Changed paths: M client/galaxy/style/less/reports.less M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/reports/controllers/workflows.py M static/style/blue/base.css M static/style/blue/reports.css M templates/page_base.mako M templates/spark_base.mako M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_in_error.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako M templates/webapps/reports/workflows_per_workflow.mako Log Message: ----------- Merge pull request #576 from Airistotal/Reports_pages Reports: Applied paging to all pages Commit: ed54c343e66d7dee79dd785da837f2ce55f69138 https://github.com/galaxyproject/galaxy/commit/ed54c343e66d7dee79dd785da837… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-16 (Sun, 16 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/galaxy_install/dependency_display.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/galaxy_install/update_repository_manager.py M lib/tool_shed/scripts/api/common.py M lib/tool_shed/scripts/deprecate_repositories_without_metadata.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Merge pull request #586 from davebx/ts_url_cleanup Cleanup of the toolshed's url handling methods. Commit: c0119de12eeeba5308c72b98811a2d140cdccbd4 https://github.com/galaxyproject/galaxy/commit/c0119de12eeeba5308c72b98811a… Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com> Date: 2015-08-17 (Mon, 17 Aug 2015) Changed paths: M client/grunt-tasks/scripts.js M static/maps/galaxy.interactive_environments.js.map M static/maps/libs/jquery/jqtouch.js.map M static/maps/libs/raven.js.map M static/maps/libs/toastr.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/data.js.map M static/maps/mvc/dataset/dataset-choice.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-repeat.js.map M static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/job/job-model.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/list/list-panel.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/tools/tools-form-workflow.js.map M static/maps/mvc/tools/tools-jobs.js.map M static/maps/mvc/ui/ui-frames.js.map M static/maps/mvc/ui/ui-select.js.map M static/maps/utils/deferred.js.map M static/maps/utils/graph.js.map M static/maps/utils/metrics-logger.js.map M static/maps/utils/utils.js.map M static/maps/viz/trackster.js.map M static/maps/viz/trackster/filters.js.map M static/maps/viz/visualization.js.map M static/scripts/galaxy.interactive_environments.js M static/scripts/libs/jquery/jqtouch.js M static/scripts/libs/raven.js M static/scripts/libs/toastr.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/data.js M static/scripts/mvc/dataset/dataset-choice.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-select-content.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/job/job-model.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/list/list-panel.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/tools/tools-form-workflow.js M static/scripts/mvc/tools/tools-jobs.js M static/scripts/mvc/ui/ui-frames.js M static/scripts/mvc/ui/ui-select.js M static/scripts/utils/deferred.js M static/scripts/utils/graph.js M static/scripts/utils/metrics-logger.js M static/scripts/utils/utils.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/visualization.js Log Message: ----------- Merge pull request #601 from dannon/grunt_develop_mode Grunt develop mode Commit: 4463676e2cf70989b4a036f155356418ef22b049 https://github.com/galaxyproject/galaxy/commit/4463676e2cf70989b4a036f15535… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-17 (Mon, 17 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M static/maps/mvc/workflow/workflow-terminals.js.map M static/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Merge branch 'release_15.07' into dev Commit: 634799803ef36b9ea1a615bc980425f224d5d958 https://github.com/galaxyproject/galaxy/commit/634799803ef36b9ea1a615bc9804… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-17 (Mon, 17 Aug 2015) Changed paths: M static/maps/mvc/history/options-menu.js.map M static/scripts/mvc/history/options-menu.js Log Message: ----------- Merge from release and rebuild. Commit: 0c3fdd2d637255e61a08f4684f63bd6b097c02eb https://github.com/galaxyproject/galaxy/commit/0c3fdd2d637255e61a08f4684f63… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-17 (Mon, 17 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-color-picker.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/utils/utils.js M static/maps/mvc/ui/ui-color-picker.js.map M static/maps/mvc/ui/ui-misc.js.map M static/maps/mvc/upload/default/default-view.js.map M static/maps/mvc/upload/upload-view.js.map M static/maps/utils/utils.js.map M static/scripts/mvc/ui/ui-color-picker.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/upload/default/default-view.js M static/scripts/utils/utils.js A test/qunit/test-app.js M test/qunit/test-common.js A test/qunit/test-data/bootstrapped.js A test/qunit/test-data/fakeserver.js A test/qunit/tests/upload_dialog_tests.html A test/qunit/tests/upload_dialog_tests.js M test/qunit/tests/workflow_editor_tests.js Log Message: ----------- Add test cases for uploader, add generic Galaxy environment to qunit Commit: ed171e95190e651434927e05f67b5a65f1c84828 https://github.com/galaxyproject/galaxy/commit/ed171e95190e651434927e05f67b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-17 (Mon, 17 Aug 2015) Changed paths: M .ci/flake8_blacklist.txt M CONTRIBUTING.md M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/style/less/reports.less M client/grunt-tasks/scripts.js M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/tools/toolbox/lineages/stock.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/reports/controllers/workflows.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy_utils/sequence/fasta.py M lib/galaxy_utils/sequence/fastq.py M lib/galaxy_utils/sequence/sequence.py M lib/galaxy_utils/sequence/transform.py M lib/galaxy_utils/sequence/vcf.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/galaxy_install/dependency_display.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/galaxy_install/update_repository_manager.py M lib/tool_shed/scripts/api/common.py M lib/tool_shed/scripts/deprecate_repositories_without_metadata.py M lib/tool_shed/tools/tool_version_manager.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/shed_util_common.py M static/maps/galaxy.interactive_environments.js.map M static/maps/libs/jquery/jqtouch.js.map M static/maps/libs/raven.js.map M static/maps/libs/toastr.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/data.js.map M static/maps/mvc/dataset/dataset-choice.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-repeat.js.map M static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/job/job-model.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/list/list-panel.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/tools/tools-form-workflow.js.map M static/maps/mvc/tools/tools-jobs.js.map M static/maps/mvc/ui/ui-frames.js.map M static/maps/mvc/ui/ui-select.js.map M static/maps/mvc/workflow/workflow-terminals.js.map M static/maps/utils/deferred.js.map M static/maps/utils/graph.js.map M static/maps/utils/metrics-logger.js.map M static/maps/utils/utils.js.map M static/maps/viz/trackster.js.map M static/maps/viz/trackster/filters.js.map M static/maps/viz/visualization.js.map M static/scripts/galaxy.interactive_environments.js M static/scripts/libs/jquery/jqtouch.js M static/scripts/libs/raven.js M static/scripts/libs/toastr.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/data.js M static/scripts/mvc/dataset/dataset-choice.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-select-content.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/job/job-model.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/list/list-panel.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/tools/tools-form-workflow.js M static/scripts/mvc/tools/tools-jobs.js M static/scripts/mvc/ui/ui-frames.js M static/scripts/mvc/ui/ui-select.js M static/scripts/mvc/workflow/workflow-terminals.js M static/scripts/utils/deferred.js M static/scripts/utils/graph.js M static/scripts/utils/metrics-logger.js M static/scripts/utils/utils.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/visualization.js M static/style/blue/base.css M static/style/blue/reports.css M templates/page_base.mako M templates/spark_base.mako A templates/webapps/galaxy/history/as_xml.mako M templates/webapps/galaxy/history/view.mako R templates/webapps/galaxy/root/history.mako R templates/webapps/galaxy/root/history_as_xml.mako M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_in_error.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako M templates/webapps/reports/workflows_per_workflow.mako Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into upload_000 Conflicts: static/maps/utils/utils.js.map static/scripts/utils/utils.js static/style/blue/base.css Commit: 89801414bbdc18f5db98c32ca462ef92f97f5647 https://github.com/galaxyproject/galaxy/commit/89801414bbdc18f5db98c32ca462… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-17 (Mon, 17 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-view.js M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/composite/composite-view.js.map M static/maps/mvc/upload/default/default-view.js.map M static/maps/mvc/upload/upload-view.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/composite/composite-view.js M static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/upload-view.js Log Message: ----------- Enhance FTP visibilty handling Commit: e9e3dd62d2178d391f5ba9f0c677063800b0f3a3 https://github.com/galaxyproject/galaxy/commit/e9e3dd62d2178d391f5ba9f0c677… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-17 (Mon, 17 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/datatypes.py Log Message: ----------- Use list comprehension to build composite_files array Commit: fe251e3c2de4d986b3654130b317fe5fe9b2cffb https://github.com/galaxyproject/galaxy/commit/fe251e3c2de4d986b3654130b317… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-08-18 (Tue, 18 Aug 2015) Changed paths: M lib/tool_shed/capsule/capsule_manager.py Log Message: ----------- Ensure removal of temporary files. Specifically, export_info.xml and manifest.xml were not being deleted after the capsule was created. Commit: ed4bb86c3355cad578354696394dd6364b5a898d https://github.com/galaxyproject/galaxy/commit/ed4bb86c3355cad578354696394d… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-08-18 (Tue, 18 Aug 2015) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py Log Message: ----------- Also delete uploaded file data after processing. API uploads, e.g. with planemo, would leave upload_file_data_XXXXXX lying around in the configured temporary directory. Forever. Commit: cac7940706f74c0104611c4bfc7860ac93802261 https://github.com/galaxyproject/galaxy/commit/cac7940706f74c0104611c4bfc78… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-08-18 (Tue, 18 Aug 2015) Changed paths: A CODE_OF_CONDUCT.md Log Message: ----------- Add a code of conduct for the project. Commit: 9c8edf106bd61851b0668ceb6047104784f2cb1a https://github.com/galaxyproject/galaxy/commit/9c8edf106bd61851b0668ceb6047… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-08-18 (Tue, 18 Aug 2015) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/tool_shed/capsule/capsule_manager.py Log Message: ----------- Merge pull request #607 from davebx/ts_tempfiles Ensure removal of temporary files. Commit: e1672f37b9bb0be4506b0df4610c14c3289df212 https://github.com/galaxyproject/galaxy/commit/e1672f37b9bb0be4506b0df4610c… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-08-18 (Tue, 18 Aug 2015) Changed paths: M client/galaxy/scripts/reports_webapp/run_stats.js Log Message: ----------- Changed refresh time on reports homepage Commit: e7a753bb6f67082b2a70ec122a2113becebad046 https://github.com/galaxyproject/galaxy/commit/e7a753bb6f67082b2a70ec122a21… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-08-18 (Tue, 18 Aug 2015) Changed paths: M static/scripts/reports_webapp/run_stats.js Log Message: ----------- Ran grunt Commit: 3ba118621d54b2b115281198a28576140507d7b0 https://github.com/galaxyproject/galaxy/commit/3ba118621d54b2b115281198a285… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-08-18 (Tue, 18 Aug 2015) Changed paths: M client/galaxy/scripts/reports_webapp/run_stats.js M static/maps/reports_webapp/run_stats.js.map Log Message: ----------- Added documentation Commit: bb7795f63c478c69e2671b2e5b4f2b12e1ff812a https://github.com/galaxyproject/galaxy/commit/bb7795f63c478c69e2671b2e5b4f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-18 (Tue, 18 Aug 2015) Changed paths: M client/galaxy/scripts/reports_webapp/run_stats.js M static/maps/reports_webapp/run_stats.js.map M static/scripts/reports_webapp/run_stats.js Log Message: ----------- Merge pull request #609 from Airistotal/dev Changed refresh time on reports homepage Commit: b6e0ba29521bbc382a9fe15493e55b2bbde1bfde https://github.com/galaxyproject/galaxy/commit/b6e0ba29521bbc382a9fe15493e5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-18 (Tue, 18 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-button-menu.js M client/galaxy/scripts/mvc/ui/ui-color-picker.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/mvc/ui/ui-popover.js A client/galaxy/scripts/mvc/upload/composite/composite-row.js A client/galaxy/scripts/mvc/upload/composite/composite-view.js A client/galaxy/scripts/mvc/upload/default/default-row.js A client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-button.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-model.js R client/galaxy/scripts/mvc/upload/upload-row.js M client/galaxy/scripts/mvc/upload/upload-settings.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/ui.less M client/galaxy/style/less/upload.less M lib/galaxy/datatypes/genetics.py M lib/galaxy/util/bunch.py M lib/galaxy/webapps/galaxy/api/datatypes.py M static/maps/mvc/ui/ui-button-menu.js.map M static/maps/mvc/ui/ui-color-picker.js.map M static/maps/mvc/ui/ui-misc.js.map M static/maps/mvc/ui/ui-modal.js.map M static/maps/mvc/ui/ui-popover.js.map A static/maps/mvc/upload/composite/composite-row.js.map A static/maps/mvc/upload/composite/composite-view.js.map A static/maps/mvc/upload/default/default-row.js.map A static/maps/mvc/upload/default/default-view.js.map M static/maps/mvc/upload/upload-button.js.map M static/maps/mvc/upload/upload-ftp.js.map M static/maps/mvc/upload/upload-model.js.map R static/maps/mvc/upload/upload-row.js.map M static/maps/mvc/upload/upload-settings.js.map M static/maps/mvc/upload/upload-view.js.map M static/maps/utils/uploadbox.js.map M static/maps/utils/utils.js.map M static/scripts/mvc/ui/ui-button-menu.js M static/scripts/mvc/ui/ui-color-picker.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-modal.js M static/scripts/mvc/ui/ui-popover.js A static/scripts/mvc/upload/composite/composite-row.js A static/scripts/mvc/upload/composite/composite-view.js A static/scripts/mvc/upload/default/default-row.js A static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/upload-button.js M static/scripts/mvc/upload/upload-ftp.js M static/scripts/mvc/upload/upload-model.js R static/scripts/mvc/upload/upload-row.js M static/scripts/mvc/upload/upload-settings.js M static/scripts/mvc/upload/upload-view.js M static/scripts/utils/uploadbox.js M static/scripts/utils/utils.js M static/style/blue/base.css A test/qunit/test-app.js M test/qunit/test-common.js A test/qunit/test-data/bootstrapped.js A test/qunit/test-data/fakeserver.js A test/qunit/tests/upload_dialog_tests.html A test/qunit/tests/upload_dialog_tests.js M test/qunit/tests/workflow_editor_tests.js Log Message: ----------- Merge pull request #605 from guerler/upload_000 Add composite file uploader Commit: aceb82247003c71565d57794d5572858d21a7712 https://github.com/galaxyproject/galaxy/commit/aceb82247003c71565d57794d557… Author: Lance Parsons <lparsons(a)genomics.princeton.edu> Date: 2015-08-18 (Tue, 18 Aug 2015) Changed paths: R tool-data/fastx_clipper_sequences.txt Log Message: ----------- Remove fastx_clipper_sequences.txt, moved to toolshed Commit: 9a376d1ae0a5bdad632b5ad0f280cddddbd2d54d https://github.com/galaxyproject/galaxy/commit/9a376d1ae0a5bdad632b5ad0f280… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-18 (Tue, 18 Aug 2015) Changed paths: M config/galaxy.ini.sample M templates/webapps/galaxy/tool_form.mako Log Message: ----------- Remove tool form downgrade option Commit: 5810a853b0370d09a3f3eb9fc80e8e90bfe8c791 https://github.com/galaxyproject/galaxy/commit/5810a853b0370d09a3f3eb9fc80e… Author: Lance Parsons <lparsons(a)genomics.princeton.edu> Date: 2015-08-18 (Tue, 18 Aug 2015) Changed paths: M .gitignore M scripts/common_startup.sh R tool-data/shared/ucsc/manual_builds.txt A tool-data/shared/ucsc/manual_builds.txt.sample Log Message: ----------- Move manual_builds.txt to manual_builds.txt.sample to allow for customization Commit: 4dc92f5fb926f024865f004df3b48e760f4ea682 https://github.com/galaxyproject/galaxy/commit/4dc92f5fb926f024865f004df3b4… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-18 (Tue, 18 Aug 2015) Changed paths: A lib/galaxy/webapps/tool_shed/api/configuration.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/config.py Log Message: ----------- expose TS version through API Commit: 5d0b2b5a87283dcd4149f780ed9093dca96c313f https://github.com/galaxyproject/galaxy/commit/5d0b2b5a87283dcd4149f780ed90… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-18 (Tue, 18 Aug 2015) Changed paths: M lib/galaxy/webapps/tool_shed/api/configuration.py Log Message: ----------- feed flake8 Commit: d98aba9c2a335df93d1d6328edef8077529cf84b https://github.com/galaxyproject/galaxy/commit/d98aba9c2a335df93d1d6328edef… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-18 (Tue, 18 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/style/less/upload.less M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/composite/composite-view.js.map M static/maps/mvc/upload/default/default-row.js.map M static/maps/mvc/upload/default/default-view.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/default/default-row.js M static/scripts/mvc/upload/default/default-view.js M static/style/blue/base.css Log Message: ----------- Fix ambiguous naming of item/model/row variables, add drag and drop helper text and styles Commit: 5c263416de4f53129bba1ef4e9947694d474d7ef https://github.com/galaxyproject/galaxy/commit/5c263416de4f53129bba1ef4e994… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-18 (Tue, 18 Aug 2015) Changed paths: A lib/galaxy/webapps/tool_shed/api/configuration.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/config.py Log Message: ----------- Merge pull request #613 from martenson/expose-api-ts-version expose TS version through API Commit: 7c0ad6b85720f0f6101f92061c19dfcd5947ff05 https://github.com/galaxyproject/galaxy/commit/7c0ad6b85720f0f6101f92061c19… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-18 (Tue, 18 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/style/less/upload.less M static/maps/mvc/upload/composite/composite-view.js.map M static/maps/mvc/upload/default/default-view.js.map M static/scripts/mvc/upload/composite/composite-view.js M static/scripts/mvc/upload/default/default-view.js M static/style/blue/base.css Log Message: ----------- Add similar helper text to composite section Commit: 5ce4f2f24d6cc6dc40318f0034e4a62ae6a2f40b https://github.com/galaxyproject/galaxy/commit/5ce4f2f24d6cc6dc40318f0034e4… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-08-18 (Tue, 18 Aug 2015) Changed paths: M lib/galaxy/managers/base.py M lib/galaxy/managers/sharable.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Managers, sharable: implement list_shared_with; API, histories: implement api/histories/shared_with_me (with order, limit, offset, and filters as index) Commit: f03840459b1ba61680999dd5ce77cd81d2189c66 https://github.com/galaxyproject/galaxy/commit/f03840459b1ba61680999dd5ce77… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-18 (Tue, 18 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/style/less/upload.less M static/maps/mvc/upload/upload-view.js.map M static/scripts/mvc/upload/upload-view.js M static/style/blue/base.css Log Message: ----------- Shorten title text, center drop helper labels Commit: ed6174a8431342aa1677311ed3c3ce8806acbf9d https://github.com/galaxyproject/galaxy/commit/ed6174a8431342aa1677311ed3c3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-19 (Wed, 19 Aug 2015) Changed paths: M lib/galaxy/managers/base.py M lib/galaxy/managers/sharable.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Merge pull request #614 from carlfeberhard/api.histories-shared-with-me Managers, sharable: implement list_shared_with; API, histories: imple… Commit: 4ff2d913ef372bd494b3c49a3726d5cfb4e80269 https://github.com/galaxyproject/galaxy/commit/4ff2d913ef372bd494b3c49a3726… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-19 (Wed, 19 Aug 2015) Changed paths: M lib/galaxy/managers/base.py M lib/galaxy/managers/sharable.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/buildapp.py A lib/galaxy/webapps/tool_shed/api/configuration.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/config.py Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into upload_001 Commit: ff0b0baf0199e28fbcfd7d876b208ec1d15af4eb https://github.com/galaxyproject/galaxy/commit/ff0b0baf0199e28fbcfd7d876b20… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-19 (Wed, 19 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/style/less/upload.less M static/scripts/mvc/upload/composite/composite-view.js M static/scripts/mvc/upload/default/default-view.js M static/style/blue/base.css Log Message: ----------- Add icon to helper message Commit: 4d7b3213c940c0d743226c348828ff6ca17b6236 https://github.com/galaxyproject/galaxy/commit/4d7b3213c940c0d743226c348828… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-19 (Wed, 19 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-view.js M static/scripts/mvc/upload/composite/composite-view.js Log Message: ----------- Change label text Commit: d89450a53c45cd9aa61e78e2931ba365d7259cdb https://github.com/galaxyproject/galaxy/commit/d89450a53c45cd9aa61e78e2931b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-19 (Wed, 19 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/style/less/upload.less M static/scripts/mvc/upload/composite/composite-view.js M static/style/blue/base.css Log Message: ----------- Remove helper text from composite dialog Commit: d44de6a4099d2d338d604f412c5b3dbf2765838f https://github.com/galaxyproject/galaxy/commit/d44de6a4099d2d338d604f412c5b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-19 (Wed, 19 Aug 2015) Changed paths: M lib/galaxy/util/jstree.py Log Message: ----------- linting broke the functionality of this module probably this commit: https://github.com/galaxyproject/galaxy/commit/5cd3e3a7e02eee03a24006b47dfb… putting it back to the former state, we did not write most of the code, we should not be linting it Commit: f47dcdda3a64d32cdb8404a78a385aea91124df2 https://github.com/galaxyproject/galaxy/commit/f47dcdda3a64d32cdb8404a78a38… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-19 (Wed, 19 Aug 2015) Changed paths: M .ci/flake8_blacklist.txt Log Message: ----------- add jstree to flake8 blacklist Commit: fb11d71984486c82eb8cec7086a86f05e7f1e1f4 https://github.com/galaxyproject/galaxy/commit/fb11d71984486c82eb8cec7086a8… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-08-19 (Wed, 19 Aug 2015) Changed paths: M .ci/flake8_blacklist.txt M lib/galaxy/util/jstree.py Log Message: ----------- Merge pull request #617 from martenson/remove-broken-linting-jstree remove linting that broke the functionality of jstree module Commit: 4f7e59aa445d1294906406f0497991e41198c6bc https://github.com/galaxyproject/galaxy/commit/4f7e59aa445d1294906406f04979… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-08-19 (Wed, 19 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Fix bug in reload API where id wasn't recognised Commit: 8cff4da9248422284f533baaf179d711a94fe739 https://github.com/galaxyproject/galaxy/commit/8cff4da9248422284f533baaf179… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-19 (Wed, 19 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/style/less/upload.less M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/default/default-row.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/default/default-row.js M static/style/blue/base.css Log Message: ----------- Improve style class naming, reduce classes Commit: e3c31db51acf9084ebb3aa87435536716d05b041 https://github.com/galaxyproject/galaxy/commit/e3c31db51acf9084ebb3aa874355… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-19 (Wed, 19 Aug 2015) Changed paths: M client/galaxy/style/less/ui.less M static/style/blue/base.css Log Message: ----------- Improve button icon visibility Commit: 312242b2171bf06bd0551b7684d9a7e89a599f17 https://github.com/galaxyproject/galaxy/commit/312242b2171bf06bd0551b7684d9… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-19 (Wed, 19 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/style/less/upload.less M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/default/default-row.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/default/default-row.js M static/style/blue/base.css Log Message: ----------- Floating icon needs special case handling Commit: 46e47dd4cb51ed43210563cfcf8ae37c999be2d0 https://github.com/galaxyproject/galaxy/commit/46e47dd4cb51ed43210563cfcf8a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-19 (Wed, 19 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/style/less/upload.less M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/default/default-row.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/default/default-row.js M static/style/blue/base.css Log Message: ----------- Use shorter style name Commit: 8c75438a5f7513c44fca8fc55ef19637122c77fd https://github.com/galaxyproject/galaxy/commit/8c75438a5f7513c44fca8fc55ef1… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-19 (Wed, 19 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Merge pull request #619 from erasche/reload_api Fix bug in reload API where id wasn't recognised Commit: 7aa54f43c40598cc5830458985f38c2598b0dcb8 https://github.com/galaxyproject/galaxy/commit/7aa54f43c40598cc5830458985f3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-19 (Wed, 19 Aug 2015) Changed paths: M client/galaxy/style/less/ui.less M client/galaxy/style/less/upload.less M static/style/blue/base.css Log Message: ----------- More css cleanup Commit: b19f4b217b7d12e4820c5bd1c6a2f0c6bae0b772 https://github.com/galaxyproject/galaxy/commit/b19f4b217b7d12e4820c5bd1c6a2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-19 (Wed, 19 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-view.js M static/maps/mvc/upload/composite/composite-view.js.map M static/scripts/mvc/upload/composite/composite-view.js Log Message: ----------- Remove unused helper code Commit: 3c555b50e6d87f73b3e6d64bd17fae8f2e460402 https://github.com/galaxyproject/galaxy/commit/3c555b50e6d87f73b3e6d64bd17f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-19 (Wed, 19 Aug 2015) Changed paths: M test/qunit/tests/upload_dialog_tests.js Log Message: ----------- Update tests Commit: 62db50bfc4fbf00d415e6ea0dca0367d2ec13873 https://github.com/galaxyproject/galaxy/commit/62db50bfc4fbf00d415e6ea0dca0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-19 (Wed, 19 Aug 2015) Changed paths: M client/galaxy/style/less/upload.less M static/style/blue/base.css Log Message: ----------- Show dashed border in composite uploader to indicate drop zone Commit: 0bfc8f0041e0ae94d46a0ea028e8683a6387e6cf https://github.com/galaxyproject/galaxy/commit/0bfc8f0041e0ae94d46a0ea028e8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-19 (Wed, 19 Aug 2015) Log Message: ----------- Merge branch 'release_15.07' into dev Commit: c429777c93680dcee449fe410f5360afbe673758 https://github.com/galaxyproject/galaxy/commit/c429777c93680dcee449fe410f53… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2015-08-19 (Wed, 19 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/style/less/ui.less M client/galaxy/style/less/upload.less M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/composite/composite-view.js.map M static/maps/mvc/upload/default/default-row.js.map M static/maps/mvc/upload/default/default-view.js.map M static/maps/mvc/upload/upload-view.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/composite/composite-view.js M static/scripts/mvc/upload/default/default-row.js M static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/upload-view.js M static/style/blue/base.css M test/qunit/tests/upload_dialog_tests.js Log Message: ----------- Merge pull request #620 from guerler/upload_001 Improve visibility of drag and drop option, simplify upload UI Commit: 6c805ccb988a47b2958e9bcaf7c56faed13c1fd0 https://github.com/galaxyproject/galaxy/commit/6c805ccb988a47b2958e9bcaf7c5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-20 (Thu, 20 Aug 2015) Changed paths: M .ci/flake8_blacklist.txt M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/reports_webapp/run_stats.js M client/galaxy/style/less/ui.less M client/galaxy/style/less/upload.less M lib/galaxy/managers/base.py M lib/galaxy/managers/sharable.py M lib/galaxy/util/jstree.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py A lib/galaxy/webapps/tool_shed/api/configuration.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/config.py M lib/tool_shed/capsule/capsule_manager.py M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/composite/composite-view.js.map M static/maps/mvc/upload/default/default-row.js.map M static/maps/mvc/upload/default/default-view.js.map M static/maps/mvc/upload/upload-view.js.map M static/maps/reports_webapp/run_stats.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/composite/composite-view.js M static/scripts/mvc/upload/default/default-row.js M static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/upload-view.js M static/scripts/reports_webapp/run_stats.js M static/style/blue/base.css M test/qunit/tests/upload_dialog_tests.js Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into tool_form_removal_000 Commit: 0f883ef776bd71348b82be29221abbbc1751d45f https://github.com/galaxyproject/galaxy/commit/0f883ef776bd71348b82be29221a… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-20 (Thu, 20 Aug 2015) Changed paths: M lib/galaxy/model/__init__.py M scripts/cleanup_datasets/cleanup_datasets.py M test/unit/test_galaxy_mapping.py Log Message: ----------- Merge branch 'release_15.07' into dev Conflicts: lib/galaxy/model/__init__.py Commit: 6ead1de53c17cb0e3e1465f2076b3c43ea81cbc4 https://github.com/galaxyproject/galaxy/commit/6ead1de53c17cb0e3e1465f2076b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-20 (Thu, 20 Aug 2015) Changed paths: R tool-data/fastx_clipper_sequences.txt Log Message: ----------- Merge pull request #611 from lparsons/fastx_clipper_sequences Remove fastx_clipper_sequences.txt, moved to toolshed Commit: 0930035a9f5629836702525822095daf598dce45 https://github.com/galaxyproject/galaxy/commit/0930035a9f562983670252582209… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-08-20 (Thu, 20 Aug 2015) Changed paths: M templates/spark_base.mako M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako Log Message: ----------- Fixed bug where max items per page was reset when changing the amount of time sparklines spanned Commit: 9fb615f83a15ae31cbc4376733831604d0d4d04b https://github.com/galaxyproject/galaxy/commit/9fb615f83a15ae31cbc437673383… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-20 (Thu, 20 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/default/default-view.js M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/default/default-row.js.map M static/maps/mvc/upload/default/default-view.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/default/default-row.js M static/scripts/mvc/upload/default/default-view.js Log Message: ----------- Change FTP icon to open folder icon Commit: 673dd2b140791fade4c2943abc399d718b789950 https://github.com/galaxyproject/galaxy/commit/673dd2b140791fade4c2943abc39… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-08-20 (Thu, 20 Aug 2015) Changed paths: M client/galaxy/scripts/reports_webapp/run_stats.js M static/maps/reports_webapp/run_stats.js.map M static/scripts/reports_webapp/run_stats.js M templates/base.mako Log Message: ----------- Refactored where d3 is coming from Commit: 94dfbaa10a783a98e7488e0aa28e7551497657db https://github.com/galaxyproject/galaxy/commit/94dfbaa10a783a98e7488e0aa28e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-20 (Thu, 20 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/default/default-view.js M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/default/default-row.js.map M static/maps/mvc/upload/default/default-view.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/default/default-row.js M static/scripts/mvc/upload/default/default-view.js Log Message: ----------- Change pencil icon to edit icon Commit: 8be164f92c6896f2d9d0297d96c8073bd2612ec6 https://github.com/galaxyproject/galaxy/commit/8be164f92c6896f2d9d0297d96c8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-20 (Thu, 20 Aug 2015) Changed paths: M test/qunit/tests/upload_dialog_tests.js Log Message: ----------- Fix tests Commit: 795e30171149e65d14e1031b2f4d652da8f5f25c https://github.com/galaxyproject/galaxy/commit/795e30171149e65d14e1031b2f4d… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-20 (Thu, 20 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/default/default-view.js M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/default/default-row.js.map M static/maps/mvc/upload/default/default-view.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/default/default-row.js M static/scripts/mvc/upload/default/default-view.js M test/qunit/tests/upload_dialog_tests.js Log Message: ----------- Merge pull request #628 from guerler/upload_002 Change uploader icons Commit: 78251936e8df0256828f22130c42922190800ecc https://github.com/galaxyproject/galaxy/commit/78251936e8df0256828f22130c42… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-08-20 (Thu, 20 Aug 2015) Changed paths: M templates/base.mako M templates/webapps/reports/run_stats.mako Log Message: ----------- Moved d3 import to run_stats Commit: 104bdcd7c8e8e5557b166d47c9dcdfdadf22cdf6 https://github.com/galaxyproject/galaxy/commit/104bdcd7c8e8e5557b166d47c9dc… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-button-check.js M client/galaxy/scripts/mvc/ui/ui-color-picker.js M client/galaxy/scripts/mvc/ui/ui-options.js M static/maps/mvc/ui/ui-button-check.js.map M static/maps/mvc/ui/ui-color-picker.js.map M static/maps/mvc/ui/ui-options.js.map M static/scripts/mvc/ui/ui-button-check.js M static/scripts/mvc/ui/ui-color-picker.js M static/scripts/mvc/ui/ui-options.js Log Message: ----------- Minor code cleanup for ui elements Commit: 5d8ad4249fc6198846bf8cdceabf3fb91acc2973 https://github.com/galaxyproject/galaxy/commit/5d8ad4249fc6198846bf8cdceabf… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-color-picker.js M static/maps/mvc/ui/ui-color-picker.js.map M static/scripts/mvc/ui/ui-color-picker.js Log Message: ----------- Remove unnecessary condition Commit: 09445359a4dbcedb2d996dd4c46469f462ca6809 https://github.com/galaxyproject/galaxy/commit/09445359a4dbcedb2d996dd4c464… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/default/default-view.js M lib/galaxy/model/__init__.py M scripts/cleanup_datasets/cleanup_datasets.py M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/default/default-row.js.map M static/maps/mvc/upload/default/default-view.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/default/default-row.js M static/scripts/mvc/upload/default/default-view.js M test/qunit/tests/upload_dialog_tests.js M test/unit/test_galaxy_mapping.py R tool-data/fastx_clipper_sequences.txt Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into tool_form_removal_000 Commit: 950f471c2326cc8d90c7efe372c063f47ed7f3e4 https://github.com/galaxyproject/galaxy/commit/950f471c2326cc8d90c7efe372c0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Merge branch 'master' into dev Commit: ea130e2c008e100de92da78fa62ac797b635baed https://github.com/galaxyproject/galaxy/commit/ea130e2c008e100de92da78fa62a… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/multi-panel.js M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/multi-panel.js.map M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/multi-panel.js M templates/webapps/galaxy/history/view_multiple.mako Log Message: ----------- Histories: move order parsing into managers; View multi: allow and pass ordering into bootstrapped histories, limit to 10; View multi, client: allow better collection setting and addition Commit: d8ee54251afbcb965c02af47d800fac1e005a004 https://github.com/galaxyproject/galaxy/commit/d8ee54251afbcb965c02af47d800… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M .ci/flake8_blacklist.txt M CONTRIBUTING.md M client/galaxy/scripts/galaxy.menu.js M 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client/galaxy/scripts/utils/uploadbox.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/reports.less M client/galaxy/style/less/ui.less M client/galaxy/style/less/upload.less M client/grunt-tasks/scripts.js M config/galaxy.ini.sample M doc/source/project/organization.rst M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/config.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/managers/base.py M lib/galaxy/managers/configuration.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/sharable.py M lib/galaxy/model/__init__.py M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/quota/__init__.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/toolbox/lineages/stock.py M lib/galaxy/util/bunch.py M lib/galaxy/util/jstree.py M lib/galaxy/version.py M lib/galaxy/webapps/galaxy/api/datatypes.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py R lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/reports/controllers/workflows.py A lib/galaxy/webapps/tool_shed/api/configuration.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/workflow/render.py M lib/galaxy_utils/sequence/fasta.py M lib/galaxy_utils/sequence/fastq.py M lib/galaxy_utils/sequence/sequence.py M lib/galaxy_utils/sequence/transform.py M lib/galaxy_utils/sequence/vcf.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/dependencies/tool/tag_attribute_handler.py M 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static/images/SetAttr.png R static/images/SetGenome.png R static/images/brochure.pdf R static/images/galaxy.png R static/images/galaxyLogo_small.png R static/images/lock.jpg R static/images/qk/quickie1_small.png R static/images/qk/quickie2_small.png R static/images/qk/quickie3_small.png R static/images/qk/quickie4_small.png R static/images/qk/quickie5_small.png R static/images/qk/quickie6_small.png R static/images/qk/quickie7_small.png R static/images/reports_webapp/bases/home-icon-active.png R static/images/reports_webapp/bases/home-icon-hov.png R static/images/reports_webapp/bases/home-icon.png R static/images/reports_webapp/home-icon-active.png R static/images/reports_webapp/home-icon-hov.png R static/images/reports_webapp/home-icon.png R static/images/screencast.png R static/images/sequencer.png R static/images/tools.gif R static/images/toolsExpandingMenu.gif R static/images/welcomePhoto.jpg M static/maps/galaxy.interactive_environments.js.map M static/maps/galaxy.menu.js.map M 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static/scripts/viz/visualization.js M static/style/blue/base.css M static/style/blue/reports.css R static/welcome.rst M templates/page_base.mako M templates/spark_base.mako R templates/webapps/galaxy/cloud/index.mako A templates/webapps/galaxy/history/as_xml.mako M templates/webapps/galaxy/history/view.mako R templates/webapps/galaxy/root/history.mako R templates/webapps/galaxy/root/history_as_xml.mako M templates/webapps/reports/base_panels.mako M templates/webapps/reports/index.mako M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_in_error.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako M templates/webapps/reports/workflows_per_workflow.mako A test/qunit/test-app.js M test/qunit/test-common.js A test/qunit/test-data/bootstrapped.js A test/qunit/test-data/fakeserver.js A test/qunit/tests/upload_dialog_tests.html A test/qunit/tests/upload_dialog_tests.js M test/qunit/tests/workflow_editor_tests.js M test/unit/test_galaxy_mapping.py M tool-data/all_fasta.loc.sample M tool-data/faseq.loc.sample R tool-data/fastx_clipper_sequences.txt M tool-data/liftOver.loc.sample M tool-data/mosaik_index.loc.sample M tool-data/ngs_sim_fasta.loc.sample M tool-data/perm_base_index.loc.sample M tool-data/perm_color_index.loc.sample M tool-data/picard_index.loc.sample M tool-data/regions.loc.sample M tool-data/srma_index.loc.sample Log Message: ----------- Merge remote-tracking branch 'origin/dev' into history.multi Commit: 68240630668848b454aa51690ed1ac7bbfbc16e2 https://github.com/galaxyproject/galaxy/commit/68240630668848b454aa51690ed1… Author: chambm <matt.chambers42(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/tool_shed/util/common_util.py Log Message: ----------- * Fix get_latest_installable_revision to use pathspec and params to work with recent changes to common_util.url_join * Fix common_util.url_join to handle a string as pathspec, instead of treating it as an a/r/r/a/y/ /o/f/ /c/h/a/r/a/c/t/e/r/s Commit: 963d3fe6591a19c3940daeb20c13a5c4566653ad https://github.com/galaxyproject/galaxy/commit/963d3fe6591a19c3940daeb20c13… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_all.mako M templates/webapps/reports/jobs_specified_month_in_error.mako M templates/webapps/reports/run_stats.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako M templates/webapps/reports/workflows_per_workflow.mako Log Message: ----------- Fixed bug where column sorting reset paging info Commit: 245a3ccd9ef5c37f45529c69f3802b7269025333 https://github.com/galaxyproject/galaxy/commit/245a3ccd9ef5c37f45529c69f380… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M templates/webapps/reports/run_stats.mako Log Message: ----------- Fixed error on homepage Commit: eb59844dd2fa28734fb0ce3a051d582e2eac723f https://github.com/galaxyproject/galaxy/commit/eb59844dd2fa28734fb0ce3a051d… Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M client/galaxy/scripts/reports_webapp/run_stats.js M static/maps/reports_webapp/run_stats.js.map M static/scripts/reports_webapp/run_stats.js M templates/base.mako M templates/spark_base.mako M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_all.mako M templates/webapps/reports/jobs_specified_month_in_error.mako M templates/webapps/reports/run_stats.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako M templates/webapps/reports/workflows_per_workflow.mako Log Message: ----------- Merge pull request #626 from Airistotal/dev Bug fix in Reports Commit: d375a8cc034acaea43e221cb60fe58ece5f5d4d6 https://github.com/galaxyproject/galaxy/commit/d375a8cc034acaea43e221cb60fe… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/tool_shed/util/common_util.py Log Message: ----------- Merge pull request #632 from chambm/bug/url_join-latest_revision-2 Cleaner commit history for #629 and array syntax for pathspec Commit: 51b3087c9c7474b0e93644f129a2ea3083e190bd https://github.com/galaxyproject/galaxy/commit/51b3087c9c7474b0e93644f129a2… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-21 (Fri, 21 Aug 2015) Log Message: ----------- Merge branch 'master' into dev Commit: 57cea58942b7887b3e95e974fbcb3ebb54e05218 https://github.com/galaxyproject/galaxy/commit/57cea58942b7887b3e95e974fbcb… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-24 (Mon, 24 Aug 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge branch 'master' into dev Commit: 9a44d780145b6a7b30b40b1a7e61b7df5e526dbc https://github.com/galaxyproject/galaxy/commit/9a44d780145b6a7b30b40b1a7e61… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-24 (Mon, 24 Aug 2015) Changed paths: M client/galaxy/scripts/reports_webapp/run_stats.js M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/workflow/render.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/util/common_util.py M static/maps/reports_webapp/run_stats.js.map M static/scripts/reports_webapp/run_stats.js M templates/base.mako M templates/spark_base.mako M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_all.mako M templates/webapps/reports/jobs_specified_month_in_error.mako M templates/webapps/reports/run_stats.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako M templates/webapps/reports/workflows_per_workflow.mako Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into tool_form_removal_000 Commit: 2ae60fbd84d87931e26227c27db36aae9b1323b0 https://github.com/galaxyproject/galaxy/commit/2ae60fbd84d87931e26227c27db3… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-24 (Mon, 24 Aug 2015) Changed paths: M config/tool_data_table_conf.xml.sample M tools/extract/liftOver_wrapper.xml Log Message: ----------- Merge pull request #588 from yhoogstrate/liftOver liftOver.loc was not accessible in local data Commit: 9444b2eb271d03c0719b6706c830404c5567e88d https://github.com/galaxyproject/galaxy/commit/9444b2eb271d03c0719b6706c830… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-08-25 (Tue, 25 Aug 2015) Changed paths: M lib/galaxy/managers/datasets.py Log Message: ----------- Dataset manager: deserialize permissions Commit: 69ea94747883f7bf2ad0ddfae84914703f6d6297 https://github.com/galaxyproject/galaxy/commit/69ea94747883f7bf2ad0ddfae849… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-25 (Tue, 25 Aug 2015) Changed paths: M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/s3.py Log Message: ----------- Merge branch 'master' into dev Commit: 7968f60d0374a15e0caf671867e711a66b8aabb4 https://github.com/galaxyproject/galaxy/commit/7968f60d0374a15e0caf671867e7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-08-25 (Tue, 25 Aug 2015) Changed paths: M CODE_OF_CONDUCT.md Log Message: ----------- Fix typo found by @nsoranzo. Commit: f9f763f430081b3f1cb1569ff3239b61e8d01f97 https://github.com/galaxyproject/galaxy/commit/f9f763f430081b3f1cb1569ff323… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-25 (Tue, 25 Aug 2015) Changed paths: M static/maps/utils/uploadbox.js.map M static/scripts/utils/uploadbox.js Log Message: ----------- add missing js build Commit: 4dc2f8ceeda68e03d3b50ee9e6f5e3ab0f21b7f0 https://github.com/galaxyproject/galaxy/commit/4dc2f8ceeda68e03d3b50ee9e6f5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-25 (Tue, 25 Aug 2015) Changed paths: M static/maps/utils/uploadbox.js.map M static/scripts/utils/uploadbox.js Log Message: ----------- Merge pull request #648 from martenson/missing-js-build add missing js build Commit: bc3ecbbae8d0161dec98d0566ad8c9eb3dfcfd97 https://github.com/galaxyproject/galaxy/commit/bc3ecbbae8d0161dec98d0566ad8… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-26 (Wed, 26 Aug 2015) Changed paths: M .ci/flake8_blacklist.txt M test/tool_shed/base/twilltestcase.py M test/tool_shed/functional/test_0000_basic_repository_features.py M test/tool_shed/functional/test_0010_repository_with_tool_dependencies.py M test/tool_shed/functional/test_0020_basic_repository_dependencies.py M test/tool_shed/functional/test_0030_repository_dependency_revisions.py M test/tool_shed/functional/test_0040_repository_circular_dependencies.py M test/tool_shed/functional/test_0050_circular_dependencies_4_levels.py M test/tool_shed/functional/test_0060_workflows.py M test/tool_shed/functional/test_0070_invalid_tool.py M test/tool_shed/functional/test_0080_advanced_circular_dependencies.py M test/tool_shed/functional/test_0090_tool_search.py M test/tool_shed/functional/test_0100_complex_repository_dependencies.py M test/tool_shed/functional/test_0110_invalid_simple_repository_dependencies.py M test/tool_shed/functional/test_0120_simple_repository_dependency_multiple_owners.py M test/tool_shed/functional/test_0130_datatype_converters.py M test/tool_shed/functional/test_0140_tool_help_images.py M test/tool_shed/functional/test_0150_prior_installation_required.py M test/tool_shed/functional/test_0160_circular_prior_installation_required.py M test/tool_shed/functional/test_0170_complex_prior_installation_required.py M test/tool_shed/functional/test_0300_reset_all_metadata.py M test/tool_shed/functional/test_0310_hg_push_from_api.py M test/tool_shed/functional/test_0400_repository_component_reviews.py M test/tool_shed/functional/test_0410_repository_component_review_access_control.py M test/tool_shed/functional/test_0420_citable_urls_for_repositories.py M test/tool_shed/functional/test_0430_browse_utilities.py M test/tool_shed/functional/test_0440_deleting_dependency_definitions.py M test/tool_shed/functional/test_0450_skip_tool_tests.py M test/tool_shed/functional/test_0460_upload_to_repository.py M test/tool_shed/functional/test_0470_tool_dependency_repository_type.py M 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test/tool_shed/functional/test_1060_install_repository_with_workflow.py M test/tool_shed/functional/test_1070_invalid_tool.py M test/tool_shed/functional/test_1080_advanced_circular_dependency_installation.py M test/tool_shed/functional/test_1085_repository_dependency_handling.py M test/tool_shed/functional/test_1087_install_updated_repository_dependencies.py M test/tool_shed/functional/test_1090_install_tool_from_tool_search.py M test/tool_shed/functional/test_1100_install_repository_with_complex_dependencies.py M test/tool_shed/functional/test_1110_install_repository_with_invalid_repository_dependency.py M test/tool_shed/functional/test_1120_simple_repository_dependency_multiple_owners.py M test/tool_shed/functional/test_1130_datatype_converters.py M test/tool_shed/functional/test_1140_tool_help_images.py M test/tool_shed/functional/test_1150_prior_installation_required.py M test/tool_shed/functional/test_1160_circular_prior_installation_required.py M test/tool_shed/functional/test_1170_complex_prior_installation_required.py M test/tool_shed/functional/test_1200_uninstall_and_reinstall_basic_repository.py M test/tool_shed/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py M test/tool_shed/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py M test/tool_shed/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py M test/tool_shed/functional/test_1300_reset_all_metadata.py M test/tool_shed/functional/test_1400_review_migration_stages.py M test/tool_shed/functional/test_1410_update_manager.py M test/tool_shed/functional/test_1420_tool_dependency_environment_inheritance.py M test/tool_shed/functional/test_1430_repair_installed_repository.py M test/tool_shed/functional/test_1440_missing_env_sh_files.py M test/tool_shed/functional/test_1450_installing_datatypes_sniffers.py M test/tool_shed/functional/test_1460_data_managers.py M test/tool_shed/functional/test_1470_updating_installed_repositories.py M test/tool_shed/functional_tests.py Log Message: ----------- flake8 test/tool_shed/ . Commit: 5701934e6520713913dced403992551eae7c6ef8 https://github.com/galaxyproject/galaxy/commit/5701934e6520713913dced403992… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-26 (Wed, 26 Aug 2015) Changed paths: M test/tool_shed/functional/test_1170_complex_prior_installation_required.py Log Message: ----------- Fix broken test_0025_install_matplotlib_repository test. Commit: 11870a96f4e73838941e29c9ae2c0f721c8c072d https://github.com/galaxyproject/galaxy/commit/11870a96f4e73838941e29c9ae2c… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-26 (Wed, 26 Aug 2015) Changed paths: M test/tool_shed/test_data/proteomics_datatypes/proteomics_datatypes.tar Log Message: ----------- Remove from proteomics_datatypes.tar test data the datatypes that have been added to Galaxy datatypes. Fix tests in test/tool_shed/functional/test_1450_installing_datatypes_sniffers.py . Commit: 6ca86b5586dea7ae88249cf66183bb44a1c9e96a https://github.com/galaxyproject/galaxy/commit/6ca86b5586dea7ae88249cf66183… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-26 (Wed, 26 Aug 2015) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/repository.py Log Message: ----------- Fix regression introduced in 0f2e2152ee17532488a8231cf1220ed9ddddb3aa . Commit: fc2861ce78204f52ec917ea73695d2b090f7b945 https://github.com/galaxyproject/galaxy/commit/fc2861ce78204f52ec917ea73695… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-26 (Wed, 26 Aug 2015) Changed paths: M test/tool_shed/base/twilltestcase.py Log Message: ----------- Fix 3 failing functional tests in test/tool_shed/ . Commit: b0f2eaec031217b8ed3c018bded274f6fbc3b155 https://github.com/galaxyproject/galaxy/commit/b0f2eaec031217b8ed3c018bded2… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-26 (Wed, 26 Aug 2015) Changed paths: M .ci/flake8_blacklist.txt M lib/galaxy/webapps/tool_shed/controllers/repository.py M test/tool_shed/base/twilltestcase.py M test/tool_shed/functional/test_0000_basic_repository_features.py M test/tool_shed/functional/test_0010_repository_with_tool_dependencies.py M test/tool_shed/functional/test_0020_basic_repository_dependencies.py M test/tool_shed/functional/test_0030_repository_dependency_revisions.py M test/tool_shed/functional/test_0040_repository_circular_dependencies.py M test/tool_shed/functional/test_0050_circular_dependencies_4_levels.py M test/tool_shed/functional/test_0060_workflows.py M test/tool_shed/functional/test_0070_invalid_tool.py M test/tool_shed/functional/test_0080_advanced_circular_dependencies.py M test/tool_shed/functional/test_0090_tool_search.py M test/tool_shed/functional/test_0100_complex_repository_dependencies.py M test/tool_shed/functional/test_0110_invalid_simple_repository_dependencies.py M test/tool_shed/functional/test_0120_simple_repository_dependency_multiple_owners.py M test/tool_shed/functional/test_0130_datatype_converters.py M test/tool_shed/functional/test_0140_tool_help_images.py M test/tool_shed/functional/test_0150_prior_installation_required.py M test/tool_shed/functional/test_0160_circular_prior_installation_required.py M test/tool_shed/functional/test_0170_complex_prior_installation_required.py M test/tool_shed/functional/test_0300_reset_all_metadata.py M test/tool_shed/functional/test_0310_hg_push_from_api.py M test/tool_shed/functional/test_0400_repository_component_reviews.py M test/tool_shed/functional/test_0410_repository_component_review_access_control.py M test/tool_shed/functional/test_0420_citable_urls_for_repositories.py M test/tool_shed/functional/test_0430_browse_utilities.py M test/tool_shed/functional/test_0440_deleting_dependency_definitions.py M test/tool_shed/functional/test_0450_skip_tool_tests.py M test/tool_shed/functional/test_0460_upload_to_repository.py M test/tool_shed/functional/test_0470_tool_dependency_repository_type.py M test/tool_shed/functional/test_0480_tool_dependency_xml_verification.py M test/tool_shed/functional/test_0490_export_import_repositories.py M test/tool_shed/functional/test_0500_export_repository_simple_dependency.py M test/tool_shed/functional/test_0510_export_import_repository_complex_dependencies.py M test/tool_shed/functional/test_0520_import_export_circular_dependencies.py M test/tool_shed/functional/test_0530_repository_admin_feature.py M test/tool_shed/functional/test_1000_install_basic_repository.py M test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py M test/tool_shed/functional/test_1020_install_repository_with_repository_dependencies.py M test/tool_shed/functional/test_1030_install_repository_with_dependency_revisions.py M test/tool_shed/functional/test_1040_install_repository_basic_circular_dependencies.py M test/tool_shed/functional/test_1050_circular_dependencies_4_levels.py M test/tool_shed/functional/test_1060_install_repository_with_workflow.py M test/tool_shed/functional/test_1070_invalid_tool.py M test/tool_shed/functional/test_1080_advanced_circular_dependency_installation.py M test/tool_shed/functional/test_1085_repository_dependency_handling.py M test/tool_shed/functional/test_1087_install_updated_repository_dependencies.py M test/tool_shed/functional/test_1090_install_tool_from_tool_search.py M test/tool_shed/functional/test_1100_install_repository_with_complex_dependencies.py M test/tool_shed/functional/test_1110_install_repository_with_invalid_repository_dependency.py M test/tool_shed/functional/test_1120_simple_repository_dependency_multiple_owners.py M test/tool_shed/functional/test_1130_datatype_converters.py M test/tool_shed/functional/test_1140_tool_help_images.py M test/tool_shed/functional/test_1150_prior_installation_required.py M test/tool_shed/functional/test_1160_circular_prior_installation_required.py M test/tool_shed/functional/test_1170_complex_prior_installation_required.py M test/tool_shed/functional/test_1200_uninstall_and_reinstall_basic_repository.py M test/tool_shed/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py M test/tool_shed/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py M test/tool_shed/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py M test/tool_shed/functional/test_1300_reset_all_metadata.py M test/tool_shed/functional/test_1400_review_migration_stages.py M test/tool_shed/functional/test_1410_update_manager.py M test/tool_shed/functional/test_1420_tool_dependency_environment_inheritance.py M test/tool_shed/functional/test_1430_repair_installed_repository.py M test/tool_shed/functional/test_1440_missing_env_sh_files.py M test/tool_shed/functional/test_1450_installing_datatypes_sniffers.py M test/tool_shed/functional/test_1460_data_managers.py M test/tool_shed/functional/test_1470_updating_installed_repositories.py M test/tool_shed/functional_tests.py M test/tool_shed/test_data/proteomics_datatypes/proteomics_datatypes.tar Log Message: ----------- Merge pull request #650 from nsoranzo/dev flake8 test/tool_shed/ . Fix 8 Tool Shed functional tests. Commit: b8362b71509013566694280cb89e967dca704a31 https://github.com/galaxyproject/galaxy/commit/b8362b71509013566694280cb89e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-26 (Wed, 26 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Include link expiration time in password reset email. Commit: 11e6c9949e2bb58874eedb81d9066c1f460fa34a https://github.com/galaxyproject/galaxy/commit/11e6c9949e2bb58874eedb81d906… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-26 (Wed, 26 Aug 2015) Changed paths: M templates/base.mako Log Message: ----------- Make sure global Galaxy object exists Commit: 6c82266546c77361f9d2265ab749db1446142150 https://github.com/galaxyproject/galaxy/commit/6c82266546c77361f9d2265ab749… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-08-26 (Wed, 26 Aug 2015) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/galaxy_install/repair_repository_manager.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Merge nearly-identical methods in shed_util_common. Commit: 7b3fbcbd7f4e4464e7471b9d634165a20e24e834 https://github.com/galaxyproject/galaxy/commit/7b3fbcbd7f4e4464e7471b9d6341… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-26 (Wed, 26 Aug 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Expose tool config file path to admins via the API. This is useful (not to mention already kinda exposed when using wrappers) for interfacing with planemo for the smc work and I would expect other automation tasks. Commit: 5e9d1becfca27882ab9a106df2ea80e3d7d96404 https://github.com/galaxyproject/galaxy/commit/5e9d1becfca27882ab9a106df2ea… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-26 (Wed, 26 Aug 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Actually use the method instead of just checking it's existence Commit: d74dfbefd4f24fa93a437b782d340d4fd152c079 https://github.com/galaxyproject/galaxy/commit/d74dfbefd4f24fa93a437b782d34… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-08-26 (Wed, 26 Aug 2015) Changed paths: M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Add missing docstring. Commit: 2fccd0c11f91fedabd979fc62064e4ea31a33ae2 https://github.com/galaxyproject/galaxy/commit/2fccd0c11f91fedabd979fc62064… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-26 (Wed, 26 Aug 2015) Changed paths: M .ci/flake8_blacklist.txt M .ci/flake8_wrapper.sh M test/base/asserts/__init__.py M test/base/interactor.py M test/base/twilltestcase.py M test/casperjs/casperjs_runner.py M test/casperjs/server_env.py M test/install_and_test_tool_shed_repositories/base/twilltestcase.py M test/install_and_test_tool_shed_repositories/base/util.py M test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py M test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py M test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py Log Message: ----------- Finish flake8 of test/ . Commit: 6f1e1cea82aae5695b669a57d870ec173f6b8d6a https://github.com/galaxyproject/galaxy/commit/6f1e1cea82aae5695b669a57d870… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-26 (Wed, 26 Aug 2015) Changed paths: M test/qunit/package.json Log Message: ----------- Add mandatory "version" field to package.json . Commit: 93716ec08a1c5aedd476b137ed2b670b2e73d114 https://github.com/galaxyproject/galaxy/commit/93716ec08a1c5aedd476b137ed2b… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-26 (Wed, 26 Aug 2015) Changed paths: M test/qunit/README.txt Log Message: ----------- Suggest to install grunt-cli globally to have grunt in PATH. Commit: dc7f7f2e3babf35dab06297245464fe16b97c8de https://github.com/galaxyproject/galaxy/commit/dc7f7f2e3babf35dab0629724546… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-26 (Wed, 26 Aug 2015) Changed paths: M test/unit/tools/test_toolbox_filters.py Log Message: ----------- Fix mock_trans to provide a user_is_admin member Commit: bb7cbc7ee556f6a0146e669792f5cc953893cf98 https://github.com/galaxyproject/galaxy/commit/bb7cbc7ee556f6a0146e669792f5… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-08-26 (Wed, 26 Aug 2015) Changed paths: M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Correct parameters. Commit: aea250334f319788aa6281bdb2d4ddfdfcb12b84 https://github.com/galaxyproject/galaxy/commit/aea250334f319788aa6281bdb2d4… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-08-26 (Wed, 26 Aug 2015) Changed paths: M lib/galaxy/tools/__init__.py M test/unit/tools/test_toolbox_filters.py Log Message: ----------- Merge pull request #652 from dannon/tool_path_expose Expose tool config file path to admins via the API. This is useful (… Commit: 299d628531bba44d403bc191b53ae09437f050be https://github.com/galaxyproject/galaxy/commit/299d628531bba44d403bc191b53a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-26 (Wed, 26 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Validate user email input prior to attempting to reset. Commit: 29d510f7dee48bf54776773f8a2f971781b08052 https://github.com/galaxyproject/galaxy/commit/29d510f7dee48bf54776773f8a2f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-26 (Wed, 26 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Force lowercase comparison for password reset. TODO: Look for more places this is potentially an issue. Commit: 785f81989627db26b3799b0e6d5123213fcec9e4 https://github.com/galaxyproject/galaxy/commit/785f81989627db26b3799b0e6d51… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-08-26 (Wed, 26 Aug 2015) Changed paths: A doc/source/dev/faq.rst A doc/source/dev/index.rst M doc/source/index.rst Log Message: ----------- Add developer documentation to docs Commit: 86c3175fcda4ff85505ecfcd78cf2b302909a7a7 https://github.com/galaxyproject/galaxy/commit/86c3175fcda4ff85505ecfcd78cf… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-08-26 (Wed, 26 Aug 2015) Changed paths: A doc/source/_api_quickstart.rst A doc/source/api/quickstart.rst M doc/source/api_doc.rst M doc/source/ts_api_doc.rst Log Message: ----------- Extract quickstart, reorg GX/TS Doc index Commit: 7f167ef3640d7bdb7e37f2b398a7d81cd15cfc83 https://github.com/galaxyproject/galaxy/commit/7f167ef3640d7bdb7e37f2b398a7… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-08-26 (Wed, 26 Aug 2015) Changed paths: A doc/source/_api_quickstart.rst A doc/source/api/quickstart.rst M doc/source/api_doc.rst A doc/source/dev/faq.rst A doc/source/dev/index.rst M doc/source/index.rst M doc/source/ts_api_doc.rst Log Message: ----------- Add developer documentation to docs - Extract quickstart - reorg GX/TS Doc index Commit: 0bfa99725463f1807816e5c0bdeacf46eb186c55 https://github.com/galaxyproject/galaxy/commit/0bfa99725463f1807816e5c0bdea… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-08-26 (Wed, 26 Aug 2015) Changed paths: R doc/source/_api_quickstart.rst Log Message: ----------- Remove unused file Commit: 1762fcde056d72414c31241c1f3965c214ad7be7 https://github.com/galaxyproject/galaxy/commit/1762fcde056d72414c31241c1f39… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-08-26 (Wed, 26 Aug 2015) Changed paths: R doc/source/_api_quickstart.rst Log Message: ----------- Remove unused file Commit: a98e3ff6de51d0fe43db97ade602ccd6b8eea468 https://github.com/galaxyproject/galaxy/commit/a98e3ff6de51d0fe43db97ade602… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Swap to config.pretty_datetime_format Commit: 9356ae5f3fa6155b68eba98b8eac9862bd53ba57 https://github.com/galaxyproject/galaxy/commit/9356ae5f3fa6155b68eba98b8eac… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Switch password reset tokens to use UTC. This is kind of a mess, we're using both UTC and localized time in various places. Commit: b339dbf585bd6f2924de516a99823e93e4f3a6e7 https://github.com/galaxyproject/galaxy/commit/b339dbf585bd6f2924de516a9982… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M doc/source/dev/faq.rst Log Message: ----------- s/python/Python in FAQ Commit: 1041cad9ec4f50837158f8bbfe5d27f9e3db7d0e https://github.com/galaxyproject/galaxy/commit/1041cad9ec4f50837158f8bbfe5d… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M client/galaxy/style/less/reports.less M static/style/blue/base.css M static/style/blue/reports.css M templates/webapps/reports/jobs_specified_month_in_error.mako Log Message: ----------- Centered headers in firefox Made page selection divs not wrap when window size is too small Changed name for action in Jobs in error per day this month which fixes crash Commit: 865d0153954e3be07d139f6100d21bdf5543a2f9 https://github.com/galaxyproject/galaxy/commit/865d0153954e3be07d139f6100d2… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M .ci/flake8_blacklist.txt M client/galaxy/scripts/mvc/ui/ui-button-menu.js M client/galaxy/scripts/mvc/ui/ui-color-picker.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/mvc/ui/ui-popover.js A client/galaxy/scripts/mvc/upload/composite/composite-row.js A client/galaxy/scripts/mvc/upload/composite/composite-view.js A client/galaxy/scripts/mvc/upload/default/default-row.js A client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-button.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-model.js R client/galaxy/scripts/mvc/upload/upload-row.js M client/galaxy/scripts/mvc/upload/upload-settings.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/ui.less M client/galaxy/style/less/upload.less M config/tool_data_table_conf.xml.sample M lib/galaxy/datatypes/genetics.py M lib/galaxy/managers/base.py M lib/galaxy/managers/sharable.py M lib/galaxy/model/__init__.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/__init__.py M lib/galaxy/util/bunch.py M lib/galaxy/util/jstree.py M lib/galaxy/webapps/galaxy/api/datatypes.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py A lib/galaxy/webapps/tool_shed/api/configuration.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/workflow/render.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/util/common_util.py M scripts/cleanup_datasets/cleanup_datasets.py M static/maps/mvc/ui/ui-button-menu.js.map M static/maps/mvc/ui/ui-color-picker.js.map M static/maps/mvc/ui/ui-misc.js.map M static/maps/mvc/ui/ui-modal.js.map M static/maps/mvc/ui/ui-popover.js.map A static/maps/mvc/upload/composite/composite-row.js.map A static/maps/mvc/upload/composite/composite-view.js.map A static/maps/mvc/upload/default/default-row.js.map A static/maps/mvc/upload/default/default-view.js.map M static/maps/mvc/upload/upload-button.js.map M static/maps/mvc/upload/upload-ftp.js.map M static/maps/mvc/upload/upload-model.js.map R static/maps/mvc/upload/upload-row.js.map M static/maps/mvc/upload/upload-settings.js.map M static/maps/mvc/upload/upload-view.js.map M static/maps/utils/uploadbox.js.map M static/maps/utils/utils.js.map M static/scripts/mvc/ui/ui-button-menu.js M static/scripts/mvc/ui/ui-color-picker.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-modal.js M static/scripts/mvc/ui/ui-popover.js A static/scripts/mvc/upload/composite/composite-row.js A static/scripts/mvc/upload/composite/composite-view.js A static/scripts/mvc/upload/default/default-row.js A static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/upload-button.js M static/scripts/mvc/upload/upload-ftp.js M static/scripts/mvc/upload/upload-model.js R static/scripts/mvc/upload/upload-row.js M static/scripts/mvc/upload/upload-settings.js M static/scripts/mvc/upload/upload-view.js M static/scripts/utils/uploadbox.js M static/scripts/utils/utils.js M static/style/blue/base.css A test/qunit/test-app.js M test/qunit/test-common.js A test/qunit/test-data/bootstrapped.js A test/qunit/test-data/fakeserver.js A test/qunit/tests/upload_dialog_tests.html A test/qunit/tests/upload_dialog_tests.js M test/qunit/tests/workflow_editor_tests.js M test/tool_shed/base/twilltestcase.py M test/tool_shed/functional/test_0000_basic_repository_features.py M test/tool_shed/functional/test_0010_repository_with_tool_dependencies.py M test/tool_shed/functional/test_0020_basic_repository_dependencies.py M test/tool_shed/functional/test_0030_repository_dependency_revisions.py M test/tool_shed/functional/test_0040_repository_circular_dependencies.py M test/tool_shed/functional/test_0050_circular_dependencies_4_levels.py M test/tool_shed/functional/test_0060_workflows.py M test/tool_shed/functional/test_0070_invalid_tool.py M test/tool_shed/functional/test_0080_advanced_circular_dependencies.py M test/tool_shed/functional/test_0090_tool_search.py M test/tool_shed/functional/test_0100_complex_repository_dependencies.py M test/tool_shed/functional/test_0110_invalid_simple_repository_dependencies.py M test/tool_shed/functional/test_0120_simple_repository_dependency_multiple_owners.py M test/tool_shed/functional/test_0130_datatype_converters.py M test/tool_shed/functional/test_0140_tool_help_images.py M test/tool_shed/functional/test_0150_prior_installation_required.py M test/tool_shed/functional/test_0160_circular_prior_installation_required.py M test/tool_shed/functional/test_0170_complex_prior_installation_required.py M test/tool_shed/functional/test_0300_reset_all_metadata.py M test/tool_shed/functional/test_0310_hg_push_from_api.py M test/tool_shed/functional/test_0400_repository_component_reviews.py M test/tool_shed/functional/test_0410_repository_component_review_access_control.py M test/tool_shed/functional/test_0420_citable_urls_for_repositories.py M test/tool_shed/functional/test_0430_browse_utilities.py M test/tool_shed/functional/test_0440_deleting_dependency_definitions.py M test/tool_shed/functional/test_0450_skip_tool_tests.py M test/tool_shed/functional/test_0460_upload_to_repository.py M test/tool_shed/functional/test_0470_tool_dependency_repository_type.py M test/tool_shed/functional/test_0480_tool_dependency_xml_verification.py M test/tool_shed/functional/test_0490_export_import_repositories.py M test/tool_shed/functional/test_0500_export_repository_simple_dependency.py M test/tool_shed/functional/test_0510_export_import_repository_complex_dependencies.py M test/tool_shed/functional/test_0520_import_export_circular_dependencies.py M test/tool_shed/functional/test_0530_repository_admin_feature.py M test/tool_shed/functional/test_1000_install_basic_repository.py M test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py M test/tool_shed/functional/test_1020_install_repository_with_repository_dependencies.py M test/tool_shed/functional/test_1030_install_repository_with_dependency_revisions.py M test/tool_shed/functional/test_1040_install_repository_basic_circular_dependencies.py M test/tool_shed/functional/test_1050_circular_dependencies_4_levels.py M test/tool_shed/functional/test_1060_install_repository_with_workflow.py M test/tool_shed/functional/test_1070_invalid_tool.py M test/tool_shed/functional/test_1080_advanced_circular_dependency_installation.py M test/tool_shed/functional/test_1085_repository_dependency_handling.py M test/tool_shed/functional/test_1087_install_updated_repository_dependencies.py M test/tool_shed/functional/test_1090_install_tool_from_tool_search.py M test/tool_shed/functional/test_1100_install_repository_with_complex_dependencies.py M test/tool_shed/functional/test_1110_install_repository_with_invalid_repository_dependency.py M test/tool_shed/functional/test_1120_simple_repository_dependency_multiple_owners.py M test/tool_shed/functional/test_1130_datatype_converters.py M test/tool_shed/functional/test_1140_tool_help_images.py M test/tool_shed/functional/test_1150_prior_installation_required.py M test/tool_shed/functional/test_1160_circular_prior_installation_required.py M test/tool_shed/functional/test_1170_complex_prior_installation_required.py M test/tool_shed/functional/test_1200_uninstall_and_reinstall_basic_repository.py M test/tool_shed/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py M test/tool_shed/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py M test/tool_shed/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py M test/tool_shed/functional/test_1300_reset_all_metadata.py M test/tool_shed/functional/test_1400_review_migration_stages.py M test/tool_shed/functional/test_1410_update_manager.py M test/tool_shed/functional/test_1420_tool_dependency_environment_inheritance.py M test/tool_shed/functional/test_1430_repair_installed_repository.py M test/tool_shed/functional/test_1440_missing_env_sh_files.py M test/tool_shed/functional/test_1450_installing_datatypes_sniffers.py M test/tool_shed/functional/test_1460_data_managers.py M test/tool_shed/functional/test_1470_updating_installed_repositories.py M test/tool_shed/functional_tests.py M test/tool_shed/test_data/proteomics_datatypes/proteomics_datatypes.tar M test/unit/test_galaxy_mapping.py M test/unit/tools/test_toolbox_filters.py R tool-data/fastx_clipper_sequences.txt M tools/extract/liftOver_wrapper.xml Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into dev Conflicts: static/style/blue/base.css Commit: c337fccbeb967c782339b5f6c812daa70014dc99 https://github.com/galaxyproject/galaxy/commit/c337fccbeb967c782339b5f6c812… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Use case-insensitive email selection only when case-sensitive comes up empty. Commit: 364a714aac3b422178b01d9bf0ac8e1a8bee6100 https://github.com/galaxyproject/galaxy/commit/364a714aac3b422178b01d9bf0ac… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M doc/source/dev/faq.rst Log Message: ----------- Merge pull request #7 from dannon/repl s/python/Python in FAQ Commit: c2fca17c98305ca24c3ec415bd9bcbe5695a382f https://github.com/galaxyproject/galaxy/commit/c2fca17c98305ca24c3ec415bd9b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: A doc/source/api/quickstart.rst M doc/source/api_doc.rst A doc/source/dev/faq.rst A doc/source/dev/index.rst M doc/source/index.rst M doc/source/ts_api_doc.rst Log Message: ----------- Merge pull request #654 from erasche/repl Galaxy Developer Documentation Commit: 7ce4bde8781645b09bb7ce54b9b7114c41ff9c36 https://github.com/galaxyproject/galaxy/commit/7ce4bde8781645b09bb7ce54b9b7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Allow accessing repeat and conditional elements in PJA parameters. Use . instead of the | that would be the actual association name. Cannot use | because it is treated as a special character in this code. Parameters with . in the names break Galaxy in subtle ways anyway and so treating them as a special character here should not be a problem. Commit: 949b3de56860242c6c20c04e0b18ffc694384b76 https://github.com/galaxyproject/galaxy/commit/949b3de56860242c6c20c04e0b18… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M .ci/flake8_blacklist.txt M .ci/flake8_wrapper.sh M test/base/asserts/__init__.py M test/base/interactor.py M test/base/twilltestcase.py M test/casperjs/casperjs_runner.py M test/casperjs/server_env.py M test/install_and_test_tool_shed_repositories/base/twilltestcase.py M test/install_and_test_tool_shed_repositories/base/util.py M test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py M test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py M test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py M test/qunit/README.txt M test/qunit/package.json Log Message: ----------- Merge pull request #653 from nsoranzo/dev Finish flake8 of test/ . Commit: f5ca24ee2baea35ad7a3bc62db7f5a996ccaa2a7 https://github.com/galaxyproject/galaxy/commit/f5ca24ee2baea35ad7a3bc62db7f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Merge pull request #655 from dannon/password_reset_tweaks Password reset tweaks Commit: 4a4ed87f11c8a47dcc838bdc6a42389def73afe9 https://github.com/galaxyproject/galaxy/commit/4a4ed87f11c8a47dcc838bdc6a42… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M client/galaxy/style/less/reports.less M static/style/blue/base.css M static/style/blue/reports.css M templates/webapps/reports/jobs_specified_month_in_error.mako Log Message: ----------- Merge pull request #656 from Airistotal/dev Reports - Small bug fixes Commit: e9580412552299d82d3e627fcf3bde45d5e95a26 https://github.com/galaxyproject/galaxy/commit/e9580412552299d82d3e627fcf3b… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M lib/galaxy/util/xml_macros.py M lib/tool_shed/metadata/metadata_generator.py M test/unit/tools/test_tool_loader.py Log Message: ----------- Merge branch 'master' into dev Conflicts: lib/tool_shed/metadata/metadata_generator.py Commit: 9711a60b82c74c697f550348e5d3fdd1f3333082 https://github.com/galaxyproject/galaxy/commit/9711a60b82c74c697f550348e5d3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M lib/galaxy/managers/base.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/rbac_secured.py M test/unit/managers/test_DatasetManager.py Log Message: ----------- Merge pull request #640 from carlfeberhard/managers Allow deserializing dataset permissions Commit: e99353bd1cb83fc55ac4678c43bbf4ce8bcbed55 https://github.com/galaxyproject/galaxy/commit/e99353bd1cb83fc55ac4678c43bb… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M lib/galaxy/webapps/tool_shed/buildapp.py Log Message: ----------- fix TS API endpoint to correctly consume full relpath of the image Commit: 23a978709528d55ab02c4127e785df909adb47c4 https://github.com/galaxyproject/galaxy/commit/23a978709528d55ab02c4127e785… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M lib/tool_shed/util/shed_util_common.py Log Message: ----------- remove replaces for static prefix in image relpaths this is not a problem when in Tool Shed and it prevents people form using these paths ping @bgruening Commit: 183ddbed3e9d01f24d66fd0d49454ecdb9e95aa6 https://github.com/galaxyproject/galaxy/commit/183ddbed3e9d01f24d66fd0d4945… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Eliminate ${static_path} from tool shed image links. I did not find a reason to use it. Commit: 3261a76828dd0e7bc834aa8a53f9e3851b59219e https://github.com/galaxyproject/galaxy/commit/3261a76828dd0e7bc834aa8a53f9… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M client/galaxy/style/less/reports.less M static/style/blue/base.css M static/style/blue/reports.css Log Message: ----------- remove reports style that affected the whole application fixes https://github.com/galaxyproject/galaxy/pull/656/files#r38132110 Commit: 0409ad6c4a54a65b666ffbd7fbc99c3a31898b3d https://github.com/galaxyproject/galaxy/commit/0409ad6c4a54a65b666ffbd7fbc9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M client/galaxy/style/less/reports.less M static/style/blue/base.css M static/style/blue/reports.css Log Message: ----------- Merge pull request #661 from martenson/remove-sideeffecting-style remove reports style that affected the whole application Commit: 5d4d32a43221d4a0725a2d16d6bac02c9b867d4d https://github.com/galaxyproject/galaxy/commit/5d4d32a43221d4a0725a2d16d6ba… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/galaxy_install/repair_repository_manager.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Merge pull request #651 from davebx/suc_cleanup Merge nearly-identical methods in shed_util_common. Commit: 396bcc782082e2965f67fc6ec87b02e79cf74859 https://github.com/galaxyproject/galaxy/commit/396bcc782082e2965f67fc6ec87b… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M lib/galaxy/webapps/tool_shed/buildapp.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Merge pull request #660 from martenson/fix-tool-image-paths Fix tool image paths. Commit: bada494b85c93c5662275ab5652e29e7bfb9a0ac https://github.com/galaxyproject/galaxy/commit/bada494b85c93c5662275ab5652e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Merge pull request #662 from jmchilton/repeat_rename Allow accessing repeat and conditional elements in PJA parameters. Commit: f28ddf779cc18ae87eff2c1d28c65622e367dbfb https://github.com/galaxyproject/galaxy/commit/f28ddf779cc18ae87eff2c1d28c6… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-28 (Fri, 28 Aug 2015) Changed paths: M lib/galaxy/web/framework/base.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/tool_shed/buildapp.py Log Message: ----------- Use new path variable syntax available since Routes 1.9 The old syntax is now documented only in the "Backward compatibility" section of Routes documentation. It is still supported, but may be removed in the future. Commit: eae62ca2cb122f5a0a674027fadc0a28d9dd179e https://github.com/galaxyproject/galaxy/commit/eae62ca2cb122f5a0a674027fadc… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-28 (Fri, 28 Aug 2015) Changed paths: M lib/galaxy/web/framework/base.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/tool_shed/buildapp.py Log Message: ----------- Merge pull request #665 from nsoranzo/dev Use new path variable syntax available since Routes 1.9 Commit: 469d8b463e4711770925f4152c95769b7c1d04dc https://github.com/galaxyproject/galaxy/commit/469d8b463e4711770925f4152c95… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-08-28 (Fri, 28 Aug 2015) Changed paths: M client/galaxy/style/less/reports.less M static/style/blue/base.css M static/style/blue/reports.css M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_all.mako M templates/webapps/reports/jobs_specified_month_in_error.mako M templates/webapps/reports/jobs_tool_per_month.mako M templates/webapps/reports/jobs_user_per_month.mako M templates/webapps/reports/registered_users.mako M templates/webapps/reports/registered_users_per_month.mako M templates/webapps/reports/registered_users_specified_date.mako M templates/webapps/reports/registered_users_specified_month.mako M templates/webapps/reports/requests_per_month_all.mako M templates/webapps/reports/requests_per_user.mako M templates/webapps/reports/requests_user_per_month.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako M templates/webapps/reports/workflows_per_workflow.mako M templates/webapps/reports/workflows_user_per_month.mako Log Message: ----------- Fixed change in class overlap Commit: ec8cba20398dcfe0fdd7a46ad93cf78fadc310ec https://github.com/galaxyproject/galaxy/commit/ec8cba20398dcfe0fdd7a46ad93c… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-08-28 (Fri, 28 Aug 2015) Changed paths: M .ci/flake8_blacklist.txt M .ci/flake8_wrapper.sh M client/galaxy/style/less/reports.less A doc/source/api/quickstart.rst M doc/source/api_doc.rst A doc/source/dev/faq.rst A doc/source/dev/index.rst M doc/source/index.rst M doc/source/ts_api_doc.rst M lib/galaxy/jobs/actions/post.py M lib/galaxy/managers/base.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/rbac_secured.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/util/xml_macros.py M lib/galaxy/web/framework/base.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/tool_shed/galaxy_install/repair_repository_manager.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/shed_util_common.py M test/base/asserts/__init__.py M test/base/interactor.py M test/base/twilltestcase.py M test/casperjs/casperjs_runner.py M test/casperjs/server_env.py M test/install_and_test_tool_shed_repositories/base/twilltestcase.py M test/install_and_test_tool_shed_repositories/base/util.py M test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py M test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py M test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py M test/qunit/README.txt M test/qunit/package.json M test/unit/managers/test_DatasetManager.py M test/unit/tools/test_tool_loader.py Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into dev Conflicts: client/galaxy/style/less/reports.less static/style/blue/base.css static/style/blue/reports.css Commit: 0fa73f2a81fed31fbfe778cf2197d46fa0d4f899 https://github.com/galaxyproject/galaxy/commit/0fa73f2a81fed31fbfe778cf2197… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-08-28 (Fri, 28 Aug 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Don't overwrite $R_LIBS path during installation. Commit: d4af323d35e4a562c6f676ebf10e63253e4d53f8 https://github.com/galaxyproject/galaxy/commit/d4af323d35e4a562c6f676ebf10e… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-08-28 (Fri, 28 Aug 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge pull request #671 from bgruening/extend_r_libs_path Don't overwrite $R_LIBS path during installation. Commit: 15fe2b7d8ff79dfbc3ac2592246401b7c6c0af52 https://github.com/galaxyproject/galaxy/commit/15fe2b7d8ff79dfbc3ac25922464… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-08-31 (Mon, 31 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/multi-panel.js M lib/galaxy/managers/histories.py M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/base-mvc.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/utils/uploadbox.js.map M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/multi-panel.js M static/scripts/utils/uploadbox.js M templates/webapps/galaxy/history/view_multiple.mako Log Message: ----------- UI, histories: lazy-load histories in the multi-history view, handle search loading indication better, move sort/comparator code into collection Commit: f61f696724a0b264a8706d6bf682fa09c178bc5e https://github.com/galaxyproject/galaxy/commit/f61f696724a0b264a8706d6bf682… Author: Nitesh Turaga <nitesh.turaga(a)gmail.com> Date: 2015-08-31 (Mon, 31 Aug 2015) Changed paths: M client/galaxy/style/less/reports.less M static/style/blue/base.css M static/style/blue/reports.css M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_all.mako M templates/webapps/reports/jobs_specified_month_in_error.mako M templates/webapps/reports/jobs_tool_per_month.mako M templates/webapps/reports/jobs_user_per_month.mako M templates/webapps/reports/registered_users.mako M templates/webapps/reports/registered_users_per_month.mako M templates/webapps/reports/registered_users_specified_date.mako M templates/webapps/reports/registered_users_specified_month.mako M templates/webapps/reports/requests_per_month_all.mako M templates/webapps/reports/requests_per_user.mako M templates/webapps/reports/requests_user_per_month.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako M templates/webapps/reports/workflows_per_workflow.mako M templates/webapps/reports/workflows_user_per_month.mako Log Message: ----------- Merge pull request #669 from Airistotal/dev Fix centering bug in firefox Commit: efc1df79f195d7479cc8a7dfb4f811e8ae82329b https://github.com/galaxyproject/galaxy/commit/efc1df79f195d7479cc8a7dfb4f8… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-08-31 (Mon, 31 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/style/less/history.less M static/maps/mvc/history/multi-panel.js.map M static/scripts/mvc/history/multi-panel.js M static/style/blue/base.css M templates/webapps/galaxy/history/view_multiple.mako Log Message: ----------- UI, histories: move load indicator style to less, use better name Commit: aa7968aa9d13ab5de9fcebd427e5eca356cc1de4 https://github.com/galaxyproject/galaxy/commit/aa7968aa9d13ab5de9fcebd427e5… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-08-31 (Mon, 31 Aug 2015) Changed paths: M client/galaxy/style/less/reports.less M static/style/blue/base.css M static/style/blue/reports.css M templates/webapps/reports/job_info.mako M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_all.mako M templates/webapps/reports/jobs_specified_month_in_error.mako M templates/webapps/reports/jobs_tool_per_month.mako M templates/webapps/reports/jobs_user_per_month.mako M templates/webapps/reports/registered_users.mako M templates/webapps/reports/registered_users_per_month.mako M templates/webapps/reports/registered_users_specified_date.mako M templates/webapps/reports/registered_users_specified_month.mako M templates/webapps/reports/requests_per_month_all.mako M templates/webapps/reports/requests_per_user.mako M templates/webapps/reports/requests_user_per_month.mako M templates/webapps/reports/run_stats.mako M templates/webapps/reports/system.mako M templates/webapps/reports/users_last_access_date.mako M templates/webapps/reports/users_user_disk_usage.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako M templates/webapps/reports/workflows_per_workflow.mako M templates/webapps/reports/workflows_user_per_month.mako Log Message: ----------- Changed class naming to reflect use Commit: 0a1617024c7923c12531fa9e18da3494833a6f1f https://github.com/galaxyproject/galaxy/commit/0a1617024c7923c12531fa9e18da… Author: Nitesh Turaga <nitesh.turaga(a)gmail.com> Date: 2015-08-31 (Mon, 31 Aug 2015) Changed paths: M client/galaxy/style/less/reports.less M static/style/blue/base.css M static/style/blue/reports.css M templates/webapps/reports/job_info.mako M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_all.mako M templates/webapps/reports/jobs_specified_month_in_error.mako M templates/webapps/reports/jobs_tool_per_month.mako M templates/webapps/reports/jobs_user_per_month.mako M templates/webapps/reports/registered_users.mako M templates/webapps/reports/registered_users_per_month.mako M templates/webapps/reports/registered_users_specified_date.mako M templates/webapps/reports/registered_users_specified_month.mako M templates/webapps/reports/requests_per_month_all.mako M templates/webapps/reports/requests_per_user.mako M templates/webapps/reports/requests_user_per_month.mako M templates/webapps/reports/run_stats.mako M templates/webapps/reports/system.mako M templates/webapps/reports/users_last_access_date.mako M templates/webapps/reports/users_user_disk_usage.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako M templates/webapps/reports/workflows_per_workflow.mako M templates/webapps/reports/workflows_user_per_month.mako Log Message: ----------- Merge pull request #675 from Airistotal/dev Changed class naming to reflect use Commit: aebf0c7fea2f276f68b77d27408c45e330aa629b https://github.com/galaxyproject/galaxy/commit/aebf0c7fea2f276f68b77d27408c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-31 (Mon, 31 Aug 2015) Changed paths: M client/galaxy/scripts/galaxy.panels.js M static/maps/galaxy.panels.js.map M templates/base.mako M templates/webapps/galaxy/root/index.mako Log Message: ----------- Add modified index handling Commit: 9a9d193eace1646c7dc0e74991ddc14ebd18c37d https://github.com/galaxyproject/galaxy/commit/9a9d193eace1646c7dc0e74991dd… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-08-31 (Mon, 31 Aug 2015) Changed paths: M client/galaxy/style/less/reports.less M static/style/blue/base.css M static/style/blue/reports.css M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_all.mako M templates/webapps/reports/jobs_specified_month_in_error.mako M templates/webapps/reports/jobs_tool_per_month.mako M templates/webapps/reports/jobs_user_per_month.mako M templates/webapps/reports/registered_users.mako M templates/webapps/reports/registered_users_per_month.mako M templates/webapps/reports/registered_users_specified_date.mako M templates/webapps/reports/registered_users_specified_month.mako M templates/webapps/reports/requests_user_per_month.mako M templates/webapps/reports/run_stats.mako M templates/webapps/reports/system.mako M templates/webapps/reports/users_last_access_date.mako M templates/webapps/reports/users_user_disk_usage.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako M templates/webapps/reports/workflows_per_workflow.mako M templates/webapps/reports/workflows_user_per_month.mako Log Message: ----------- Refactored line lengths Fixed sorting bug in workflows per user sorting Commit: c057bfa1d8fe4c921e80260f5205fe35f5d1e8b8 https://github.com/galaxyproject/galaxy/commit/c057bfa1d8fe4c921e80260f5205… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-08-31 (Mon, 31 Aug 2015) Changed paths: M client/galaxy/style/less/reports.less M static/style/blue/base.css M static/style/blue/reports.css M templates/webapps/reports/users_last_access_date.mako Log Message: ----------- Fixed format issue in date of last login page Commit: 8cf76bd27e30a7b35ad3c7867fdc43bd44a4b661 https://github.com/galaxyproject/galaxy/commit/8cf76bd27e30a7b35ad3c7867fdc… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-01 (Tue, 01 Sep 2015) Changed paths: M client/galaxy/scripts/galaxy.panels.js M static/maps/galaxy.panels.js.map M static/maps/utils/uploadbox.js.map M static/scripts/galaxy.panels.js M static/scripts/utils/uploadbox.js M templates/base.mako Log Message: ----------- Note root in Galaxy object Commit: b1841e22d924b53a3a75306bf773b0b0ad4f02a6 https://github.com/galaxyproject/galaxy/commit/b1841e22d924b53a3a75306bf773… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-09-01 (Tue, 01 Sep 2015) Changed paths: M client/grunt-tasks/scripts.js M static/maps/galaxy.interactive_environments.js.map M static/maps/libs/jquery/jqtouch.js.map M static/maps/libs/raven.js.map M static/maps/libs/toastr.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/data.js.map M static/maps/mvc/dataset/dataset-choice.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-repeat.js.map M static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/job/job-model.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/list/list-panel.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/tools/tools-form-workflow.js.map M static/maps/mvc/tools/tools-jobs.js.map M static/maps/mvc/ui/ui-frames.js.map M static/maps/mvc/ui/ui-select.js.map M static/maps/utils/deferred.js.map M static/maps/utils/graph.js.map M static/maps/utils/metrics-logger.js.map M static/maps/utils/uploadbox.js.map M static/maps/utils/utils.js.map M static/maps/viz/trackster.js.map M static/maps/viz/trackster/filters.js.map M static/maps/viz/visualization.js.map M static/scripts/galaxy.interactive_environments.js M static/scripts/libs/jquery/jqtouch.js M static/scripts/libs/raven.js M static/scripts/libs/toastr.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/data.js M static/scripts/mvc/dataset/dataset-choice.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-select-content.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/job/job-model.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/list/list-panel.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/tools/tools-form-workflow.js M static/scripts/mvc/tools/tools-jobs.js M static/scripts/mvc/ui/ui-frames.js M static/scripts/mvc/ui/ui-select.js M static/scripts/utils/deferred.js M static/scripts/utils/graph.js M static/scripts/utils/metrics-logger.js M static/scripts/utils/uploadbox.js M static/scripts/utils/utils.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/visualization.js Log Message: ----------- Client build: do not drop console when compressing, when not compressing do not mangle variable names Commit: ee46947c3d58a98d0c6640ba3eea3ef405d8c9c3 https://github.com/galaxyproject/galaxy/commit/ee46947c3d58a98d0c6640ba3eea… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2015-09-01 (Tue, 01 Sep 2015) Changed paths: M lib/tool_shed/galaxy_install/install_manager.py Log Message: ----------- Fix issue #525. Repo info dicts and tsr_ids were filtered for pre-installed tools, but the unfiltered info_dict was passed on, causing misalignment of repository and tsr_id. Commit: 15d9dfd3073b8da1684b10ec489d9d7f0f6b5939 https://github.com/galaxyproject/galaxy/commit/15d9dfd3073b8da1684b10ec489d… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-09-01 (Tue, 01 Sep 2015) Changed paths: M lib/galaxy/managers/collections.py Log Message: ----------- Managers, collections: return copied hdca from copy method Commit: c47d4a715ed4acf2ed72693f9659730b402fd001 https://github.com/galaxyproject/galaxy/commit/c47d4a715ed4acf2ed72693f9659… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-01 (Tue, 01 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/style/less/history.less M lib/galaxy/managers/histories.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/base-mvc.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/multi-panel.js.map M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/multi-panel.js M static/style/blue/base.css M templates/webapps/galaxy/history/view_multiple.mako Log Message: ----------- Merge pull request #676 from carlfeberhard/history.multi Lazy-load histories into multi-history view Commit: d00b5507c0d33ea334ab9db5677b461b998c74ab https://github.com/galaxyproject/galaxy/commit/d00b5507c0d33ea334ab9db5677b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-01 (Tue, 01 Sep 2015) Changed paths: M lib/galaxy/managers/collections.py Log Message: ----------- Merge pull request #682 from carlfeberhard/fix.copied-collection-hid Managers, collections: return copied hdca from copy method Commit: 85d4b747297f8bb2a2d7e39c8995d92e6e91911b https://github.com/galaxyproject/galaxy/commit/85d4b747297f8bb2a2d7e39c8995… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-01 (Tue, 01 Sep 2015) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Slight refactoring of parse_int, move to galaxy.util and use default in invocation. Commit: 67322c5a440e2912be02c88d4d77e525fe8a7638 https://github.com/galaxyproject/galaxy/commit/67322c5a440e2912be02c88d4d77… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-01 (Tue, 01 Sep 2015) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Don't overload language builtins min, max in parse_int Commit: 6273fa8a5da7bae8c4f4cdda281cc096ee21f70a https://github.com/galaxyproject/galaxy/commit/6273fa8a5da7bae8c4f4cdda281c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-01 (Tue, 01 Sep 2015) Changed paths: M client/galaxy/style/less/base.less M static/style/blue/base.css Log Message: ----------- Use standard Galaxy message box styles on tool help texts that use rST admonitions. Commit: e584a3527323a0b801e50a86f6fc2032d84b06ed https://github.com/galaxyproject/galaxy/commit/e584a3527323a0b801e50a86f6fc… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-09-02 (Wed, 02 Sep 2015) Changed paths: M lib/tool_shed/galaxy_install/install_manager.py Log Message: ----------- Merge pull request #681 from mvdbeek/dev Fix issue #525. Repo info dicts and tsr_ids were filtered for pre-ins… Commit: 291d16f3fcf7f4b7c70f47aa568a08f60262a806 https://github.com/galaxyproject/galaxy/commit/291d16f3fcf7f4b7c70f47aa568a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-02 (Wed, 02 Sep 2015) Changed paths: M client/galaxy/style/less/base.less M static/style/blue/base.css Log Message: ----------- Merge pull request #685 from natefoo/help-message-css Use standard Galaxy message box styles on tool help texts that use rST admonitions Commit: f48dd9942567b23326227b2538d350cd4c118ba3 https://github.com/galaxyproject/galaxy/commit/f48dd9942567b23326227b2538d3… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-02 (Wed, 02 Sep 2015) Changed paths: M client/galaxy/style/less/reports.less M static/style/blue/base.css M static/style/blue/reports.css M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_all.mako M templates/webapps/reports/jobs_specified_month_in_error.mako M templates/webapps/reports/jobs_tool_per_month.mako M templates/webapps/reports/jobs_user_per_month.mako M templates/webapps/reports/registered_users.mako M templates/webapps/reports/registered_users_per_month.mako M templates/webapps/reports/registered_users_specified_date.mako M templates/webapps/reports/registered_users_specified_month.mako M templates/webapps/reports/requests_user_per_month.mako M templates/webapps/reports/run_stats.mako M templates/webapps/reports/system.mako M templates/webapps/reports/users_last_access_date.mako M templates/webapps/reports/users_user_disk_usage.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako M templates/webapps/reports/workflows_per_workflow.mako M templates/webapps/reports/workflows_user_per_month.mako Log Message: ----------- Merge pull request #678 from Airistotal/dev Reports Refactoring Commit: 65182d3a623630a783aff3a1d4ebba14bb106e81 https://github.com/galaxyproject/galaxy/commit/65182d3a623630a783aff3a1d4eb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-02 (Wed, 02 Sep 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Include second file of commit fixing min/max overloading Commit: bcbeb75a68952597e89563d316dc0ec2d945f49c https://github.com/galaxyproject/galaxy/commit/bcbeb75a68952597e89563d316dc… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-02 (Wed, 02 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-form.js A doc/source/releases/15.07.rst M doc/source/releases/15.07_announce.rst A doc/source/releases/15.10_announce.rst M doc/source/releases/index.rst M lib/galaxy/datatypes/tabular.py M lib/tool_shed/dependencies/attribute_handlers.py M lib/tool_shed/dependencies/tool/tag_attribute_handler.py M scripts/bootstrap_history.py A scripts/bootstrap_history_announce_template.rst M static/maps/mvc/tools/tools-form.js.map M static/scripts/mvc/tools/tools-form.js Log Message: ----------- Merge branch 'master' into dev Conflicts: lib/tool_shed/dependencies/tool/tag_attribute_handler.py Commit: 2625bc4bc02f3b109c2340ca46b376fc9fbd9017 https://github.com/galaxyproject/galaxy/commit/2625bc4bc02f3b109c2340ca46b3… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-02 (Wed, 02 Sep 2015) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Fix flake8 broken when merging 041c94bf788bea0990401dab14e0ab717cec0c55 from release_15.07 . Commit: 88c57bf16b52c8d7edbe0c91eb30dda277d4f24b https://github.com/galaxyproject/galaxy/commit/88c57bf16b52c8d7edbe0c91eb30… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-02 (Wed, 02 Sep 2015) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #688 from nsoranzo/dev Fix flake8 broken when merging from release_15.07 . Commit: b1949c5805730d2f4ce53759dd5636449a0b08f5 https://github.com/galaxyproject/galaxy/commit/b1949c5805730d2f4ce53759dd56… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-02 (Wed, 02 Sep 2015) Changed paths: A client/galaxy/scripts/mvc/app/app-panel-center.js A client/galaxy/scripts/mvc/app/app-panel-history.js A client/galaxy/scripts/mvc/app/app-panel-tool.js A client/galaxy/scripts/mvc/app/app-view.js A static/maps/mvc/app/app-panel-center.js.map A static/maps/mvc/app/app-panel-history.js.map A static/maps/mvc/app/app-panel-tool.js.map A static/maps/mvc/app/app-view.js.map A static/scripts/mvc/app/app-panel-center.js A static/scripts/mvc/app/app-panel-history.js A static/scripts/mvc/app/app-panel-tool.js A static/scripts/mvc/app/app-view.js M templates/base.mako M templates/webapps/galaxy/root/index.mako Log Message: ----------- Add script files, continue ui replication Commit: 8444838a3eda2b2e361c32e165cb65ad3a198cc5 https://github.com/galaxyproject/galaxy/commit/8444838a3eda2b2e361c32e165cb… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-02 (Wed, 02 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-panel-history.js M client/galaxy/scripts/mvc/app/app-panel-tool.js M client/galaxy/scripts/mvc/app/app-view.js M static/maps/mvc/app/app-panel-history.js.map M static/maps/mvc/app/app-panel-tool.js.map M static/maps/mvc/app/app-view.js.map M static/scripts/mvc/app/app-panel-history.js M static/scripts/mvc/app/app-panel-tool.js M static/scripts/mvc/app/app-view.js Log Message: ----------- Fix panel handlers Commit: 8d8df1ab5d741758a195eaa34b75b49c1339a948 https://github.com/galaxyproject/galaxy/commit/8d8df1ab5d741758a195eaa34b75… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-panel-history.js M client/galaxy/scripts/mvc/app/app-panel-tool.js M client/galaxy/scripts/mvc/app/app-view.js R client/galaxy/scripts/mvc/ui/ui-button-check.js R client/galaxy/scripts/mvc/ui/ui-button-menu.js A client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M static/maps/mvc/app/app-panel-history.js.map M static/maps/mvc/app/app-panel-tool.js.map M static/maps/mvc/app/app-view.js.map R static/maps/mvc/ui/ui-button-check.js.map R static/maps/mvc/ui/ui-button-menu.js.map A static/maps/mvc/ui/ui-buttons.js.map M static/maps/mvc/ui/ui-misc.js.map M static/maps/mvc/ui/ui-options.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/mvc/app/app-panel-history.js M static/scripts/mvc/app/app-panel-tool.js M static/scripts/mvc/app/app-view.js R static/scripts/mvc/ui/ui-button-check.js R static/scripts/mvc/ui/ui-button-menu.js A static/scripts/mvc/ui/ui-buttons.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-options.js M static/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Revise/unify buttons, cleanup default ui element code, add panel button Commit: c7bb8873ca46a67993ad5cb25a85bc81bb780777 https://github.com/galaxyproject/galaxy/commit/c7bb8873ca46a67993ad5cb25a85… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-panel-history.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M static/maps/mvc/app/app-panel-history.js.map M static/maps/mvc/ui/ui-buttons.js.map M static/scripts/mvc/app/app-panel-history.js M static/scripts/mvc/ui/ui-buttons.js Log Message: ----------- Add buttons to panel history builder, apply coding conventions Commit: d546d08c86fc506edb7912adefe723c60e0738fb https://github.com/galaxyproject/galaxy/commit/d546d08c86fc506edb7912adefe7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-panel-history.js M static/maps/mvc/app/app-panel-history.js.map M static/scripts/mvc/app/app-panel-history.js Log Message: ----------- Minor fix Commit: 910f95188c3ea5fffc36e80aa5f8d689e4450ddf https://github.com/galaxyproject/galaxy/commit/910f95188c3ea5fffc36e80aa5f8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-panel-tool.js M client/galaxy/scripts/mvc/app/app-view.js M client/galaxy/scripts/mvc/upload/upload-button.js M client/galaxy/scripts/mvc/upload/upload-view.js M static/maps/mvc/app/app-panel-tool.js.map M static/maps/mvc/app/app-view.js.map M static/maps/mvc/upload/upload-button.js.map M static/maps/mvc/upload/upload-view.js.map M static/scripts/mvc/app/app-panel-tool.js M static/scripts/mvc/app/app-view.js M static/scripts/mvc/upload/upload-button.js M static/scripts/mvc/upload/upload-view.js Log Message: ----------- Fix tool panel handling Commit: ad6fdc3dc226af9238b4e366ddc3f246db1e5a87 https://github.com/galaxyproject/galaxy/commit/ad6fdc3dc226af9238b4e366ddc3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-panel-history.js M client/galaxy/scripts/mvc/app/app-panel-tool.js M client/galaxy/scripts/mvc/app/app-view.js M static/maps/mvc/app/app-panel-history.js.map M static/maps/mvc/app/app-view.js.map M static/scripts/mvc/app/app-panel-history.js M static/scripts/mvc/app/app-view.js Log Message: ----------- Add history panel specific css style Commit: b99b8f2853c49f432eb6e400c734ef087ce36af2 https://github.com/galaxyproject/galaxy/commit/b99b8f2853c49f432eb6e400c734… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-view.js M static/maps/mvc/app/app-view.js.map M static/scripts/mvc/app/app-view.js Log Message: ----------- Remove unnecessary div Commit: df52c62f4d662cd73587cd8450c33f86799ff79e 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doc/source/api/quickstart.rst M doc/source/api_doc.rst A doc/source/dev/faq.rst A doc/source/dev/index.rst M doc/source/index.rst A doc/source/releases/15.07.rst M doc/source/releases/15.07_announce.rst A doc/source/releases/15.10_announce.rst M doc/source/releases/index.rst M doc/source/ts_api_doc.rst M lib/galaxy/datatypes/tabular.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/managers/base.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/rbac_secured.py M lib/galaxy/model/__init__.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/util/xml_macros.py M lib/galaxy/web/framework/base.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/buildapp.py M 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test/tool_shed/functional/test_1420_tool_dependency_environment_inheritance.py M test/tool_shed/functional/test_1430_repair_installed_repository.py M test/tool_shed/functional/test_1440_missing_env_sh_files.py M test/tool_shed/functional/test_1450_installing_datatypes_sniffers.py M test/tool_shed/functional/test_1460_data_managers.py M test/tool_shed/functional/test_1470_updating_installed_repositories.py M test/tool_shed/functional_tests.py M test/tool_shed/test_data/proteomics_datatypes/proteomics_datatypes.tar M test/unit/managers/test_DatasetManager.py M test/unit/tools/test_tool_loader.py M test/unit/tools/test_toolbox_filters.py M tools/extract/liftOver_wrapper.xml Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into ui_revision_000 Commit: a8ffdc523eebe21162e8e29cb6311200d7a2816b https://github.com/galaxyproject/galaxy/commit/a8ffdc523eebe21162e8e29cb631… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) 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53b84fd17f662ba595d0a72ca79a24d5792ec0f8 https://github.com/galaxyproject/galaxy/commit/53b84fd17f662ba595d0a72ca79a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-view.js M client/galaxy/style/less/base.less M static/maps/mvc/app/app-view.js.map M static/scripts/mvc/app/app-view.js M static/style/blue/base.css M templates/webapps/galaxy/root/index.mako Log Message: ----------- Style fixes, generalizations Commit: 92bdf0de2436549546951645a7f1e8d852715e49 https://github.com/galaxyproject/galaxy/commit/92bdf0de2436549546951645a7f1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M templates/webapps/galaxy/root/index.mako Log Message: ----------- Remove unused styles Commit: 3a94f35468622b6819c7f07c2a2f95a85ca03870 https://github.com/galaxyproject/galaxy/commit/3a94f35468622b6819c7f07c2a2f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: R templates/webapps/galaxy/root/tool_menu.mako Log Message: ----------- Remove tool menu mako Commit: 6edaf458e89b3db7115c65f0242b781df7c77faa https://github.com/galaxyproject/galaxy/commit/6edaf458e89b3db7115c65f0242b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: A CODE_OF_CONDUCT.md Log Message: ----------- Merge pull request #646 from natefoo/code-of-conduct [PROCEDURES] Create a project code of conduct Commit: b8304e1ab7538b5bcc315f87905d242554b2171a https://github.com/galaxyproject/galaxy/commit/b8304e1ab7538b5bcc315f87905d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M templates/webapps/galaxy/root/index.mako Log Message: ----------- Reinsert active view identifier Commit: 4dc5ed52f9a85770e1652557a021a3e531f471c8 https://github.com/galaxyproject/galaxy/commit/4dc5ed52f9a85770e1652557a021… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M README.rst Log Message: ----------- add alt to images; include GitHub issues for reporting Commit: 05f2c4bad0eaffa55782033a2c956f615ce955d8 https://github.com/galaxyproject/galaxy/commit/05f2c4bad0eaffa55782033a2c95… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M README.rst Log Message: ----------- switch links to https Commit: 0785dedd854c7f71c3360f1cbd8dfe3c1a9fb205 https://github.com/galaxyproject/galaxy/commit/0785dedd854c7f71c3360f1cbd8d… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M README.rst Log Message: ----------- Merge pull request #690 from martenson/readme-changes Readme changes Commit: 94e8b312d4548be90f7ae4e899080298f87380f5 https://github.com/galaxyproject/galaxy/commit/94e8b312d4548be90f7ae4e89908… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-view.js M static/maps/mvc/app/app-view.js.map M static/scripts/mvc/app/app-view.js M templates/webapps/galaxy/root/index.mako Log Message: ----------- Reinsert message classes Commit: 2afcc658c7f4b7f945413050b5b7bdcdd0b3abaf https://github.com/galaxyproject/galaxy/commit/2afcc658c7f4b7f945413050b5b7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Support 'None' and raise the ValueError when appropriate. Commit: 93be500441a5c454168de3c504db341709be7191 https://github.com/galaxyproject/galaxy/commit/93be500441a5c454168de3c504db… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: A client/galaxy/scripts/mvc/app/app-analysis.js A static/maps/mvc/app/app-analysis.js.map A static/scripts/mvc/app/app-analysis.js Log Message: ----------- Add unified panel script Commit: 152c81cf8acc45b1c686e26eba04ec87488c52a1 https://github.com/galaxyproject/galaxy/commit/152c81cf8acc45b1c686e26eba04… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M templates/webapps/galaxy/history/copy.mako Log Message: ----------- Set a default value for copy history dialog radio input (to copy *all*). Commit: 39c2854f652524f784a5179a7a2762fd375d67e5 https://github.com/galaxyproject/galaxy/commit/39c2854f652524f784a5179a7a27… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M templates/webapps/galaxy/history/copy.mako Log Message: ----------- Merge pull request #693 from dannon/copy_history_default Set a default value for copy history dialog radio input (to copy *all*). Commit: 9df1dfafebe31c84d546aee4146be1239cc793dc https://github.com/galaxyproject/galaxy/commit/9df1dfafebe31c84d546aee4146b… Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Merge pull request #684 from dannon/minor_parseint_tweaks Minor parseint refactoring, tweaks Commit: 8f1d3cac8d4506053d252687194962b7ee81538d https://github.com/galaxyproject/galaxy/commit/8f1d3cac8d4506053d2526871949… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/repository.py Log Message: ----------- Dedupe one of the worse offenders Commit: 5415e295ac4bf00e9ed9a903ae908c06f57ee0d4 https://github.com/galaxyproject/galaxy/commit/5415e295ac4bf00e9ed9a903ae90… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M lib/galaxy/jobs/deferred/__init__.py M lib/galaxy/jobs/transfer_manager.py Log Message: ----------- Refactor sleeper duplications Commit: 673c1cdbca1ce3bf9ce561c3041d5fa33a8275e8 https://github.com/galaxyproject/galaxy/commit/673c1cdbca1ce3bf9ce561c3041d… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M lib/galaxy/security/__init__.py Log Message: ----------- Refactor identical role queries into a single function Commit: a71ac4ee3144e1463064730a297627c9797382f6 https://github.com/galaxyproject/galaxy/commit/a71ac4ee3144e1463064730a2976… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/tool_shed/buildapp.py A lib/galaxy/webapps/util.py Log Message: ----------- Refactor copy-pasted function into separate module Commit: 7cd241f0d9dfb0d4b20bd1c3902a1405258f682d https://github.com/galaxyproject/galaxy/commit/7cd241f0d9dfb0d4b20bd1c3902a… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M lib/galaxy/jobs/deferred/__init__.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/security/__init__.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/tool_shed/buildapp.py A lib/galaxy/webapps/util.py Log Message: ----------- Merge branch 'big-dedup' into deduplication Commit: 1a2413f8793dee35ae237003f743ac80df17ef74 https://github.com/galaxyproject/galaxy/commit/1a2413f8793dee35ae237003f743… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M lib/galaxy/webapps/reports/controllers/jobs.py Log Message: ----------- Refactor duplicate calculation code in reports Commit: 6dd4b2b11f14882e3d129261de950e6b61e5bbc0 https://github.com/galaxyproject/galaxy/commit/6dd4b2b11f14882e3d129261de95… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/repository.py Log Message: ----------- Correct copy-pasted typo Commit: 28143581d9270dc880433dd80687a47076d9ccd1 https://github.com/galaxyproject/galaxy/commit/28143581d9270dc880433dd80687… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/tool_shed/buildapp.py Log Message: ----------- Make flake8 happy Commit: 1aa7ef12ec88e469f5e635b9c28cd4f9055ceb33 https://github.com/galaxyproject/galaxy/commit/1aa7ef12ec88e469f5e635b9c28c… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py M lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py Log Message: ----------- Refactor into a single method and flake Commit: a437083d429f605485745ce82b19c4825c57c161 https://github.com/galaxyproject/galaxy/commit/a437083d429f605485745ce82b19… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M lib/galaxy/util/topsort.py Log Message: ----------- refactor completely duplicated numpreds/successor processing Commit: 8430ca4e3fc506db41357312db0cced248ee43dd https://github.com/galaxyproject/galaxy/commit/8430ca4e3fc506db41357312db0c… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/multi-panel.js M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/multi-panel.js.map M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/multi-panel.js Log Message: ----------- UI, histories: correct allFetched setting in setCollection to allow fetching after changing collection order Commit: 15edae24c8e3fae058aa7c7d017d47467febb5ff https://github.com/galaxyproject/galaxy/commit/15edae24c8e3fae058aa7c7d017d… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M lib/galaxy/util/topsort.py Log Message: ----------- Fix formatting error Commit: b325966e65398b6f7ff6bf493c44e2ab691cd042 https://github.com/galaxyproject/galaxy/commit/b325966e65398b6f7ff6bf493c44… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M client/galaxy/style/less/history.less M static/style/blue/base.css Log Message: ----------- UI, histories: try to correct bootstrap popover dropdown width to keep caret inside button Commit: 99e7ba43a0c45a8777aafb0c5d0d9e773793d201 https://github.com/galaxyproject/galaxy/commit/99e7ba43a0c45a8777aafb0c5d0d… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/style/less/history.less M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/multi-panel.js.map M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/multi-panel.js M static/style/blue/base.css Log Message: ----------- Merge pull request #695 from carlfeberhard/multi-history.all-fetched Fix multi-history fetch flag to allow re-fetching after collection sort Commit: 2867f1149a019f840bc6f4d1da23b98aad702839 https://github.com/galaxyproject/galaxy/commit/2867f1149a019f840bc6f4d1da23… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-04 (Fri, 04 Sep 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge branch 'master' into dev Commit: 5fc366f7f7fa1231b2c1c643f2e3ff4bae2d26de https://github.com/galaxyproject/galaxy/commit/5fc366f7f7fa1231b2c1c643f2e3… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-04 (Fri, 04 Sep 2015) Changed paths: M lib/galaxy/security/__init__.py Log Message: ----------- Correct typo'd _get_roles function Commit: 060fdffda8b2d4b0c7aad3e460248b3793fdb69d https://github.com/galaxyproject/galaxy/commit/060fdffda8b2d4b0c7aad3e46024… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-04 (Fri, 04 Sep 2015) Changed paths: M lib/galaxy/webapps/util.py Log Message: ----------- Correct import for @nsoranzo Commit: 16a98b50cce48150272289b409ae5a2a70fb9425 https://github.com/galaxyproject/galaxy/commit/16a98b50cce48150272289b409ae… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-04 (Fri, 04 Sep 2015) Changed paths: M config/auth_conf.xml.sample Log Message: ----------- Fixes to LDAP auth config sample. Commit: b962a8ded0661b1df940400cb544a0ddbcfb0686 https://github.com/galaxyproject/galaxy/commit/b962a8ded0661b1df940400cb544… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-04 (Fri, 04 Sep 2015) Changed paths: M lib/galaxy/auth/__init__.py Log Message: ----------- Style fixes. Commit: 5043dd2b7265e7b489428f2858936cd7edac75d3 https://github.com/galaxyproject/galaxy/commit/5043dd2b7265e7b489428f285893… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-04 (Fri, 04 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-view.js M client/galaxy/scripts/mvc/upload/upload-view.js M static/maps/mvc/app/app-view.js.map M static/maps/mvc/upload/upload-view.js.map M static/scripts/mvc/app/app-view.js M templates/webapps/galaxy/root/index.mako Log Message: ----------- Fix panel notifications Commit: c08aab0bd358a8568841a4b43af2e416dec5a513 https://github.com/galaxyproject/galaxy/commit/c08aab0bd358a8568841a4b43af2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-04 (Fri, 04 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-view.js M static/maps/mvc/app/app-view.js.map Log Message: ----------- Code style fix Commit: 474d58809ab1a001a64cb2f540e896d2de22cda5 https://github.com/galaxyproject/galaxy/commit/474d58809ab1a001a64cb2f540e8… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-04 (Fri, 04 Sep 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/mobile.py Log Message: ----------- Fix commented-out code. Commit: cafe2ece1e0a71870be6c368e569ff2b4ceab096 https://github.com/galaxyproject/galaxy/commit/cafe2ece1e0a71870be6c368e569… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-04 (Fri, 04 Sep 2015) Changed paths: M config/auth_conf.xml.sample M lib/galaxy/auth/__init__.py M lib/galaxy/webapps/galaxy/controllers/mobile.py Log Message: ----------- Merge pull request #696 from nsoranzo/dev Small fixes for LDAP auth. Commit: 823fd4ae47ccbf6ed1d19665a7a921d53441833c https://github.com/galaxyproject/galaxy/commit/823fd4ae47ccbf6ed1d19665a7a9… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-04 (Fri, 04 Sep 2015) Changed paths: A CODE_OF_CONDUCT.md M README.rst M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/style/less/history.less M config/auth_conf.xml.sample M lib/galaxy/auth/__init__.py M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/mobile.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/multi-panel.js.map M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/multi-panel.js M static/style/blue/base.css M templates/webapps/galaxy/history/copy.mako Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into ui_revision_000 Conflicts: static/style/blue/base.css Commit: 192239f8d7832e24e9cca55f2ec20c6e3f8e4773 https://github.com/galaxyproject/galaxy/commit/192239f8d7832e24e9cca55f2ec2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-04 (Fri, 04 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-color-picker.js M static/maps/mvc/ui/ui-color-picker.js.map Log Message: ----------- Fix codestyle color picker Commit: bcf77efb5aa79f20afd4cb1104013892fac97959 https://github.com/galaxyproject/galaxy/commit/bcf77efb5aa79f20afd4cb110401… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-04 (Fri, 04 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-analysis.js M static/maps/mvc/app/app-analysis.js.map M static/scripts/mvc/app/app-analysis.js M templates/webapps/galaxy/root/index.mako Log Message: ----------- Remove fixed message Commit: 2f08578ff607c67ddcfcf15f299e26ea99008ecb https://github.com/galaxyproject/galaxy/commit/2f08578ff607c67ddcfcf15f299e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-04 (Fri, 04 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-analysis.js M static/maps/mvc/app/app-analysis.js.map M static/scripts/mvc/app/app-analysis.js M templates/webapps/galaxy/root/index.mako Log Message: ----------- Fix center panel Commit: c948bc70caa9f241c56df0a0e1ff7e542bdabee3 https://github.com/galaxyproject/galaxy/commit/c948bc70caa9f241c56df0a0e1ff… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-04 (Fri, 04 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-analysis.js M static/maps/mvc/app/app-analysis.js.map Log Message: ----------- Remove gap Commit: 759c2142e744476c7bfa3164c34ac351bfb37fa0 https://github.com/galaxyproject/galaxy/commit/759c2142e744476c7bfa3164c34a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-04 (Fri, 04 Sep 2015) Changed paths: M client/galaxy/scripts/galaxy.menu.js M client/galaxy/scripts/mvc/app/app-analysis.js M client/galaxy/scripts/mvc/app/app-view.js M static/maps/galaxy.menu.js.map M static/maps/mvc/app/app-analysis.js.map M static/maps/mvc/app/app-view.js.map M static/scripts/galaxy.menu.js M static/scripts/mvc/app/app-analysis.js M static/scripts/mvc/app/app-view.js M templates/webapps/galaxy/root/index.mako Log Message: ----------- Fix user object usage Commit: 359e812f4fbea0e207537b482b7ab601aa5a3d8f https://github.com/galaxyproject/galaxy/commit/359e812f4fbea0e207537b482b7a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-04 (Fri, 04 Sep 2015) Changed paths: M templates/webapps/galaxy/galaxy.masthead.mako Log Message: ----------- Adjust old masthead config Commit: ac3fc394571da6d33eca6943d58f18aeb5e00814 https://github.com/galaxyproject/galaxy/commit/ac3fc394571da6d33eca6943d58f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-04 (Fri, 04 Sep 2015) Changed paths: M templates/webapps/galaxy/galaxy.masthead.mako Log Message: ----------- Fix masthead Commit: 200c2e640b3665b7c63ce487ccdee044b7c9b054 https://github.com/galaxyproject/galaxy/commit/200c2e640b3665b7c63ce487ccde… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-04 (Fri, 04 Sep 2015) Changed paths: M client/galaxy/scripts/galaxy.menu.js M client/galaxy/scripts/mvc/app/app-analysis.js M static/maps/galaxy.menu.js.map M static/maps/mvc/app/app-analysis.js.map M static/scripts/mvc/app/app-analysis.js Log Message: ----------- Fix tabs Commit: fcbd8b241024ea5a419287759f33b622e94af4fa https://github.com/galaxyproject/galaxy/commit/fcbd8b241024ea5a419287759f33… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-04 (Fri, 04 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-view.js M static/maps/mvc/app/app-view.js.map M static/scripts/mvc/app/app-view.js M templates/webapps/galaxy/root/index.mako Log Message: ----------- Remove unused user json Commit: 00806d484b2007aaf0adb1efbf83db49c8dc5ff4 https://github.com/galaxyproject/galaxy/commit/00806d484b2007aaf0adb1efbf83… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-04 (Fri, 04 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-analysis.js M client/galaxy/scripts/mvc/app/app-view.js M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/scripts/mvc/upload/upload-view.js M static/maps/mvc/app/app-analysis.js.map M static/maps/mvc/app/app-view.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/upload/upload-view.js.map M static/scripts/mvc/app/app-analysis.js M static/scripts/mvc/app/app-view.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/upload/upload-view.js Log Message: ----------- Use Galaxy object instead of galaxy_config Commit: e9009f63936cbef0248ef60638c9de7d6ffb034b https://github.com/galaxyproject/galaxy/commit/e9009f63936cbef0248ef60638c9… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-04 (Fri, 04 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-analysis.js M static/maps/mvc/app/app-analysis.js.map M static/scripts/mvc/app/app-analysis.js Log Message: ----------- Start adding workflows back into tool panel Commit: a47a5e89da8ef30b10115a96ade74e2efb6fbf1f https://github.com/galaxyproject/galaxy/commit/a47a5e89da8ef30b10115a96ade7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-05 (Sat, 05 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-analysis.js M static/maps/mvc/app/app-analysis.js.map M static/scripts/mvc/app/app-analysis.js M templates/webapps/galaxy/root/index.mako Log Message: ----------- Fix workflow links in tool panel Commit: cfbe362cb985f873bb7733e92542bf97ee2ec1bc https://github.com/galaxyproject/galaxy/commit/cfbe362cb985f873bb7733e92542… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-05 (Sat, 05 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-analysis.js M static/maps/mvc/app/app-analysis.js.map M static/scripts/mvc/app/app-analysis.js Log Message: ----------- Fix links Commit: af6a51f0046e10aad46045fc513b3ea2af77995b https://github.com/galaxyproject/galaxy/commit/af6a51f0046e10aad46045fc513b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-05 (Sat, 05 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-form-base.js M static/maps/mvc/tools/tools-form-base.js.map M static/scripts/mvc/tools/tools-form-base.js Log Message: ----------- Fix admin check Commit: 4971a8f54003f38b427d6ebb3398f88182912174 https://github.com/galaxyproject/galaxy/commit/4971a8f54003f38b427d6ebb3398… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-05 (Sat, 05 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-analysis.js M client/galaxy/scripts/mvc/app/app-view.js M client/galaxy/scripts/mvc/tools.js M client/galaxy/scripts/mvc/tools/tools-form-base.js M static/maps/mvc/app/app-analysis.js.map M static/maps/mvc/app/app-view.js.map M static/maps/mvc/tools.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/scripts/mvc/app/app-analysis.js M static/scripts/mvc/app/app-view.js M static/scripts/mvc/tools.js M static/scripts/mvc/tools/tools-form-base.js Log Message: ----------- Disable iframe for tool form Commit: 1b86748a97c8eaa96882d370970d99603c967303 https://github.com/galaxyproject/galaxy/commit/1b86748a97c8eaa96882d370970d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-05 (Sat, 05 Sep 2015) Changed paths: M templates/webapps/galaxy/root/index.mako Log Message: ----------- Insert bibtex support Commit: ce3e7931f6cb19a4a0c1e7cd2bdcbe301c9060f3 https://github.com/galaxyproject/galaxy/commit/ce3e7931f6cb19a4a0c1e7cd2bdc… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2015-09-05 (Sat, 05 Sep 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Use setup.py for all installations instead of the depreceated easy_install method. Commit: 9850e45f07ebca6109084cfe3bd1338b47b361ae https://github.com/galaxyproject/galaxy/commit/9850e45f07ebca6109084cfe3bd1… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-07 (Mon, 07 Sep 2015) Changed paths: M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Fix regression introduced in 6c82266546c77361f9d2265ab749db1446142150 . Fix traceback when calling galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed.update_to_changeset_revision() due to repository being None. Commit: d3fa5066ca6e9ee23a25427050d3573f522bb1e0 https://github.com/galaxyproject/galaxy/commit/d3fa5066ca6e9ee23a25427050d3… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-07 (Mon, 07 Sep 2015) Changed paths: M lib/galaxy/webapps/util.py Log Message: ----------- Fix wrong local import of galaxy. Commit: f2d7917cfca995ba6c8ea77e0475360b59496576 https://github.com/galaxyproject/galaxy/commit/f2d7917cfca995ba6c8ea77e0475… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-07 (Mon, 07 Sep 2015) Changed paths: M lib/galaxy/webapps/util.py Log Message: ----------- Merge pull request #8 from nsoranzo/fix_for_erasche Fix wrong local import of galaxy. Commit: 1f3486cb517a54c7dd9ae4a8c9020d07745774f6 https://github.com/galaxyproject/galaxy/commit/1f3486cb517a54c7dd9ae4a8c902… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-07 (Mon, 07 Sep 2015) Changed paths: M lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py Log Message: ----------- Initialized variables Commit: d95b1cd37a564f6f72e6bfc453b09ed010c3e19a https://github.com/galaxyproject/galaxy/commit/d95b1cd37a564f6f72e6bfc453b0… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-07 (Mon, 07 Sep 2015) Changed paths: M lib/galaxy/webapps/util.py Log Message: ----------- Merge branch 'deduplication' of github.com:erasche/galaxy into deduplication Commit: 471664c2692315b6699c586efccb6c7522fd6b56 https://github.com/galaxyproject/galaxy/commit/471664c2692315b6699c586efccb… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-07 (Mon, 07 Sep 2015) Changed paths: M CONTRIBUTING.md M README.rst Log Message: ----------- Merge "Issues" and "Galaxy Development" from README.rst in CONTRIBUTING.md . Commit: 3f40b7ca8f41403cc00e9fbbc88d8b48b6be6259 https://github.com/galaxyproject/galaxy/commit/3f40b7ca8f41403cc00e9fbbc88d… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-07 (Mon, 07 Sep 2015) Changed paths: M CONTRIBUTING.md M doc/source/project/organization.rst Log Message: ----------- Move "Handling Pull Requests" from CONTRIBUTING.md to organization.rst . Commit: 6f8dd18ede82d35b60f2b8c99e6d8781f9b9d085 https://github.com/galaxyproject/galaxy/commit/6f8dd18ede82d35b60f2b8c99e6d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-07 (Mon, 07 Sep 2015) Changed paths: M templates/webapps/galaxy/root/index.mako Log Message: ----------- Fix style Commit: f99ff868657161a79e760760b73fba0ad1368c9e https://github.com/galaxyproject/galaxy/commit/f99ff868657161a79e760760b73f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-07 (Mon, 07 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-view.js M static/maps/mvc/app/app-view.js.map M static/scripts/mvc/app/app-view.js Log Message: ----------- Fix select2 leak Commit: 26c79e4aab5b8f9f0f7d0c5908352c776f12cef0 https://github.com/galaxyproject/galaxy/commit/26c79e4aab5b8f9f0f7d0c590835… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-08 (Tue, 08 Sep 2015) Changed paths: M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Merge pull request #701 from nsoranzo/fix_for_6c82266546c77361f9d2265ab749db1446142150 Fix regression introduced in 6c82266546c77361f9d2265ab749db1446142150 . Commit: d55c47a14cca837ed775ff47a0c41a170c591c67 https://github.com/galaxyproject/galaxy/commit/d55c47a14cca837ed775ff47a0c4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-08 (Tue, 08 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/tools/tools-form-workflow.js M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/tools/tools-form-workflow.js.map M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/tools/tools-form-workflow.js Log Message: ----------- Optional argument id display (in workflow editor PJAs we don't care to see this, for example -- and this has been toggled off here) Commit: 434caeaf9515cee99e1f5ac4f9610bcc6a5e00cd https://github.com/galaxyproject/galaxy/commit/434caeaf9515cee99e1f5ac4f961… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-08 (Tue, 08 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/form/form-section.js Log Message: ----------- Minor cleanup. Commit: e212f224703d4f63721eb51aa7214640c9e86c53 https://github.com/galaxyproject/galaxy/commit/e212f224703d4f63721eb51aa721… Author: Richard Burhans <burhans(a)bx.psu.edu> Date: 2015-09-08 (Tue, 08 Sep 2015) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/tabular.py Log Message: ----------- TabularData.set_peek() was missing parameters present in Text.set_peek() Changed default value of skipchars in Text.set_peek() from [] to None Commit: e2542d7296adf1e9e5cf15fb7c9bc5f68db05002 https://github.com/galaxyproject/galaxy/commit/e2542d7296adf1e9e5cf15fb7c9b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-08 (Tue, 08 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/tools/tools-form-workflow.js M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/tools/tools-form-workflow.js.map M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/tools/tools-form-workflow.js Log Message: ----------- Swap argument to pja_arg, being more indicative of how this is used. This also obviates the need for the togglable show_arg. Commit: ca5717d203cf93e0bc4dcb9bd6febd0d8c73d083 https://github.com/galaxyproject/galaxy/commit/ca5717d203cf93e0bc4dcb9bd6fe… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-08 (Tue, 08 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-form-workflow.js M static/maps/mvc/tools/tools-form-workflow.js.map M static/scripts/mvc/tools/tools-form-workflow.js Log Message: ----------- Address the regression in #674, add input name list back to rename PJA helptext. Commit: 514da84b07a78a24767d9f9318c735d52fc77d32 https://github.com/galaxyproject/galaxy/commit/514da84b07a78a24767d9f9318c7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-08 (Tue, 08 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/form/form-view.js M static/maps/mvc/form/form-view.js.map M static/scripts/mvc/form/form-view.js Log Message: ----------- Fix scrolling Commit: 4bcc60b04484d7dc54a6bab3ab7c48de27838f9e https://github.com/galaxyproject/galaxy/commit/4bcc60b04484d7dc54a6bab3ab7c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-08 (Tue, 08 Sep 2015) Changed paths: M templates/webapps/galaxy/root/index.mako Log Message: ----------- Fix stored workflow list Commit: b62bf77d9612e98c6dbe39af0035e0c7f6b18875 https://github.com/galaxyproject/galaxy/commit/b62bf77d9612e98c6dbe39af0035… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-08 (Tue, 08 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-analysis.js M static/maps/mvc/app/app-analysis.js.map M static/scripts/mvc/app/app-analysis.js Log Message: ----------- Empty center div before hiding it Commit: 65f6d83459cd82c22b7308d7fdb9ba35b973aca7 https://github.com/galaxyproject/galaxy/commit/65f6d83459cd82c22b7308d7fdb9… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-08 (Tue, 08 Sep 2015) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/tabular.py Log Message: ----------- Merge pull request #705 from richard-burhans/tabulardata Fix to get custom datatypes working after TabularData class was added Commit: bef379dfea1ec7b130fd20dc9dfce59f009ce6e4 https://github.com/galaxyproject/galaxy/commit/bef379dfea1ec7b130fd20dc9dfc… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-09 (Wed, 09 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/tools.js M static/maps/mvc/tools.js.map M static/scripts/mvc/tools.js Log Message: ----------- Avoid blank screen when switching between tools Commit: 8205bade71e1c4977ff9069bae22662fb5af159f https://github.com/galaxyproject/galaxy/commit/8205bade71e1c4977ff9069bae22… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-09-09 (Wed, 09 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/tools/tools-form-workflow.js M static/maps/mvc/tools/tools-form-workflow.js.map M static/scripts/mvc/tools/tools-form-workflow.js Log Message: ----------- Merge pull request #703 from dannon/optional_wf_args Workflow Editor PJA Argument Display + fix #674 Commit: 5bcc452a3718139f511d2097d18ab5644e0a86c2 https://github.com/galaxyproject/galaxy/commit/5bcc452a3718139f511d2097d18a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-09 (Wed, 09 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-analysis.js M static/maps/mvc/app/app-analysis.js.map M static/scripts/mvc/app/app-analysis.js Log Message: ----------- Reset scrolling when display is called Commit: 2b43a271ed5987040731ae63df0fe997b9af28e6 https://github.com/galaxyproject/galaxy/commit/2b43a271ed5987040731ae63df0f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-09 (Wed, 09 Sep 2015) Changed paths: M client/galaxy/scripts/galaxy.menu.js M client/galaxy/scripts/galaxy.panels.js A client/galaxy/scripts/mvc/app/app-analysis.js A client/galaxy/scripts/mvc/app/app-view.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/tools.js M client/galaxy/scripts/mvc/tools/tools-form-base.js R client/galaxy/scripts/mvc/ui/ui-button-check.js R client/galaxy/scripts/mvc/ui/ui-button-menu.js A client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-color-picker.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/upload/upload-button.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/style/less/base.less M config/galaxy.ini.sample M static/maps/galaxy.menu.js.map M static/maps/galaxy.panels.js.map A static/maps/mvc/app/app-analysis.js.map A static/maps/mvc/app/app-view.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/tools.js.map M static/maps/mvc/tools/tools-form-base.js.map R static/maps/mvc/ui/ui-button-check.js.map R static/maps/mvc/ui/ui-button-menu.js.map A static/maps/mvc/ui/ui-buttons.js.map M static/maps/mvc/ui/ui-color-picker.js.map M static/maps/mvc/ui/ui-misc.js.map M static/maps/mvc/ui/ui-options.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/mvc/upload/upload-button.js.map M static/maps/mvc/upload/upload-view.js.map M static/scripts/galaxy.menu.js M static/scripts/galaxy.panels.js A static/scripts/mvc/app/app-analysis.js A static/scripts/mvc/app/app-view.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/tools.js M static/scripts/mvc/tools/tools-form-base.js R static/scripts/mvc/ui/ui-button-check.js R static/scripts/mvc/ui/ui-button-menu.js A static/scripts/mvc/ui/ui-buttons.js M static/scripts/mvc/ui/ui-color-picker.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-options.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/upload/upload-button.js M static/scripts/mvc/upload/upload-view.js M static/style/blue/base.css M templates/base.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/root/index.mako R templates/webapps/galaxy/root/tool_menu.mako M templates/webapps/galaxy/tool_form.mako Log Message: ----------- Merge pull request #706 from guerler/ui_revision_000 UI revision (panel rendering, iframes and tool forms) Commit: af2f93b23609b367d15619471a18e3e6fd0c90e8 https://github.com/galaxyproject/galaxy/commit/af2f93b23609b367d15619471a18… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-09 (Wed, 09 Sep 2015) Changed paths: M .ci/flake8_blacklist.txt M contrib/galaxy_config_merger.py M contrib/nagios/check_galaxy.py Log Message: ----------- flake8 contrib/ . Commit: df808d0c1e8c46e45adebaafbd30e0a8a1cf9b55 https://github.com/galaxyproject/galaxy/commit/df808d0c1e8c46e45adebaafbd30… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-09 (Wed, 09 Sep 2015) Changed paths: M .ci/flake8_blacklist.txt M lib/tool_shed/dependencies/repository/relation_builder.py M lib/tool_shed/dependencies/tool/tag_attribute_handler.py M lib/tool_shed/galaxy_install/datatypes/custom_datatype_manager.py M lib/tool_shed/galaxy_install/dependency_display.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/migrate/check.py M lib/tool_shed/galaxy_install/migrate/common.py M lib/tool_shed/galaxy_install/migrate/versions/0001_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0002_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0003_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0004_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0005_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0006_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0007_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0008_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0009_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0010_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0011_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0012_tools.py M lib/tool_shed/galaxy_install/tool_dependencies/env_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/asynchronous_reader.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/galaxy_install/tools/data_manager.py M lib/tool_shed/galaxy_install/utility_containers/__init__.py M lib/tool_shed/grids/repository_grid_filter_manager.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/util.py M lib/tool_shed/repository_types/metadata.py M lib/tool_shed/repository_types/repository_suite_definition.py M lib/tool_shed/repository_types/tool_dependency_definition.py M lib/tool_shed/repository_types/util.py M lib/tool_shed/scripts/api/add_repository_registry_entry.py M lib/tool_shed/scripts/api/common.py M lib/tool_shed/scripts/api/create_categories.py M lib/tool_shed/scripts/api/create_users.py M lib/tool_shed/scripts/api/export.py M lib/tool_shed/scripts/api/get_filtered_repository_revisions.py M lib/tool_shed/scripts/api/import_capsule.py M lib/tool_shed/scripts/api/remove_repository_registry_entry.py M lib/tool_shed/scripts/api/reset_metadata_on_repositories.py M lib/tool_shed/scripts/api/tool_shed_repository_revision_update.py M lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py M lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py M lib/tool_shed/scripts/check_filesystem_for_empty_tool_dependency_installation_paths.py M lib/tool_shed/scripts/check_repositories_for_functional_tests.py M lib/tool_shed/scripts/check_s3_for_empty_tool_dependency_installation_paths.py M lib/tool_shed/scripts/check_tool_dependency_definition_repositories.py M lib/tool_shed/scripts/clean_up_tool_dependency_directory.py M lib/tool_shed/scripts/deprecate_repositories_without_metadata.py M lib/tool_shed/scripts/show_tool_dependency_installation_dir_contents.py M lib/tool_shed/tool_shed_registry.py M lib/tool_shed/tools/data_table_manager.py M lib/tool_shed/util/basic_util.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/container_util.py M lib/tool_shed/util/encoding_util.py M lib/tool_shed/util/hg_util.py M lib/tool_shed/util/metadata_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/xml_util.py M lib/tool_shed/utility_containers/__init__.py M lib/tool_shed/utility_containers/utility_container_manager.py Log Message: ----------- flake8 lib/tool_shed/ . Also: - use sys.exit() instead of exit() - fix sys.path manipulations. Commit: fa82f2ded3d07ec9a60631809ad4596310d22bca https://github.com/galaxyproject/galaxy/commit/fa82f2ded3d07ec9a60631809ad4… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-09-10 (Thu, 10 Sep 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge pull request #457 from davebx/td_regex_replace Add regex_replace tool dependency action. Commit: 076af9bf487bfcef105a058c3f10cbe5c2e709b4 https://github.com/galaxyproject/galaxy/commit/076af9bf487bfcef105a058c3f10… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-10 (Thu, 10 Sep 2015) Changed paths: M eggs.ini Log Message: ----------- Upgrade sqlalchemy to 1.0.8. This was primarily done in an attempt to fix a mysql-specific unicode bug (which it didn't fix). Commit: 5d79823a2d6703297503ed07e42cba75bec4b3df https://github.com/galaxyproject/galaxy/commit/5d79823a2d6703297503ed07e42c… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-09-10 (Thu, 10 Sep 2015) Changed paths: M eggs.ini Log Message: ----------- Merge pull request #709 from dannon/sqlalchemy_update_108 Upgrade sqlalchemy to 1.0.8. Commit: b1b710925a4c54f3081fc4b79963085e0c362d42 https://github.com/galaxyproject/galaxy/commit/b1b710925a4c54f3081fc4b79963… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-10 (Thu, 10 Sep 2015) Changed paths: M .ci/flake8_blacklist.txt M contrib/galaxy_config_merger.py M contrib/nagios/check_galaxy.py M lib/tool_shed/dependencies/repository/relation_builder.py M lib/tool_shed/dependencies/tool/tag_attribute_handler.py M lib/tool_shed/galaxy_install/datatypes/custom_datatype_manager.py M lib/tool_shed/galaxy_install/dependency_display.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/migrate/check.py M lib/tool_shed/galaxy_install/migrate/common.py M lib/tool_shed/galaxy_install/migrate/versions/0001_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0002_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0003_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0004_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0005_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0006_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0007_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0008_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0009_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0010_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0011_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0012_tools.py M lib/tool_shed/galaxy_install/tool_dependencies/env_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/asynchronous_reader.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/galaxy_install/tools/data_manager.py M lib/tool_shed/galaxy_install/utility_containers/__init__.py M lib/tool_shed/grids/repository_grid_filter_manager.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/util.py M lib/tool_shed/repository_types/metadata.py M lib/tool_shed/repository_types/repository_suite_definition.py M lib/tool_shed/repository_types/tool_dependency_definition.py M lib/tool_shed/repository_types/util.py M lib/tool_shed/scripts/api/add_repository_registry_entry.py M lib/tool_shed/scripts/api/common.py M lib/tool_shed/scripts/api/create_categories.py M lib/tool_shed/scripts/api/create_users.py M lib/tool_shed/scripts/api/export.py M lib/tool_shed/scripts/api/get_filtered_repository_revisions.py M lib/tool_shed/scripts/api/import_capsule.py M lib/tool_shed/scripts/api/remove_repository_registry_entry.py M lib/tool_shed/scripts/api/reset_metadata_on_repositories.py M lib/tool_shed/scripts/api/tool_shed_repository_revision_update.py M lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py M lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py M lib/tool_shed/scripts/check_filesystem_for_empty_tool_dependency_installation_paths.py M lib/tool_shed/scripts/check_repositories_for_functional_tests.py M lib/tool_shed/scripts/check_s3_for_empty_tool_dependency_installation_paths.py M lib/tool_shed/scripts/check_tool_dependency_definition_repositories.py M lib/tool_shed/scripts/clean_up_tool_dependency_directory.py M lib/tool_shed/scripts/deprecate_repositories_without_metadata.py M lib/tool_shed/scripts/show_tool_dependency_installation_dir_contents.py M lib/tool_shed/tool_shed_registry.py M lib/tool_shed/tools/data_table_manager.py M lib/tool_shed/util/basic_util.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/container_util.py M lib/tool_shed/util/encoding_util.py M lib/tool_shed/util/hg_util.py M lib/tool_shed/util/metadata_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/xml_util.py M lib/tool_shed/utility_containers/__init__.py M lib/tool_shed/utility_containers/utility_container_manager.py Log Message: ----------- Merge pull request #708 from nsoranzo/flake8_fixes flake8 contrib/ and lib/tool_shed/ . Commit: 1e4b4070ce14af06860ee6eb0b963b159097cc39 https://github.com/galaxyproject/galaxy/commit/1e4b4070ce14af06860ee6eb0b96… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-10 (Thu, 10 Sep 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- I think this was broken in #457 Commit: 54d4c266bd7c724256f44f0057021d0da2dba3b6 https://github.com/galaxyproject/galaxy/commit/54d4c266bd7c724256f44f005702… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-10 (Thu, 10 Sep 2015) Changed paths: M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_exporter.xml M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_file_browser_dev.xml M tools/genomespace/genomespace_file_browser_prod.xml M tools/genomespace/genomespace_file_browser_test.xml M tools/genomespace/genomespace_importer.py M tools/genomespace/genomespace_importer.xml Log Message: ----------- Have GenomeSpace tools report the GS tool name (for their internal metrics). Default is "Galaxy", but can be overridden by setting "GENOMESPACE_TOOLNAME" environment variable. Commit: e6a603decec5fb3f3b4756c20d0e5cf53700d435 https://github.com/galaxyproject/galaxy/commit/e6a603decec5fb3f3b4756c20d0e… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-10 (Thu, 10 Sep 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge pull request #710 from martenson/fix-double-import fix double import for travis Commit: b79555264e6f1d7b042bd5650efeed1483252095 https://github.com/galaxyproject/galaxy/commit/b79555264e6f1d7b042bd5650efe… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-10 (Thu, 10 Sep 2015) Changed paths: M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_exporter.xml M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_file_browser_dev.xml M tools/genomespace/genomespace_file_browser_prod.xml M tools/genomespace/genomespace_file_browser_test.xml M tools/genomespace/genomespace_importer.py M tools/genomespace/genomespace_importer.xml Log Message: ----------- Merge pull request #711 from blankenberg/genomespace_toolname Have GenomeSpace tools report the GS tool name Commit: 451196e4d39800995d7b1ea1f69b177294c3c632 https://github.com/galaxyproject/galaxy/commit/451196e4d39800995d7b1ea1f69b… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-10 (Thu, 10 Sep 2015) Changed paths: M templates/user/login.mako Log Message: ----------- Fix for logging in using OpenID when the OpenID isn't associated with a user yet. Commit: c9ef883db64bbf9e2d4f9b8bc2dea11f8e4be60d https://github.com/galaxyproject/galaxy/commit/c9ef883db64bbf9e2d4f9b8bc2de… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-10 (Thu, 10 Sep 2015) Changed paths: M templates/user/login.mako Log Message: ----------- Merge pull request #712 from blankenberg/openid_associate_fix Fix for logging in using OpenID when the OpenID isn't associated Commit: 91799c3891fe60f94fc52501541326904cc96071 https://github.com/galaxyproject/galaxy/commit/91799c3891fe60f94fc525015413… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-11 (Fri, 11 Sep 2015) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/webapps/tool_shed/controllers/admin.py M lib/pulsar/client/action_mapper.py M lib/pulsar/client/amqp_exchange.py M lib/pulsar/client/amqp_exchange_factory.py M lib/pulsar/client/client.py M lib/pulsar/client/config_util.py M lib/pulsar/client/decorators.py M lib/pulsar/client/interface.py M lib/pulsar/client/manager.py M lib/pulsar/client/staging/__init__.py M lib/pulsar/client/staging/down.py M lib/pulsar/client/staging/up.py M lib/pulsar/client/transport/curl.py M lib/pulsar/client/util.py Log Message: ----------- Merge branch 'release_15.07' into dev Commit: 36809cd6f37f65e9b571a0eb3e663419930e5871 https://github.com/galaxyproject/galaxy/commit/36809cd6f37f65e9b571a0eb3e66… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-11 (Fri, 11 Sep 2015) Changed paths: M lib/pulsar/client/amqp_exchange.py Log Message: ----------- Merge branch 'amqp_ack' into test Commit: 63a715f27c5ee31de6bdd0cd4222b309b3f2ce23 https://github.com/galaxyproject/galaxy/commit/63a715f27c5ee31de6bdd0cd4222… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-11 (Fri, 11 Sep 2015) Changed paths: M test/tool_shed/functional/test_1140_tool_help_images.py Log Message: ----------- Fix Tool Shed test broken with PR #706. Commit: ed92a12e78dad1d7290fde30b23768b613e68232 https://github.com/galaxyproject/galaxy/commit/ed92a12e78dad1d7290fde30b237… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-11 (Fri, 11 Sep 2015) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Specify the tool_id of the missing tool when raising MissingToolException. Commit: 760899f9c0ce717df4e6c789e36693973d048c7d https://github.com/galaxyproject/galaxy/commit/760899f9c0ce717df4e6c789e366… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-11 (Fri, 11 Sep 2015) Changed paths: M test/api/test_workflows.py Log Message: ----------- Fix MissingToolException when running "./run_tests.sh -api" without "-with_framework_test_tools". Commit: 65519718b37a0a08c802c131b92ca0335a0b7eda https://github.com/galaxyproject/galaxy/commit/65519718b37a0a08c802c131b92c… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-11 (Fri, 11 Sep 2015) Changed paths: M test/api/yaml_to_workflow.py Log Message: ----------- Fix "KeyError: name" error when running "./run_tests.sh -api". Example traceback for test/api/test_workflows.py:WorkflowsApiTestCase.test_workflow_run_dynamic_output_collections : galaxy.web.framework.decorators: ERROR: Uncaught exception in exposed API method: Traceback (most recent call last): File "/opt/galaxy/lib/galaxy/web/framework/decorators.py", line 260, in decorator rval = func( self, trans, *args, **kwargs) File "/opt/galaxy/lib/galaxy/webapps/galaxy/api/workflows.py", line 182, in create return self.__api_import_new_workflow( trans, payload, **kwd ) File "/opt/galaxy/lib/galaxy/webapps/galaxy/api/workflows.py", line 374, in __api_import_new_workflow workflow, missing_tool_tups = self._workflow_from_dict( trans, data, **from_dict_kwds ) File "/opt/galaxy/lib/galaxy/web/base/controller.py", line 1111, in _workflow_from_dict publish=publish File "/opt/galaxy/lib/galaxy/managers/workflows.py", line 165, in build_workflow_from_dict missing_tool_tup = ( step_dict[ 'tool_id' ], step_dict[ 'name' ], step_dict[ 'tool_version' ] ) KeyError: 'name' Commit: cd456e186dc1ba6f51e3cafb0c54d6b1f1651817 https://github.com/galaxyproject/galaxy/commit/cd456e186dc1ba6f51e3cafb0c54… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-11 (Fri, 11 Sep 2015) Changed paths: M cron/add_manual_builds.py M cron/build_chrom_db.py M cron/cleanup_datasets.py M scripts/check_galaxy.py Log Message: ----------- Print to stderr when calling sys.exit(1) Commit: c01cf85d450a83c4f235ba488b84d2c7a60c4209 https://github.com/galaxyproject/galaxy/commit/c01cf85d450a83c4f235ba488b84… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-11 (Fri, 11 Sep 2015) Changed paths: M doc/source/conf.py M lib/galaxy/main.py M lib/galaxy_ext/metadata/set_metadata.py M test/base/tool_shed_util.py M test/install_and_test_tool_shed_repositories/base/util.py M test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py M test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py M test/manual/workflows_scaling.py M test/tool_shed/functional_tests.py M test/unit/unittest_utils/utility.py Log Message: ----------- Use __file__ when adding paths to sys.path instead of os.getcwd() . Also insert additional paths in position 1 unless strictly necessary. Commit: fef28884fc6f46efb01816c9466667840947f372 https://github.com/galaxyproject/galaxy/commit/fef28884fc6f46efb01816c94666… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-09-11 (Fri, 11 Sep 2015) Changed paths: M cron/add_manual_builds.py M cron/build_chrom_db.py M cron/cleanup_datasets.py M doc/source/conf.py M lib/galaxy/main.py M lib/galaxy/workflow/modules.py M lib/galaxy_ext/metadata/set_metadata.py M scripts/check_galaxy.py M test/api/test_workflows.py M test/api/yaml_to_workflow.py M test/base/tool_shed_util.py M test/install_and_test_tool_shed_repositories/base/util.py M test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py M test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py M test/manual/workflows_scaling.py M test/tool_shed/functional/test_1140_tool_help_images.py M test/tool_shed/functional_tests.py M test/unit/unittest_utils/utility.py Log Message: ----------- Merge pull request #720 from nsoranzo/misc_fixes Misc fixes Commit: 76ad959f16e0f30a8e306056ab8042ba8512b9a9 https://github.com/galaxyproject/galaxy/commit/76ad959f16e0f30a8e306056ab80… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-13 (Sun, 13 Sep 2015) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/admin.py Log Message: ----------- Fix lint failure in toolshed/admin. Commit: 51979deefbd98858987d7c93495743300845c90c https://github.com/galaxyproject/galaxy/commit/51979deefbd98858987d7c934957… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-09-13 (Sun, 13 Sep 2015) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/admin.py Log Message: ----------- Merge pull request #722 from dannon/style_fix Fix lint failure in toolshed/admin. Commit: 4064d0c5980644f29ac06b83f28e7064479f28db https://github.com/galaxyproject/galaxy/commit/4064d0c5980644f29ac06b83f28e… Author: Michael R. Crusoe <crusoe(a)ucdavis.edu> Date: 2015-09-13 (Sun, 13 Sep 2015) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py Log Message: ----------- add Oxli datatypes Commit: cecea3ebc6e9043df85989cd74899779a06c1e41 https://github.com/galaxyproject/galaxy/commit/cecea3ebc6e9043df85989cd7489… Author: Michael R. Crusoe <michael.crusoe(a)gmail.com> Date: 2015-09-13 (Sun, 13 Sep 2015) Changed paths: M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/oxli_countgraph.oxlicg A lib/galaxy/datatypes/test/oxli_graphlabels.oxligl A lib/galaxy/datatypes/test/oxli_nodegraph.oxling A lib/galaxy/datatypes/test/oxli_stoptags.oxlist A lib/galaxy/datatypes/test/oxli_subset.oxliss A lib/galaxy/datatypes/test/oxli_tagset.oxlits Log Message: ----------- added doctests + 1 fix + cleanup Made helper function a proper @staticmethod fixed error in sniffer (thank you doctests) Moved registration lines after their respective classes Added test data Commit: 383e9e01817483b819e770e22cf9d2d0beebbd5b https://github.com/galaxyproject/galaxy/commit/383e9e01817483b819e770e22cf9… Author: Michael R. Crusoe <michael.crusoe(a)gmail.com> Date: 2015-09-13 (Sun, 13 Sep 2015) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- OxliLabelSet->OxliGraphLabels even in the config Commit: 02df796c7236b51382f7b1f77d50cc1709c76356 https://github.com/galaxyproject/galaxy/commit/02df796c7236b51382f7b1f77d50… Author: Michael R. Crusoe <michael.crusoe(a)gmail.com> Date: 2015-09-13 (Sun, 13 Sep 2015) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- drop trailing whitespace Commit: 8c2ab4180b218c3cffcf5c739ccbe4d22c52edaa https://github.com/galaxyproject/galaxy/commit/8c2ab4180b218c3cffcf5c739ccb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-14 (Mon, 14 Sep 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Extend root controller to allow specifing a history id. It currently allows hoping straight to a given workflow or tool by id, this commit extends that to allow histories as well. Simply add history_id=<history_id> to the query string. Commit: 17d8e15e4ee696610799a46abdf3d0379e9d23d5 https://github.com/galaxyproject/galaxy/commit/17d8e15e4ee696610799a46abdf3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-14 (Mon, 14 Sep 2015) Changed paths: M lib/galaxy/jobs/deferred/__init__.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/security/__init__.py M lib/galaxy/util/topsort.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/controllers/repository.py A lib/galaxy/webapps/util.py M lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py M lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py Log Message: ----------- Merge remote-tracking branch 'erasche/deduplication' into deduplication-merge Conflicts: lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py Commit: 57634f43ea4ed82bf2603df80545604d795e3896 https://github.com/galaxyproject/galaxy/commit/57634f43ea4ed82bf2603df80545… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-14 (Mon, 14 Sep 2015) Changed paths: M lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py M lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py Log Message: ----------- Fix lint problems from merge. How did that happen, those pieces of code were largely unrelated. Ekkk... Commit: b51294efba3ba018bab6b7f5d9234196f7712adc https://github.com/galaxyproject/galaxy/commit/b51294efba3ba018bab6b7f5d923… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-14 (Mon, 14 Sep 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge pull request #725 from jmchilton/history_id_entry Extend root controller to allow specifying a history id. Commit: 222d7805e9a36b5d9b1e31377f1fb35f3405f084 https://github.com/galaxyproject/galaxy/commit/222d7805e9a36b5d9b1e31377f1f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-14 (Mon, 14 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-analysis.js M static/maps/mvc/app/app-analysis.js.map M static/scripts/mvc/app/app-analysis.js Log Message: ----------- Fix history options menu Commit: 08fef5843894317b791559e7dc2aa54bb720aed3 https://github.com/galaxyproject/galaxy/commit/08fef5843894317b791559e7dc2a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-14 (Mon, 14 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-analysis.js M static/maps/mvc/app/app-analysis.js.map M static/scripts/mvc/app/app-analysis.js Log Message: ----------- Fix purge flag in history options Commit: 2844d8579b5e84c81b22a662ca4d1211f96f39d3 https://github.com/galaxyproject/galaxy/commit/2844d8579b5e84c81b22a662ca4d… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2015-09-14 (Mon, 14 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-analysis.js M static/maps/mvc/app/app-analysis.js.map M static/scripts/mvc/app/app-analysis.js Log Message: ----------- Merge pull request #726 from guerler/fix_history_000 Fix history option flags Commit: 857755284db6ba2c6a773e01050222ba9748e616 https://github.com/galaxyproject/galaxy/commit/857755284db6ba2c6a773e010502… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-09-14 (Mon, 14 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/history/history-model.js M static/maps/mvc/history/history-model.js.map M static/scripts/mvc/history/history-model.js Log Message: ----------- Fix multi-history copy/new to set the history as current Commit: 1ba64709e668f08ce757606a784aec19f7a840d1 https://github.com/galaxyproject/galaxy/commit/1ba64709e668f08ce757606a784a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-14 (Mon, 14 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/history/history-model.js M static/maps/mvc/history/history-model.js.map M static/scripts/mvc/history/history-model.js Log Message: ----------- Merge pull request #727 from carlfeberhard/fix.multi-new Fix multi-history copy/new to set the history as current Commit: 85480e72bfa62306d19ac03ff60b4406f01146e0 https://github.com/galaxyproject/galaxy/commit/85480e72bfa62306d19ac03ff60b… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-09-14 (Mon, 14 Sep 2015) Changed paths: M templates/webapps/galaxy/galaxy.masthead.mako Log Message: ----------- Fix Galaxy.user to be available when not using 1 require Commit: ba25057922594b1d2878ccf5e96dd83ffc0843a3 https://github.com/galaxyproject/galaxy/commit/ba25057922594b1d2878ccf5e96d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-14 (Mon, 14 Sep 2015) Changed paths: M lib/galaxy/jobs/deferred/__init__.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/security/__init__.py M lib/galaxy/util/topsort.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/controllers/repository.py A lib/galaxy/webapps/util.py M lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py M lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py Log Message: ----------- Merge pull request #694 from erasche/deduplication Deduplication PR Commit: 08668104e5aa9c564dba561bab403439a65cd0fd https://github.com/galaxyproject/galaxy/commit/08668104e5aa9c564dba561bab40… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2015-09-14 (Mon, 14 Sep 2015) Changed paths: M templates/webapps/galaxy/galaxy.masthead.mako Log Message: ----------- Merge pull request #728 from carlfeberhard/fix.galaxy-user Fix Galaxy.user to be available when not using 1 require Commit: 34165913ba1e70ee72db363aeea74cc1824301ec https://github.com/galaxyproject/galaxy/commit/34165913ba1e70ee72db363aeea7… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-14 (Mon, 14 Sep 2015) Changed paths: M CONTRIBUTING.md M README.rst M doc/source/project/organization.rst Log Message: ----------- Merge pull request #702 from nsoranzo/readme_contributing [PROCEDURES] Reorganize content Commit: 8dadfdcaa0492bce485fb786aed0d29243356258 https://github.com/galaxyproject/galaxy/commit/8dadfdcaa0492bce485fb786aed0… Author: Michael R. Crusoe <crusoe(a)ucdavis.edu> Date: 2015-09-14 (Mon, 14 Sep 2015) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- remove no-op __init__ methods Commit: 1ea1da02291d3d9abbec32a09d63a16ddcef1084 https://github.com/galaxyproject/galaxy/commit/1ea1da02291d3d9abbec32a09d63… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-15 (Tue, 15 Sep 2015) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Merge pull request #729 from mr-c/drop-noop-init remove no-op __init__ methods from lib/galaxy/datatypes/binary.py Commit: 23051da68c88f1173be8094c2597cc60cb054f27 https://github.com/galaxyproject/galaxy/commit/23051da68c88f1173be8094c2597… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-15 (Tue, 15 Sep 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- When rerunning a job w/ remap, reassociate PostJobActions when possible to the new job. Commit: 555b6d745d245d5fa6d6868e92cc3797d6855343 https://github.com/galaxyproject/galaxy/commit/555b6d745d245d5fa6d6868e92cc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-15 (Tue, 15 Sep 2015) Changed paths: M lib/galaxy/managers/collections.py Log Message: ----------- Fix for 13ea86753ad778aaaf6e6470a9370190fc2e91a0. Fixes tests and functionality broken with 13ea86753ad778aaaf6e6470a9370190fc2e91a0 as spotted by eagle eye @nsoranzo here https://github.com/galaxyproject/galaxy/commit/13ea86753ad778aaaf6e6470a937…. Commit: 4671ae8d45092824db2f7b19b7d6896e6524c672 https://github.com/galaxyproject/galaxy/commit/4671ae8d45092824db2f7b19b7d6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-15 (Tue, 15 Sep 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Merge pull request #730 from dannon/pja_wf_rerun_fix When rerunning a job w/ remap, reassociate PostJobActions when possib… Commit: 3fafbb5e34ed3f6f547bf1f184782b0f6967cf2f https://github.com/galaxyproject/galaxy/commit/3fafbb5e34ed3f6f547bf1f18478… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-15 (Tue, 15 Sep 2015) Changed paths: M test/api/test_workflow_extraction.py Log Message: ----------- Fix more MissingToolException when running "./run_tests.sh -api" without "-with_framework_test_tools". Commit: 63d1715679fb714f4c8f5ae426106edf6988e7ab https://github.com/galaxyproject/galaxy/commit/63d1715679fb714f4c8f5ae42610… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-15 (Tue, 15 Sep 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix API tests using collection_creates_pair tool. Commit: 89cc67baf67e295b3eaa2449e6fd6727317df942 https://github.com/galaxyproject/galaxy/commit/89cc67baf67e295b3eaa2449e6fd… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-15 (Tue, 15 Sep 2015) Changed paths: M client/galaxy/scripts/galaxy-app-base.js M client/galaxy/scripts/mvc/app/app-analysis.js M static/maps/mvc/app/app-analysis.js.map M static/scripts/mvc/app/app-analysis.js Log Message: ----------- Trigger iframe event for history Commit: 89b42bf0603433b2b66a264c9a3a3d3fe4e12280 https://github.com/galaxyproject/galaxy/commit/89b42bf0603433b2b66a264c9a3a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-15 (Tue, 15 Sep 2015) Changed paths: M lib/galaxy/tools/__init__.py M test/api/test_workflow_extraction.py Log Message: ----------- Merge pull request #731 from nsoranzo/dev Fix more API tests. Commit: 71a1def3219db8763e76b87a4bb1aefdfdc082d3 https://github.com/galaxyproject/galaxy/commit/71a1def3219db8763e76b87a4bb1… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-15 (Tue, 15 Sep 2015) Changed paths: M lib/galaxy/managers/collections.py Log Message: ----------- Merge pull request #735 from jmchilton/collection_fix Fix for 13ea86753ad778aaaf6e6470a9370190fc2e91a0. Commit: d3e14ec6731d6f0524ff8f2575a100555de2fe25 https://github.com/galaxyproject/galaxy/commit/d3e14ec6731d6f0524ff8f2575a1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-15 (Tue, 15 Sep 2015) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Check to make sure a job is actually part of a workflow invocation prior to attempting to clean other workflow steps. This prevents an error when a 'clean intermediates' type job is remapped. TODO: Perhaps the job should actually be replaced in the workflow invocation as well, but this is a decent defensive check anyway. Commit: 1e2adc6b57034fb27b3a12f0a13d6f0ace1b096a https://github.com/galaxyproject/galaxy/commit/1e2adc6b57034fb27b3a12f0a13d… Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com> Date: 2015-09-15 (Tue, 15 Sep 2015) Changed paths: M client/galaxy/scripts/galaxy-app-base.js M client/galaxy/scripts/mvc/app/app-analysis.js M static/maps/mvc/app/app-analysis.js.map M static/scripts/mvc/app/app-analysis.js Log Message: ----------- Merge pull request #732 from guerler/fix_history_001 Trigger iframe event for history Commit: bd55650f0624e4218cbf898a73579979e7bc6072 https://github.com/galaxyproject/galaxy/commit/bd55650f0624e4218cbf898a7357… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-16 (Wed, 16 Sep 2015) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M scripts/functional_tests.py A test/base/test_logging.py Log Message: ----------- Add testing environment variable GALAXY_TEST_LOGGING_CONFIG. Unifies logging through the testing process. Requires adding a Galaxy option to disable its own attempts to configure a different root logger. Commit: 1a5ef156d9d58966bee8dba95ac2cf2803fe16a7 https://github.com/galaxyproject/galaxy/commit/1a5ef156d9d58966bee8dba95ac2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-16 (Wed, 16 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/tools/tools-form-base.js M lib/galaxy/managers/hdas.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/tools.py M static/maps/galaxy-app-base.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/scripts/galaxy-app-base.js M static/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- First pass of updating rerun to use the new modal. Pretty hacky, needs cleanup. Commit: 43c13ee1626779a4127f67b564ee88bb6b9af3ca https://github.com/galaxyproject/galaxy/commit/43c13ee1626779a4127f67b564ee… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-16 (Wed, 16 Sep 2015) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/model/__init__.py Log Message: ----------- Merge branch 'release_15.07' into dev Conflicts: lib/galaxy/model/__init__.py Commit: c51bfaa51aefff1e6be5c54b72fc51c4fc666264 https://github.com/galaxyproject/galaxy/commit/c51bfaa51aefff1e6be5c54b72fc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-16 (Wed, 16 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-form-base.js M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/mvc/tools/tools-form-base.js.map M static/scripts/mvc/tools/tools-form-base.js Log Message: ----------- Flip API endpoint to the jobs API instead of hacking it into the existing tools api. Commit: 5953fb592202cd12cf4cfb78900a4f1b89e85c79 https://github.com/galaxyproject/galaxy/commit/5953fb592202cd12cf4cfb78900a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-16 (Wed, 16 Sep 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py Log Message: ----------- Use tool.to_json optional kwd to parse old job inputs instead of doing it manually. Commit: 3348715971bc85901553fe8b87f9d3962962b40c https://github.com/galaxyproject/galaxy/commit/3348715971bc85901553fe8b87f9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-17 (Thu, 17 Sep 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py Log Message: ----------- Add documentation to new API endpoint. Commit: 4d4e19b37904907201217bff7a6d295411b93968 https://github.com/galaxyproject/galaxy/commit/4d4e19b37904907201217bff7a6d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-17 (Thu, 17 Sep 2015) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Merge pull request #736 from dannon/pja_wf_rerun_fix Check to make sure a job is actually part of a workflow invocation pr… Commit: a7ca9586bb8bffaf61d751e6b21da46a187bbad1 https://github.com/galaxyproject/galaxy/commit/a7ca9586bb8bffaf61d751e6b21d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-17 (Thu, 17 Sep 2015) Changed paths: M lib/galaxy/managers/hdas.py M lib/galaxy/webapps/galaxy/api/jobs.py Log Message: ----------- Allow serialization of hdas without 'creating job', though we should probably look into how/why this can ever happen. Seems like there's a bug hidden here somewhere, but this allows the existing functionality to work and pass tests. Commit: 7c78e01b7da020d11cad29c906536e1ff95b484d https://github.com/galaxyproject/galaxy/commit/7c78e01b7da020d11cad29c90653… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2015-09-17 (Thu, 17 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/tools/tools-form-base.js M lib/galaxy/managers/hdas.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/galaxy-app-base.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/scripts/galaxy-app-base.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/tools/tools-form-base.js Log Message: ----------- Merge pull request #739 from dannon/rerun_newform Swap rerun to use iframe-less Galaxy.display. Commit: 4e063e793f6ddea0ae4c36183b8b4ad96d193f08 https://github.com/galaxyproject/galaxy/commit/4e063e793f6ddea0ae4c36183b8b… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2015-09-17 (Thu, 17 Sep 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- add mkdir as safeguard and remove old warning Commit: c74cda3c60b0b0e8c8698946c373999fac300b4c https://github.com/galaxyproject/galaxy/commit/c74cda3c60b0b0e8c8698946c373… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-17 (Thu, 17 Sep 2015) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M scripts/functional_tests.py A test/base/test_logging.py Log Message: ----------- Merge pull request #738 from jmchilton/logging Add testing environment variable GALAXY_TEST_LOGGING_CONFIG. Commit: d717ec833de5615fdb949fdfd0a3c69ab90a7a7f https://github.com/galaxyproject/galaxy/commit/d717ec833de5615fdb949fdfd0a3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-17 (Thu, 17 Sep 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge pull request #698 from bgruening/pip_install Use setup.py for Python all installations Commit: 150c17b9e8adc03fe8684962ca76f19bf0c93705 https://github.com/galaxyproject/galaxy/commit/150c17b9e8adc03fe8684962ca76… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-17 (Thu, 17 Sep 2015) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/web/framework/__init__.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py M scripts/transfer.py Log Message: ----------- Do not explicitly require pexpect. If anyone wants to use the old and mostly unused features that depend on it (namely remote sequencer transfers via scp) they can pip install pexpect. Commit: 63e35965401a2eac2ef3308913fb48be89961c10 https://github.com/galaxyproject/galaxy/commit/63e35965401a2eac2ef3308913fb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-17 (Thu, 17 Sep 2015) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/web/framework/__init__.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py M scripts/transfer.py Log Message: ----------- Merge pull request #741 from natefoo/drop-pexpect Do not explicitly require pexpect Commit: e71826889f1c4f8f4cab68ac7adab40bf53d3094 https://github.com/galaxyproject/galaxy/commit/e71826889f1c4f8f4cab68ac7ada… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-09-17 (Thu, 17 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/multi-panel.js M lib/galaxy/webapps/galaxy/api/histories.py M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/multi-panel.js.map M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/multi-panel.js Log Message: ----------- API, histories: correct copy to copy both non-deleted and deleted contents by default, add all_datasets flag to support copying only non-deleted; UI, histories: separate out history copy dialog for use in multi-panel (and later: the options menu), include deleted filter in choices Commit: de8bdaf44f0d304ce715e7ff43cf43b1b920f28a https://github.com/galaxyproject/galaxy/commit/de8bdaf44f0d304ce715e7ff43cf… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-09-17 (Thu, 17 Sep 2015) Changed paths: A client/galaxy/scripts/mvc/history/copy-dialog.js A static/maps/mvc/history/copy-dialog.js.map A static/scripts/mvc/history/copy-dialog.js Log Message: ----------- Fix to e718268: add copy-dialog files Commit: 3f71220bcfd6d17593e1f8d7aa7e09e6e5bd9997 https://github.com/galaxyproject/galaxy/commit/3f71220bcfd6d17593e1f8d7aa7e… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-09-17 (Thu, 17 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/history/copy-dialog.js M static/maps/mvc/history/copy-dialog.js.map M static/scripts/mvc/history/copy-dialog.js Log Message: ----------- UI, history: clean up copy dialog Commit: fec26b39c26d1687622dbfc999d244f34afcf264 https://github.com/galaxyproject/galaxy/commit/fec26b39c26d1687622dbfc999d2… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-17 (Thu, 17 Sep 2015) Changed paths: A client/galaxy/scripts/mvc/history/copy-dialog.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/multi-panel.js M lib/galaxy/webapps/galaxy/api/histories.py A static/maps/mvc/history/copy-dialog.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/multi-panel.js.map A static/scripts/mvc/history/copy-dialog.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/multi-panel.js Log Message: ----------- Merge pull request #742 from carlfeberhard/history.copy-dialog History copy dialog & API fix Commit: 0ea4ad69a013a51b1327a275864a0471ec55c070 https://github.com/galaxyproject/galaxy/commit/0ea4ad69a013a51b1327a275864a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-18 (Fri, 18 Sep 2015) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Remove deprecated objectstore options from sample; the new way is to set object_store_conf and use it. Commit: 4fb4873934ea8857a2e4a694194a97137ba7ae35 https://github.com/galaxyproject/galaxy/commit/4fb4873934ea8857a2e4a694194a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-18 (Fri, 18 Sep 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py Log Message: ----------- Jobs API docstring {job_id} to {id} convention fix. Elsewhere we refer to a member's id as simply 'id' in docs, and this is the parameter name. Commit: 35621ca118d278559dee31ff0ac53f77184be7c1 https://github.com/galaxyproject/galaxy/commit/35621ca118d278559dee31ff0ac5… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-09-18 (Fri, 18 Sep 2015) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Merge pull request #748 from dannon/sample_cleanup Remove deprecated objectstore options from sample; the new way is to … Commit: ef23abc6df1dfc1b5ca10d380c2e7a840862c76a https://github.com/galaxyproject/galaxy/commit/ef23abc6df1dfc1b5ca10d380c2e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-18 (Fri, 18 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/history/hdca-li.js M lib/galaxy/model/__init__.py M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/history/hdca-li.js.map M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/history/hdca-li.js M test/api/test_dataset_collections.py Log Message: ----------- WIP: Improved state tracking of HDCA in history panel. For tools which dynamically discover datasets for an output collection, keep the collection yellow until the structure of the HDCA has been fully defined. HDCAs still have the problem that they will always be green even if datasets contained within are in error, running, or queued states - but at least the structure is now reflected in the color. Commit: 3de7bb66993c0094f8ff138fcb768a75fd5f3a0a https://github.com/galaxyproject/galaxy/commit/3de7bb66993c0094f8ff138fcb76… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-09-18 (Fri, 18 Sep 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py Log Message: ----------- Merge pull request #751 from dannon/api_docstrings Jobs API docstring {job_id} to {id} convention fix. Elsewhere we ref… Commit: 989191d3cef70999661668ca9031e6cf39aaca61 https://github.com/galaxyproject/galaxy/commit/989191d3cef70999661668ca9031… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-18 (Fri, 18 Sep 2015) Changed paths: M test/functional/tools/output_format.xml Log Message: ----------- Fix output_format framework test. Commit: 92a152d89c507168a6085cc34acfa13566b6eda9 https://github.com/galaxyproject/galaxy/commit/92a152d89c507168a6085cc34acf… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-18 (Fri, 18 Sep 2015) Changed paths: M test/api/helpers.py Log Message: ----------- Uniform and slight increase the default timeout of API tests. Commit: d585a4a03d6956404830d63fc6b8872fba241d83 https://github.com/galaxyproject/galaxy/commit/d585a4a03d6956404830d63fc6b8… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-18 (Fri, 18 Sep 2015) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Clearer error message when setting metadata for BCF and SAM/BAM files. When the shutil.move() fails. Commit: ca733d33f9c52a630a30132d24974ed1143e6945 https://github.com/galaxyproject/galaxy/commit/ca733d33f9c52a630a30132d2497… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-18 (Fri, 18 Sep 2015) Changed paths: M lib/galaxy/datatypes/binary.py M test/api/helpers.py M test/functional/tools/output_format.xml Log Message: ----------- Merge pull request #752 from nsoranzo/dev Fixes for #744. Commit: b2e9c8a36f9b1ba394b0d27bdc8287880abe27cd https://github.com/galaxyproject/galaxy/commit/b2e9c8a36f9b1ba394b0d27bdc82… Author: nitesh1989 <nitesh.turaga(a)gmail.com> Date: 2015-09-18 (Fri, 18 Sep 2015) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Fixed broken RData sniffer Commit: 304e569730c84f54176b06a175a49b7bce225325 https://github.com/galaxyproject/galaxy/commit/304e569730c84f54176b06a175a4… Author: nitesh1989 <nitesh.turaga(a)gmail.com> Date: 2015-09-18 (Fri, 18 Sep 2015) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Revert "Fixed broken RData sniffer" This reverts commit b2e9c8a36f9b1ba394b0d27bdc8287880abe27cd. Commit: ce9fe44b939a693a87b18ab4dfaa1dfff4a715f4 https://github.com/galaxyproject/galaxy/commit/ce9fe44b939a693a87b18ab4dfaa… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-09-18 (Fri, 18 Sep 2015) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/oxli_countgraph.oxlicg A lib/galaxy/datatypes/test/oxli_graphlabels.oxligl A lib/galaxy/datatypes/test/oxli_nodegraph.oxling A lib/galaxy/datatypes/test/oxli_stoptags.oxlist A lib/galaxy/datatypes/test/oxli_subset.oxliss A lib/galaxy/datatypes/test/oxli_tagset.oxlits Log Message: ----------- Merge pull request #721 from dib-lab/add-oxli-datatypes add Oxli datatypes Commit: 98f6dcc4dea061db7c04fbe8e2cd86898d10343b https://github.com/galaxyproject/galaxy/commit/98f6dcc4dea061db7c04fbe8e2cd… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-09-18 (Fri, 18 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/history/hdca-li.js M static/maps/mvc/history/hdca-li.js.map M static/scripts/mvc/history/hdca-li.js Log Message: ----------- Render HDCAs when their models change Commit: d4534bb814bb5716152dad8dfc9bfc53c3983ebb https://github.com/galaxyproject/galaxy/commit/d4534bb814bb5716152dad8dfc9b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-18 (Fri, 18 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/history/hdca-li.js M static/maps/mvc/history/hdca-li.js.map M static/scripts/mvc/history/hdca-li.js Log Message: ----------- Merge pull request #11 from carlfeberhard/jmchilton Render HDCAs when their models change Commit: cb303a46ef71c1b13d7760d2c8b840afff973b9e https://github.com/galaxyproject/galaxy/commit/cb303a46ef71c1b13d7760d2c8b8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-18 (Fri, 18 Sep 2015) Changed paths: M lib/galaxy/managers/hdas.py Log Message: ----------- Fix the fix I added to make the unit tests pass. Commit: 31c2d33ede1b97672ff0a05faa6928a8d05b1422 https://github.com/galaxyproject/galaxy/commit/31c2d33ede1b97672ff0a05faa69… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-09-19 (Sat, 19 Sep 2015) Changed paths: M lib/galaxy/managers/hdas.py Log Message: ----------- Merge pull request #756 from dannon/oops Fix lack of a return in hda manager Commit: 2b02677e85e57792a2aab52333ccc3f24c65393e https://github.com/galaxyproject/galaxy/commit/2b02677e85e57792a2aab52333cc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-19 (Sat, 19 Sep 2015) Changed paths: A test-data/3.bam M test/functional/tools/metadata_bam.xml Log Message: ----------- Workaround for metadata_bam.xml failure. Commit: c6be0bc12c6300f839d4b9dace05f567c493637d https://github.com/galaxyproject/galaxy/commit/c6be0bc12c6300f839d4b9dace05… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-19 (Sat, 19 Sep 2015) Changed paths: R test/functional/tools/compare_bam_as_sam.xml Log Message: ----------- Remove compare_bam_as_sam.xml test. It never passed, it was originally used by me to test failing tests compared output of bams as sam files. Now that we want all these tests to pass we need to rethink how to test that aspect of the testing framework. Commit: 45d5e29c1dcc30e896ed3fc408b2005a35d11ba6 https://github.com/galaxyproject/galaxy/commit/45d5e29c1dcc30e896ed3fc408b2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-19 (Sat, 19 Sep 2015) Changed paths: M test/api/test_tools.py Log Message: ----------- Extend test_map_over_two_collections timeout. May be the cause of intermittent test failure on jenkins (https://jenkins.galaxyproject.org/job/G-API/lastCompletedBuild/default/test…) Commit: 69f4ace0bcdaedc4f2077baeaffe605eb7538d79 https://github.com/galaxyproject/galaxy/commit/69f4ace0bcdaedc4f2077baeaffe… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-19 (Sat, 19 Sep 2015) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Fix failing workflow to_dict editor test. Generating form HTML as part of this request requires a history now (since https://github.com/galaxyproject/galaxy/commit/a00461eaf61bdeeea0c42b8098ae…) This is a less than ideal since it should definitely not require a history, but it is also less than idea to be shipping HTML via the API for non-web transactions. So rather than solving the former problem, this solves the latter and just doesn't attach form HTML for API requests. Fixes #734. Commit: c7d7736472d06b4b8df169f6017f7a4afe97d7b3 https://github.com/galaxyproject/galaxy/commit/c7d7736472d06b4b8df169f6017f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-19 (Sat, 19 Sep 2015) Changed paths: A test-data/3.bam R test/functional/tools/compare_bam_as_sam.xml M test/functional/tools/metadata_bam.xml Log Message: ----------- Merge pull request #757 from jmchilton/framework_tests Fix failing framework tests. Commit: 134c985f90a538eef623e6bc58c540228658d599 https://github.com/galaxyproject/galaxy/commit/134c985f90a538eef623e6bc58c5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-19 (Sat, 19 Sep 2015) Changed paths: M run_tests.sh M test/docker/README.md M test/docker/base/Dockerfile Log Message: ----------- Updates and fixes for dockerized Galaxy testing. Commit: 2e55eb11e5513cf76cb970e16ea2102bc557865a https://github.com/galaxyproject/galaxy/commit/2e55eb11e5513cf76cb970e16ea2… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-19 (Sat, 19 Sep 2015) Changed paths: M lib/galaxy/managers/workflows.py M test/api/test_tools.py Log Message: ----------- Merge pull request #758 from jmchilton/framework_tests API Test Fixes Commit: 1f1eed0e05600e7d89e36a0b152c87d609c85a3d https://github.com/galaxyproject/galaxy/commit/1f1eed0e05600e7d89e36a0b152c… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-19 (Sat, 19 Sep 2015) Changed paths: M run_tests.sh M test/docker/README.md M test/docker/base/Dockerfile Log Message: ----------- Merge pull request #759 from jmchilton/dockerize_test Updates and fixes for dockerized Galaxy testing. Commit: 311100ff9e40128b4da158fbb404a0b781765e11 https://github.com/galaxyproject/galaxy/commit/311100ff9e40128b4da158fbb404… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-21 (Mon, 21 Sep 2015) Changed paths: M test/base/interactor.py Log Message: ----------- Bugfix in test error reporting handling code. The code for showing status of histories in error would fail if there are collections in the history. This fixes that and skips over collections. Commit: 07dd69edd5472afef305fb170f18628a0cf3402d https://github.com/galaxyproject/galaxy/commit/07dd69edd5472afef305fb170f18… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-21 (Mon, 21 Sep 2015) Changed paths: M lib/galaxy/tools/parameters/output_collect.py M test/functional/tools/multi_output_configured.xml Log Message: ----------- Allow discover_datasets tag to use format attribute (instead of ext). https://github.com/TGAC/tgac-galaxytools/commit/93514438cb50fab48d0e211f1e1…. Commit: 2bfc12d666946a3e057aa3801fde2df90c6ab990 https://github.com/galaxyproject/galaxy/commit/2bfc12d666946a3e057aa3801fde… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-09-21 (Mon, 21 Sep 2015) Changed paths: M test/base/interactor.py Log Message: ----------- Merge pull request #760 from jmchilton/test_error Bugfix in test error reporting handling code. Commit: 87d5063a0dff35d6cddda3f17a8cadb6b04ff5e9 https://github.com/galaxyproject/galaxy/commit/87d5063a0dff35d6cddda3f17a8c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-21 (Mon, 21 Sep 2015) Changed paths: M lib/galaxy/tools/parameters/basic.py M test/api/test_tools.py M test/functional/tools/multi_data_param.xml Log Message: ----------- Implement min/max for multiple data input parameters. Commit: b9913d29316de4058197739b2ae4cfed5c5ae2f3 https://github.com/galaxyproject/galaxy/commit/b9913d29316de4058197739b2ae4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-21 (Mon, 21 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-form-base.js M static/maps/mvc/tools/tools-form-base.js.map M static/scripts/mvc/tools/tools-form-base.js Log Message: ----------- Swap tool form to use Galaxy.modal Commit: 83bd9dd541079f0571b90044e1a64d8318377039 https://github.com/galaxyproject/galaxy/commit/83bd9dd541079f0571b90044e1a6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-21 (Mon, 21 Sep 2015) Changed paths: M static/maps/mvc/tools/tools-form-base.js.map M static/scripts/mvc/tools/tools-form-base.js Log Message: ----------- repack without --develop Commit: b89c6e56a5559186d126afdf09ea1565a146f178 https://github.com/galaxyproject/galaxy/commit/b89c6e56a5559186d126afdf09ea… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-21 (Mon, 21 Sep 2015) Changed paths: M lib/galaxy/tools/errors.py Log Message: ----------- When submitting tool error reports, include 'old' tool id as part of subject line. Makes sifting through bug report emails easier, old id is used for brevity, but full guid is still included in text of report. Commit: c7394bd0b31f4ecab36a144897e26871eedde008 https://github.com/galaxyproject/galaxy/commit/c7394bd0b31f4ecab36a144897e2… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-21 (Mon, 21 Sep 2015) Changed paths: M lib/galaxy/tools/errors.py Log Message: ----------- Merge pull request #761 from blankenberg/error-tool-id When submitting tool error reports, include 'old' tool id as part of subject line. Commit: 56f10c9a1d7fa984aa1c286abaf4fadd26f1746a https://github.com/galaxyproject/galaxy/commit/56f10c9a1d7fa984aa1c286abaf4… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-21 (Mon, 21 Sep 2015) Changed paths: M lib/galaxy/tools/errors.py Log Message: ----------- make except catch just Exceptions, not everything I am not sure when these are hapenning (error initialized with encoded id & tool without id) but this should be safe fix Commit: 4525b4b911fcaaf6ce2daed04cdd25c7bea2d24e https://github.com/galaxyproject/galaxy/commit/4525b4b911fcaaf6ce2daed04cdd… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-21 (Mon, 21 Sep 2015) Changed paths: M lib/galaxy/tools/errors.py Log Message: ----------- Merge pull request #763 from martenson/fix-bare-exceptions make except catch just Exceptions, not everything Commit: 5e419197d1da6122d51ded0c1782d5b1c59126ee https://github.com/galaxyproject/galaxy/commit/5e419197d1da6122d51ded0c1782… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-09-21 (Mon, 21 Sep 2015) Changed paths: M lib/galaxy/tools/parameters/output_collect.py M test/functional/tools/multi_output_configured.xml Log Message: ----------- Merge pull request #764 from jmchilton/format_discover Allow discover_datasets tag to use format attribute (instead of ext). Commit: 7ca661bb010e4106e4fac910612810b99f741805 https://github.com/galaxyproject/galaxy/commit/7ca661bb010e4106e4fac9106128… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-21 (Mon, 21 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-form-base.js M static/maps/mvc/tools/tools-form-base.js.map M static/scripts/mvc/tools/tools-form-base.js Log Message: ----------- Fix for displaying tool form errors caused by http exceptions and when tool form doesn't exist. Commit: aed76f3744aba7b6c83659a9ad7dd079b9be1b70 https://github.com/galaxyproject/galaxy/commit/aed76f3744aba7b6c83659a9ad7d… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-21 (Mon, 21 Sep 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py Log Message: ----------- Do not attempt to rerun non-rerunable tools. Commit: fb54be77678c409d12e935b28ee7068c18999263 https://github.com/galaxyproject/galaxy/commit/fb54be77678c409d12e935b28ee7… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-09-21 (Mon, 21 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-form-base.js M lib/galaxy/webapps/galaxy/api/jobs.py M static/maps/mvc/tools/tools-form-base.js.map M static/scripts/mvc/tools/tools-form-base.js Log Message: ----------- Merge pull request #766 from blankenberg/toolform-rerun Tool form error messages and rerun fixes Commit: acfd8673b6817cc9d4b94947bb13293d1e384968 https://github.com/galaxyproject/galaxy/commit/acfd8673b6817cc9d4b94947bb13… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-21 (Mon, 21 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-form-base.js M lib/galaxy/tools/errors.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/webapps/galaxy/api/jobs.py M static/maps/mvc/tools/tools-form-base.js.map M static/scripts/mvc/tools/tools-form-base.js M test/functional/tools/multi_output_configured.xml Log Message: ----------- Merge from dev." Commit: 248ce3075b24a8da4e4142244f81c82c63a4cbff https://github.com/galaxyproject/galaxy/commit/248ce3075b24a8da4e4142244f81… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-09-22 (Tue, 22 Sep 2015) Changed paths: M lib/galaxy/tools/parameters/basic.py M test/api/test_tools.py M test/functional/tools/multi_data_param.xml Log Message: ----------- Merge pull request #765 from jmchilton/multi_min_max Implement min/max for multiple data input parameters. Commit: aeda77c6005f58f4df2939098151d376bf6515a9 https://github.com/galaxyproject/galaxy/commit/aeda77c6005f58f4df2939098151… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-22 (Tue, 22 Sep 2015) Changed paths: M templates/webapps/galaxy/root/index.mako Log Message: ----------- Add "Galaxy" title to templates/webapps/galaxy/root/index.mako Commit: 419d94e8b05c3d5979415c46671126422f5d68ad https://github.com/galaxyproject/galaxy/commit/419d94e8b05c3d5979415c466711… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-22 (Tue, 22 Sep 2015) Changed paths: M templates/webapps/galaxy/root/index.mako Log Message: ----------- Merge pull request #769 from blankenberg/ui-fixes Add "Galaxy" title to templates/webapps/galaxy/root/index.mako Commit: 3d697937c7f9d3aff0178f013692d795c3b73eb6 https://github.com/galaxyproject/galaxy/commit/3d697937c7f9d3aff0178f013692… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-22 (Tue, 22 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M lib/galaxy/managers/hdas.py M static/maps/mvc/dataset/dataset-li-edit.js.map M static/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Rerun improvement -- instead of allowing someone to try to rerun the upload tool and showing an error message, just don't provide the option for it in the first place. Commit: 7b7359b57ba213049d1c4f4a3cfa363f4a70a2b9 https://github.com/galaxyproject/galaxy/commit/7b7359b57ba213049d1c4f4a3cfa… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-22 (Tue, 22 Sep 2015) Changed paths: M .ci/flake8_blacklist.txt M lib/galaxy/webapps/tool_shed/model/migrate/versions/0001_initial_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0002_add_tool_suite_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0003_review_and_review_association_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0004_repository_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0005_drop_tool_related_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0006_add_email_alerts_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0007_add_long_description_times_downloaded_columns.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0008_add_repository_metadata_table.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0009_add_malicious_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0010_add_new_repo_alert_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0011_add_tool_versions_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0012_add_downloadable_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0013_add_review_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0014_add_deprecated_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0015_add_api_keys_table.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0016_add_do_not_test_tools_functionally_correct_errors_columns.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0017_add_galaxy_utility_columns_to_repository_metadata_table.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0018_add_repository_metadata_flag_columns.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0019_add_skip_tool_test_table_and_test_install_error_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0020_add_repository_type_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0021_change_repository_type_value.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0022_add_repository_admin_roles.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0023_add_repository_url_and_hompeage_url.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0024_password_reset.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0025_session_timeout.py Log Message: ----------- flake8 lib/galaxy/webapps/tool_shed/model/migrate/versions/ . Fix 227 linting errors. Commit: b2433f077d0de6925792e9e2c3d04cfa13308d8d https://github.com/galaxyproject/galaxy/commit/b2433f077d0de6925792e9e2c3d0… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-22 (Tue, 22 Sep 2015) Changed paths: M lib/galaxy/tools/errors.py Log Message: ----------- Add encoded IDs to job error reports and also include a direct link to dataset's show_params. Commit: eac449ed1e733cb0aa01b527a2518dc712efe443 https://github.com/galaxyproject/galaxy/commit/eac449ed1e733cb0aa01b527a251… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-22 (Tue, 22 Sep 2015) Changed paths: M lib/galaxy/tools/errors.py Log Message: ----------- white space fix Commit: 21f777d6081565fc1abfcc8a6aa91d163667db9d https://github.com/galaxyproject/galaxy/commit/21f777d6081565fc1abfcc8a6aa9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-22 (Tue, 22 Sep 2015) Changed paths: M lib/galaxy/tools/errors.py Log Message: ----------- Merge pull request #771 from blankenberg/error-report Add encoded IDs to job error reports and also include a link to show_params Commit: 02e61226b5681186426809d3497fdb2f0d46e466 https://github.com/galaxyproject/galaxy/commit/02e61226b5681186426809d3497f… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-22 (Tue, 22 Sep 2015) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- In log of collecting job metrics, print id, if available, in addition to the string representation of the has_metrics object. Commit: 03062478a9c381514a61240f25f54681f3cc733c https://github.com/galaxyproject/galaxy/commit/03062478a9c381514a61240f25f5… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-22 (Tue, 22 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M lib/galaxy/managers/libraries.py M lib/galaxy/model/__init__.py M lib/galaxy/util/__init__.py M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- expose lib create time; show error message when deleting folders Commit: fe642fe7fa66a53b4fbb1f89e200c10ead7854a6 https://github.com/galaxyproject/galaxy/commit/fe642fe7fa66a53b4fbb1f89e200… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-22 (Tue, 22 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-jobs.js M static/maps/mvc/tools/tools-jobs.js.map M static/scripts/mvc/tools/tools-jobs.js Log Message: ----------- Tweak tool execution to automatically pull detail ids for new hdas on execution success model update so rerun can be immediate. Commit: c96f0e35859beecfc76df92dee4ed11bece438bb https://github.com/galaxyproject/galaxy/commit/c96f0e35859beecfc76df92dee4e… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-22 (Tue, 22 Sep 2015) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Quote value to fix configparser error Commit: 130b3f2d75f7f6af4087078f4f653c3ee645774b https://github.com/galaxyproject/galaxy/commit/130b3f2d75f7f6af4087078f4f65… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Add docker command wrapper. For example, to change the current group to docker, which is needed when user belongs to (too) many groups) Commit: ce16573897ca471e8fd431029ae19861439bce5c https://github.com/galaxyproject/galaxy/commit/ce16573897ca471e8fd431029ae1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Merge remote-tracking branch 'jmchilton/release_15.07' into sniff_test Commit: 684be5f6a5c4ac91d6df2c5ec4f1e2866a538965 https://github.com/galaxyproject/galaxy/commit/684be5f6a5c4ac91d6df2c5ec4f1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M test/api/helpers.py M test/api/test_tools.py M test/base/test_data.py M test/base/twilltestcase.py Log Message: ----------- Functional test to verify RData is not decompressed in upload process. Commit: 91da5f806805fcc3661f985d843793f1785b7e64 https://github.com/galaxyproject/galaxy/commit/91da5f806805fcc3661f985d8437… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge pull request #775 from erasche/462-followup Quote value to fix configparser error in GIEs Commit: 292642ed91de908bf4e1e3f8705147bc7fd2ca1b https://github.com/galaxyproject/galaxy/commit/292642ed91de908bf4e1e3f87051… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/upload/default/default-row.js M static/maps/mvc/upload/default/default-row.js.map M static/scripts/mvc/upload/default/default-row.js Log Message: ----------- Fix upload event binding to be input and change instead of just relying on keyup. This fixes https://github.com/galaxyproject/galaxy/issues/762 Commit: 8b404205c07bcc7971cdc3d38cb369a0fc7d4940 https://github.com/galaxyproject/galaxy/commit/8b404205c07bcc7971cdc3d38cb3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M client/grunt-tasks/scripts.js M static/maps/galaxy.interactive_environments.js.map M static/maps/libs/jquery/jqtouch.js.map M static/maps/libs/raven.js.map M static/maps/libs/toastr.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/data.js.map M static/maps/mvc/dataset/dataset-choice.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-repeat.js.map M static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/job/job-model.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/list/list-panel.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/tools/tools-form-workflow.js.map M static/maps/mvc/tools/tools-jobs.js.map M static/maps/mvc/ui/ui-frames.js.map M static/maps/mvc/ui/ui-select.js.map M static/maps/utils/deferred.js.map M static/maps/utils/graph.js.map M static/maps/utils/metrics-logger.js.map M static/maps/utils/uploadbox.js.map M static/maps/utils/utils.js.map M static/maps/viz/trackster.js.map M static/maps/viz/trackster/filters.js.map M static/maps/viz/visualization.js.map M static/scripts/galaxy.interactive_environments.js M static/scripts/libs/jquery/jqtouch.js M static/scripts/libs/raven.js M static/scripts/libs/toastr.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/data.js M static/scripts/mvc/dataset/dataset-choice.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-select-content.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/job/job-model.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/list/list-panel.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/tools/tools-form-workflow.js M static/scripts/mvc/tools/tools-jobs.js M static/scripts/mvc/ui/ui-frames.js M static/scripts/mvc/ui/ui-select.js M static/scripts/utils/deferred.js M static/scripts/utils/graph.js M static/scripts/utils/metrics-logger.js M static/scripts/utils/uploadbox.js M static/scripts/utils/utils.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/visualization.js Log Message: ----------- Resolve client merge conflict, repack. Commit: 76a683e878246b54e14dc4f9fcf3d17916b17564 https://github.com/galaxyproject/galaxy/commit/76a683e878246b54e14dc4f9fcf3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M client/grunt-tasks/scripts.js M lib/galaxy/web/base/interactive_environments.py M static/maps/galaxy.interactive_environments.js.map M static/maps/libs/jquery/jqtouch.js.map M static/maps/libs/raven.js.map M static/maps/libs/toastr.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/data.js.map M static/maps/mvc/dataset/dataset-choice.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-repeat.js.map M static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/job/job-model.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/list/list-panel.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/tools/tools-form-workflow.js.map M static/maps/mvc/tools/tools-jobs.js.map M static/maps/mvc/ui/ui-frames.js.map M static/maps/mvc/ui/ui-select.js.map M static/maps/utils/deferred.js.map M static/maps/utils/graph.js.map M static/maps/utils/metrics-logger.js.map M static/maps/utils/uploadbox.js.map M static/maps/utils/utils.js.map M static/maps/viz/trackster.js.map M static/maps/viz/trackster/filters.js.map M static/maps/viz/visualization.js.map M static/scripts/galaxy.interactive_environments.js M static/scripts/libs/jquery/jqtouch.js M static/scripts/libs/raven.js M static/scripts/libs/toastr.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/data.js M static/scripts/mvc/dataset/dataset-choice.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-select-content.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/job/job-model.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/list/list-panel.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/tools/tools-form-workflow.js M static/scripts/mvc/tools/tools-jobs.js M static/scripts/mvc/ui/ui-frames.js M static/scripts/mvc/ui/ui-select.js M static/scripts/utils/deferred.js M static/scripts/utils/graph.js M static/scripts/utils/metrics-logger.js M static/scripts/utils/uploadbox.js M static/scripts/utils/utils.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/visualization.js Log Message: ----------- Merge branch 'dev' into upload_fix Commit: 61fda5f23dce31da353bbee209c8cf260427a400 https://github.com/galaxyproject/galaxy/commit/61fda5f23dce31da353bbee209c8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: A test-data/1.RData Log Message: ----------- Add missing file from previous commit. Commit: 2ee34167921a92a8c14c3f1694e43bce3efc27cf https://github.com/galaxyproject/galaxy/commit/2ee34167921a92a8c14c3f1694e4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M static/maps/mvc/upload/composite/composite-row.js.map M static/scripts/mvc/upload/composite/composite-row.js Log Message: ----------- One more location where keyup should be replaced Commit: e9ddc21661ffe27ed87e04a6c852c9914a22bacc https://github.com/galaxyproject/galaxy/commit/e9ddc21661ffe27ed87e04a6c852… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Merge pull request #772 from blankenberg/job-metrics In log of collecting job metrics, print id of has_metrics object Commit: 6804ce681be29baca1c1d50737b427b95b0a66ee https://github.com/galaxyproject/galaxy/commit/6804ce681be29baca1c1d50737b4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M client/grunt-tasks/scripts.js M lib/galaxy/tools/errors.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/web/base/interactive_environments.py M static/maps/galaxy.interactive_environments.js.map M static/maps/libs/jquery/jqtouch.js.map M static/maps/libs/raven.js.map M static/maps/libs/toastr.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/data.js.map M static/maps/mvc/dataset/dataset-choice.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-repeat.js.map M static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/job/job-model.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/list/list-panel.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/tools/tools-form-workflow.js.map M static/maps/mvc/tools/tools-jobs.js.map M static/maps/mvc/ui/ui-frames.js.map M static/maps/mvc/ui/ui-select.js.map M static/maps/utils/deferred.js.map M static/maps/utils/graph.js.map M static/maps/utils/metrics-logger.js.map M static/maps/utils/uploadbox.js.map M static/maps/utils/utils.js.map M static/maps/viz/trackster.js.map M static/maps/viz/trackster/filters.js.map M static/maps/viz/visualization.js.map M static/scripts/galaxy.interactive_environments.js M static/scripts/libs/jquery/jqtouch.js M static/scripts/libs/raven.js M static/scripts/libs/toastr.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/data.js M static/scripts/mvc/dataset/dataset-choice.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-select-content.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/job/job-model.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/list/list-panel.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/tools/tools-form-workflow.js M static/scripts/mvc/tools/tools-jobs.js M static/scripts/mvc/ui/ui-frames.js M static/scripts/mvc/ui/ui-select.js M static/scripts/utils/deferred.js M static/scripts/utils/graph.js M static/scripts/utils/metrics-logger.js M static/scripts/utils/uploadbox.js M static/scripts/utils/utils.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/visualization.js M templates/webapps/galaxy/root/index.mako M test/api/test_tools.py M test/functional/tools/multi_data_param.xml Log Message: ----------- Merge dev, resolve conflicts from console re-enablement. Commit: 6a450b9c31788586ec6d781984a145c7ce570d8a https://github.com/galaxyproject/galaxy/commit/6a450b9c31788586ec6d781984a1… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/default/default-row.js M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/default/default-row.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/default/default-row.js Log Message: ----------- Merge pull request #778 from dannon/upload_fix Fix upload event binding to be input and change instead of just relyi… Commit: 54c4861b0d0f405b3c12348d40ed29fab8ff03b1 https://github.com/galaxyproject/galaxy/commit/54c4861b0d0f405b3c12348d40ed… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- space issue fixed Commit: 53f7ac02d23939c8b17ad93ead787527dc1c805b https://github.com/galaxyproject/galaxy/commit/53f7ac02d23939c8b17ad93ead78… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-form-base.js M static/maps/mvc/tools/tools-form-base.js.map M static/scripts/mvc/tools/tools-form-base.js Log Message: ----------- Don't use a local reference to modal -- the intent here was to allow component-isolated modals as in other places, but we can do (or not) that at a later time. Commit: 3167b426265d89e500fe50cd145004cdb5d4bc5c https://github.com/galaxyproject/galaxy/commit/3167b426265d89e500fe50cd1450… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/grunt-tasks/scripts.js M lib/galaxy/jobs/__init__.py M lib/galaxy/web/base/interactive_environments.py M static/maps/galaxy.interactive_environments.js.map M static/maps/libs/jquery/jqtouch.js.map M static/maps/libs/raven.js.map M static/maps/libs/toastr.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/data.js.map M static/maps/mvc/dataset/dataset-choice.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-repeat.js.map M static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/job/job-model.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/list/list-panel.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/tools/tools-form-workflow.js.map M static/maps/mvc/tools/tools-jobs.js.map M static/maps/mvc/ui/ui-frames.js.map M static/maps/mvc/ui/ui-select.js.map M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/default/default-row.js.map M static/maps/utils/deferred.js.map M static/maps/utils/graph.js.map M static/maps/utils/metrics-logger.js.map M static/maps/utils/uploadbox.js.map M static/maps/utils/utils.js.map M static/maps/viz/trackster.js.map M static/maps/viz/trackster/filters.js.map M static/maps/viz/visualization.js.map M static/scripts/galaxy.interactive_environments.js M static/scripts/libs/jquery/jqtouch.js M static/scripts/libs/raven.js M static/scripts/libs/toastr.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/data.js M static/scripts/mvc/dataset/dataset-choice.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-select-content.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/job/job-model.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/list/list-panel.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/tools/tools-form-workflow.js M static/scripts/mvc/tools/tools-jobs.js M static/scripts/mvc/ui/ui-frames.js M static/scripts/mvc/ui/ui-select.js M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/default/default-row.js M static/scripts/utils/deferred.js M static/scripts/utils/graph.js M static/scripts/utils/metrics-logger.js M static/scripts/utils/uploadbox.js M static/scripts/utils/utils.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/visualization.js Log Message: ----------- fixed merge conflict - but is this correct? Commit: 183e5cd7c6fe20cb9682fa78260c6466c9851497 https://github.com/galaxyproject/galaxy/commit/183e5cd7c6fe20cb9682fa78260c… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge pull request #777 from scholtalbers/docker-cmd-wrapper Add docker command wrapper. Commit: dc0dd6ec4b7a5f47595d43133e5f9d3d999a7e15 https://github.com/galaxyproject/galaxy/commit/dc0dd6ec4b7a5f47595d43133e5f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M static/maps/mvc/dataset/dataset-li-edit.js.map M static/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Simplify logic. Commit: 15a516b57799e61eaca90a3b7d9dc188a012b808 https://github.com/galaxyproject/galaxy/commit/15a516b57799e61eaca90a3b7d9d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M static/maps/mvc/dataset/dataset-li-edit.js.map M static/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Remove 'disabled' cruft, since we opted to simply not show the button rather than disable it. Commit: 52dfd589b986397852d6700a4ca8d8afa7235416 https://github.com/galaxyproject/galaxy/commit/52dfd589b986397852d6700a4ca8… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Unify the docker command, command_inject, and command_wrapper Commit: e4c1e8b23226f901495ab4d3ab3689d5bc2344af https://github.com/galaxyproject/galaxy/commit/e4c1e8b23226f901495ab4d3ab36… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: A static/maps/mvc/upload/upload-row.js.map A static/scripts/mvc/upload/upload-row.js Log Message: ----------- Merge master->dev Commit: 56ac2c0f137523c320ca12c684579b75d4b76dfc https://github.com/galaxyproject/galaxy/commit/56ac2c0f137523c320ca12c68457… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Revert command inject and document rationale Commit: 595d7d5fd8f0efc51b93e35018839831f6eac7f7 https://github.com/galaxyproject/galaxy/commit/595d7d5fd8f0efc51b93e3501883… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/scripts/mvc/tools/tools-jobs.js M lib/galaxy/managers/hdas.py M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/tools/tools-jobs.js.map M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/tools/tools-jobs.js Log Message: ----------- Merge pull request #781 from dannon/rerun_tweaks Rerun/toolform tweaks Commit: a90a4fcebaee0a1c975bf0c90598bd72a7e7f833 https://github.com/galaxyproject/galaxy/commit/a90a4fcebaee0a1c975bf0c90598… Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/history/hdca-li.js M lib/galaxy/model/__init__.py M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/history/hdca-li.js.map M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/history/hdca-li.js M test/api/test_dataset_collections.py Log Message: ----------- Merge pull request #755 from jmchilton/hdca_structure_state_tracking Improved state tracking of HDCA in history panel. Commit: 484578936bc7ee04c6b28cb848772a4b6ded2b03 https://github.com/galaxyproject/galaxy/commit/484578936bc7ee04c6b28cb84877… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M config/plugins/interactive_environments/ipython/templates/ipython.mako M config/plugins/interactive_environments/rstudio/templates/rstudio.mako M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Refactor to use -P This is a major refactoring to use the -P option of docker which should simplify some of our deployment like running docker containers on another host. In support of #372 Commit: 175f89bdc8df1550d34bc5084df45185ef633057 https://github.com/galaxyproject/galaxy/commit/175f89bdc8df1550d34bc5084df4… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Hardcode defaults, per @jmchilton's comments Commit: bab1e3b562814c4091200e27ff579c6c54502a13 https://github.com/galaxyproject/galaxy/commit/bab1e3b562814c4091200e27ff57… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M lib/galaxy/managers/folders.py M lib/galaxy/managers/libraries.py Log Message: ----------- add update method to folder manager; update root folder name when lib name is updated; refactor exception imports Commit: 04c5e6864cc77fa1952d1acd88bac5df93f5ac44 https://github.com/galaxyproject/galaxy/commit/04c5e6864cc77fa1952d1acd88ba… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge branch 'gie-docker-cmd' into gie-docker-launch Commit: c9e9c95514e50f9a260b5ed342a715d2846fd4fe https://github.com/galaxyproject/galaxy/commit/c9e9c95514e50f9a260b5ed342a7… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Correct small logic bugs, add logging Commit: a02df53f3356a03f3784070a4c50accfbc00187f https://github.com/galaxyproject/galaxy/commit/a02df53f3356a03f3784070a4c50… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M config/plugins/interactive_environments/ipython/templates/ipython.mako Log Message: ----------- Correct IPython notebooks to new URL Commit: a5b296b8ecd262d58a17049f5a9aeeecb7649621 https://github.com/galaxyproject/galaxy/commit/a5b296b8ecd262d58a17049f5a9a… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Include user email Fixes bgruening/docker-ipython-notebook#51 Commit: 38823c61db7b3d43c620752dc215dc5af6f76576 https://github.com/galaxyproject/galaxy/commit/38823c61db7b3d43c620752dc215… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M lib/galaxy/datatypes/binary.py M test/api/helpers.py M test/api/test_tools.py M test/base/test_data.py M test/base/twilltestcase.py Log Message: ----------- Merge pull request #784 from jmchilton/sniff_test Test case to prevent regression of #753. Commit: b28810444d60dabccee8239a8bff0febc3fc8876 https://github.com/galaxyproject/galaxy/commit/b28810444d60dabccee8239a8bff… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M lib/galaxy/managers/folders.py M lib/galaxy/webapps/galaxy/api/folders.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- expose API to update lib folder; make manager not update when nothing changes Commit: bf0ab52e75e7a51f696262bc33b1d82ba4acd98c https://github.com/galaxyproject/galaxy/commit/bf0ab52e75e7a51f696262bc33b1… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: A test-data/1.RData Log Message: ----------- Merge pull request #787 from jmchilton/sniff_test Add missing file from #784 Commit: 10af45012735603385ac076f7b517dfe70314484 https://github.com/galaxyproject/galaxy/commit/10af45012735603385ac076f7b51… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Move run into python from template Commit: a76ba39321e71cab8a0ecd3a610bcd861827815c https://github.com/galaxyproject/galaxy/commit/a76ba39321e71cab8a0ecd3a610b… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Update against gie-docker-cmd Commit: d7bff96778b11a3ed2838103aea6cceca43bdfb4 https://github.com/galaxyproject/galaxy/commit/d7bff96778b11a3ed2838103aea6… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Correct stupid mistake from lack of testing Commit: 06a67c8c109dcf59425b53b80dcb5419f5e814af https://github.com/galaxyproject/galaxy/commit/06a67c8c109dcf59425b53b80dcb… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/web/proxy/__init__.py Log Message: ----------- Add dynamic_proxy_prefix configuration Normally the proxy binds to :8800 and runs containers under :8800/ipython/... which is great... until you have an upstream proxy like apache wrapping that at the url FQDN/ipython and suddenly your cookies aren't available because they're specific to /galaxy. Thus, when an upstream proxy is in use, we correct the proxy's path to: with :8800/{cookie_path}/gie_proxy/ipython/... which behaves much more nicely with upstraem proxies. Commit: 5a2b1ec322f0808ba4e7925effe87a467f6b467a https://github.com/galaxyproject/galaxy/commit/5a2b1ec322f0808ba4e7925effe8… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge branch 'gie-docker-cmd' into gie-docker-launch Commit: 1ad3308b49a6f5a25ef357300b47791987acbb22 https://github.com/galaxyproject/galaxy/commit/1ad3308b49a6f5a25ef357300b47… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample Log Message: ----------- Remove small formatting issue Commit: 1d78033625259bc50413393422feab38116b8884 https://github.com/galaxyproject/galaxy/commit/1d78033625259bc50413393422fe… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample Log Message: ----------- Merge branch 'gie-docker-cmd' into gie-docker-launch Commit: 57f023529aef13723cb1555dc3ad5ea59aef009c https://github.com/galaxyproject/galaxy/commit/57f023529aef13723cb1555dc3ad… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-analysis.js M client/galaxy/scripts/mvc/app/app-view.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/scripts/mvc/tools/tools-form.js M lib/galaxy/tools/__init__.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/controllers/tool_runner.py M static/maps/mvc/app/app-analysis.js.map M static/maps/mvc/app/app-view.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/tools/tools-form.js.map M static/scripts/mvc/app/app-analysis.js M static/scripts/mvc/app/app-view.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/tools/tools-form.js R templates/webapps/galaxy/tool_form.mako M test/unit/tools/test_execution.py Log Message: ----------- Remove tool form mako Fix new-line Commit: e8db8a1932ab058d83331b547d9ef6e6e49bb934 https://github.com/galaxyproject/galaxy/commit/e8db8a1932ab058d83331b547d9e… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Add docker_galaxy_temp_dir This is useful for if the normal tmp dir is located on NFS. In this case it's useful to override the temporary directory with an sshfs mount for example. Commit: b1d642a6ecd324c6c519fb391f7747a05d709bb7 https://github.com/galaxyproject/galaxy/commit/b1d642a6ecd324c6c519fb391f77… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M config/plugins/interactive_environments/ipython/config/ipython.ini.sample Log Message: ----------- Update ipython.ini.sample Commit: a7c1c53f5352323abdb422fc8a9557e16e3f7993 https://github.com/galaxyproject/galaxy/commit/a7c1c53f5352323abdb422fc8a95… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample Log Message: ----------- Update rstudio.ini.sample Commit: 03ee295e7be09d53f7c1c3ff03988e0e82aa254d https://github.com/galaxyproject/galaxy/commit/03ee295e7be09d53f7c1c3ff0398… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge pull request #9 from erasche/docker_galaxy_temp_dir Add docker_galaxy_temp_dir Commit: b4bbd1c2f161959fabdb62962aa63fb630c1ca2d https://github.com/galaxyproject/galaxy/commit/b4bbd1c2f161959fabdb62962aa6… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M config/plugins/interactive_environments/ipython/templates/ipython.mako M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.py Log Message: ----------- Make use of proxy path in appropriate places Commit: 4a4a7ca51b195ac9d9a718448d65c89c02ae118c https://github.com/galaxyproject/galaxy/commit/4a4a7ca51b195ac9d9a718448d65… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M config/plugins/interactive_environments/rstudio/templates/rstudio.mako Log Message: ----------- Update URLs for rstudio Commit: baf25e07b809d1f7ce0c1c7b6b9b5f8ab7011a24 https://github.com/galaxyproject/galaxy/commit/baf25e07b809d1f7ce0c1c7b6b9b… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-24 (Thu, 24 Sep 2015) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Print has_metrics class name instead of object memory address. Commit: cc1d7a509cf75f49516c8e2a664cf81a15d1f7e9 https://github.com/galaxyproject/galaxy/commit/cc1d7a509cf75f49516c8e2a664c… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-24 (Thu, 24 Sep 2015) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Merge pull request #791 from nsoranzo/772_followup Print has_metrics class name instead of object memory address. Commit: f0ea4be88477d1baf3d4793af3fa173ec431a418 https://github.com/galaxyproject/galaxy/commit/f0ea4be88477d1baf3d4793af3fa… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-24 (Thu, 24 Sep 2015) Changed paths: M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge pull request #782 from erasche/gie-docker-cmd Unify the docker command, command_inject, and command_wrapper Commit: e8eb46b65d76a2b7645aa325e321d135df02e802 https://github.com/galaxyproject/galaxy/commit/e8eb46b65d76a2b7645aa325e321… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-09-24 (Thu, 24 Sep 2015) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Use a backport for check_output that is not part of python 2.6 Commit: fa0c3a4bbc9995b0f20638984d0395b442c33c92 https://github.com/galaxyproject/galaxy/commit/fa0c3a4bbc9995b0f20638984d03… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-24 (Thu, 24 Sep 2015) Changed paths: M test/api/test_workflows.py M test/functional/tools/min_repeat.xml Log Message: ----------- Implement failing workflow test case. For galaxyproject/galaxy#776. Commit: 0e521fd39822f9488392ef0485a40ded3606f0f2 https://github.com/galaxyproject/galaxy/commit/0e521fd39822f9488392ef0485a4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-24 (Thu, 24 Sep 2015) Changed paths: M lib/galaxy/workflow/run.py Log Message: ----------- Fix problem maintaining input maps when rescheduling workflows. Fixes #776. I suspect the problem has very little to do with dynamic output collections and in fact exhibits itself when workflow rescheduling occurs, it is just that workflow rescheduling is forced when using dynamic output collections. Commit: d4d439f51ebd2343e111d912499f336778e590c5 https://github.com/galaxyproject/galaxy/commit/d4d439f51ebd2343e111d912499f… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-24 (Thu, 24 Sep 2015) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge pull request #10 from erasche/check_output_backport Use a backport for check_output that is not part of python 2.6 Commit: 5f15b0d94c4a9703315f96fe3ce63b9b3906ea84 https://github.com/galaxyproject/galaxy/commit/5f15b0d94c4a9703315f96fe3ce6… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-24 (Thu, 24 Sep 2015) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Replace backported one with just the code used Sorry bjoern, ripped out what you'd added and just used the code because the doctest was failing for some unknown reason and we didn't ever need to reuse the function, so ... easier this way Commit: b58c7203d0b874ef2d266a96c33e44aabdec61ed https://github.com/galaxyproject/galaxy/commit/b58c7203d0b874ef2d266a96c33e… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-09-24 (Thu, 24 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/tools/tools-jobs.js M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/tools/tools-jobs.js.map M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/tools/tools-jobs.js Log Message: ----------- UI, datasets: Move support for rerunnable to dataset-li expansion; remove redundant listener set up Commit: e1aad977597996f0e60422ba8b3fdd0275cc56fe https://github.com/galaxyproject/galaxy/commit/e1aad977597996f0e60422ba8b3f… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-09-24 (Thu, 24 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li.js M static/maps/mvc/dataset/dataset-li.js.map M static/scripts/mvc/dataset/dataset-li.js Log Message: ----------- Fix to b58c720: add creating_job to info needed for re-run button Commit: 7f3ee5b1670b80ec2fa14943950eac7cfe5bbd76 https://github.com/galaxyproject/galaxy/commit/7f3ee5b1670b80ec2fa14943950e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-24 (Thu, 24 Sep 2015) Changed paths: M .gitignore M scripts/common_startup.sh R tool-data/shared/ucsc/manual_builds.txt A tool-data/shared/ucsc/manual_builds.txt.sample Log Message: ----------- Merge pull request #612 from lparsons/manual_builds Move manual_builds.txt to manual_builds.txt.sample Commit: ace8c8864b552f3104774c45ca13a6f057545625 https://github.com/galaxyproject/galaxy/commit/ace8c8864b552f3104774c45ca13… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-24 (Thu, 24 Sep 2015) Changed paths: M lib/galaxy/workflow/run.py M test/api/test_workflows.py M test/functional/tools/min_repeat.xml Log Message: ----------- Merge pull request #795 from jmchilton/workflow_output_collect Regression test case and fix for #776 Commit: 12ada39cdd17cb19bc16aa096a1d0984bac49e4e https://github.com/galaxyproject/galaxy/commit/12ada39cdd17cb19bc16aa096a1d… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-09-24 (Thu, 24 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li.js M static/maps/mvc/dataset/dataset-li.js.map M static/scripts/mvc/dataset/dataset-li.js Log Message: ----------- Fix to b58c720: only request creating_job and rerunnable Commit: 0428de04fba3fa695304a2a42d396ad64c7beb50 https://github.com/galaxyproject/galaxy/commit/0428de04fba3fa695304a2a42d39… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-24 (Thu, 24 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/tools/tools-jobs.js M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/tools/tools-jobs.js.map M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/tools/tools-jobs.js Log Message: ----------- Merge pull request #793 from carlfeberhard/fix.rerun-details-take2 UI, datasets: Move support for rerunnable to dataset-li expansion; re… Commit: f935d27bdfb4ff66e841de2667a40d3d65c0175d https://github.com/galaxyproject/galaxy/commit/f935d27bdfb4ff66e841de2667a4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M config/job_conf.xml.sample_advanced Log Message: ----------- Fix _JAVA_OPTIONS example in job_conf.xml. Thanks detailed bug report by Damion Dooley (http://dev.list.galaxyproject.org/JAVA-OPTIONS-config-parameter-in-job-conf…) Commit: 86c4263b344f1bdd3c316a579a30f157f88eadf7 https://github.com/galaxyproject/galaxy/commit/86c4263b344f1bdd3c316a579a30… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M test/unit/jobs/test_job_configuration.py Log Message: ----------- Fix unit tests broken with f935d27bdfb4ff66e841de2667a40d3d65c0175d. Commit: 5ff102507b7b461d404f5747532e21caf551ac9c https://github.com/galaxyproject/galaxy/commit/5ff102507b7b461d404f5747532e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M test/api/test_tools.py M test/functional/tools/validation_repeat.xml Log Message: ----------- Add regression test for issue in #798. Commit: 0fefff07b34c2b16793a3ae1c68849119abfa244 https://github.com/galaxyproject/galaxy/commit/0fefff07b34c2b16793a3ae1c688… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M config/job_conf.xml.sample_advanced Log Message: ----------- Merge pull request #796 from jmchilton/java_opts_doc Fix _JAVA_OPTIONS example in job_conf.xml.sample_advanced Commit: 6d3ea7ee0086707bbf3f6d54cfa0ee1e2221341c https://github.com/galaxyproject/galaxy/commit/6d3ea7ee0086707bbf3f6d54cfa0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M config/galaxy.ini.sample M config/plugins/interactive_environments/ipython/templates/ipython.mako M config/plugins/interactive_environments/rstudio/templates/rstudio.mako M lib/galaxy/config.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.py Log Message: ----------- Merge pull request #790 from erasche/gie-docker-launch Refactor GIE Launching to use -P Commit: a5610d6845f4bf016a0ac6a9a2d3d17a11e9b83b https://github.com/galaxyproject/galaxy/commit/a5610d6845f4bf016a0ac6a9a2d3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M test/unit/jobs/test_job_configuration.py Log Message: ----------- Merge pull request #797 from jmchilton/java_opts_doc Fix unit tests broken with f935d27bdfb4ff66e841de2667a40d3d65c0175d. Commit: 3fcf3210462a64ca3112295926240d04a99f3d24 https://github.com/galaxyproject/galaxy/commit/3fcf3210462a64ca311229592624… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Add sentry configuration option and doc to galaxy.ini.sample Commit: 3f91a9a381868910a1f5d3e8daf784dc960ffded https://github.com/galaxyproject/galaxy/commit/3f91a9a381868910a1f5d3e8daf7… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Merge pull request #799 from dannon/sample_sentry Add sentry configuration option and doc to galaxy.ini.sample Commit: ac8b5eae02155a7364e4131ba88d983c69bd000b https://github.com/galaxyproject/galaxy/commit/ac8b5eae02155a7364e4131ba88d… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M lib/galaxy/tools/parser/yaml.py M test/functional/tools/disambiguate_cond.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Fix errors when starting "./run_tests.sh -with_framework_test_tools -api" Commit: ba43e95f41c3220df05aac0be7bc117c6acda362 https://github.com/galaxyproject/galaxy/commit/ba43e95f41c3220df05aac0be7bc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M lib/galaxy/tools/parser/yaml.py M test/functional/tools/disambiguate_cond.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #800 from nsoranzo/functional_tests_fixes Fix errors when starting "./run_tests.sh -with_framework_test_tools -api" Commit: 0260d753c76d7305f6c1f05d08af43e61faa7641 https://github.com/galaxyproject/galaxy/commit/0260d753c76d7305f6c1f05d08af… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-25 (Fri, 25 Sep 2015) Log Message: ----------- Merge branch 'master' into dev Conflicts: config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample Commit: 6d5ee0b6c8c2eb8b343a4473e253bb14e34b1da0 https://github.com/galaxyproject/galaxy/commit/6d5ee0b6c8c2eb8b343a4473e253… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge branch 'master' into dev Commit: bd3e86c046bf5609b95a7b82f0751ee97bfd637c https://github.com/galaxyproject/galaxy/commit/bd3e86c046bf5609b95a7b82f075… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M test/api/test_tools.py M test/functional/tools/validation_repeat.xml Log Message: ----------- Merge pull request #801 from jmchilton/validator_repeat_test Add regression test for issue in #798. Commit: b6105acd2b7f0957c315a63bcf083a596189383b https://github.com/galaxyproject/galaxy/commit/b6105acd2b7f0957c315a63bcf08… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M doc/source/dev/faq.rst Log Message: ----------- merge... Commit: f7a68ec29567a4dc3067ab0b3bccdc6c32c975d3 https://github.com/galaxyproject/galaxy/commit/f7a68ec29567a4dc3067ab0b3bcc… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M .gitignore M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/scripts/mvc/tools/tools-jobs.js M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/ipython/templates/ipython.mako M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample M config/plugins/interactive_environments/rstudio/templates/rstudio.mako M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/jobs/__init__.py M lib/galaxy/managers/hdas.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/workflow/run.py M scripts/common_startup.sh M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/history/hdca-li.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/tools/tools-jobs.js.map A static/maps/mvc/upload/upload-row.js.map M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/tools/tools-jobs.js A static/scripts/mvc/upload/upload-row.js A test-data/1.RData M test/api/helpers.py M test/api/test_dataset_collections.py M test/api/test_tools.py M test/api/test_workflows.py M test/base/test_data.py M test/base/twilltestcase.py M test/functional/tools/disambiguate_cond.xml M test/functional/tools/min_repeat.xml M test/functional/tools/samples_tool_conf.xml M test/functional/tools/validation_repeat.xml M test/unit/jobs/test_job_configuration.py R tool-data/shared/ucsc/manual_builds.txt A tool-data/shared/ucsc/manual_builds.txt.sample Log Message: ----------- Merge branch 'dev' of github.com:galaxyproject/galaxy into dev Commit: 2166f876bc938e9837bbb974e24a670e1e12fe98 https://github.com/galaxyproject/galaxy/commit/2166f876bc938e9837bbb974e24a… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: A doc/source/admin/index.rst A doc/source/admin/interactive_environments.png A doc/source/admin/interactive_environments.rst A doc/source/admin/interactive_environments.svg M doc/source/index.rst Log Message: ----------- First draft of GIE admin docs Commit: 79c75e6e21aa894c949540160d87f1b7a6c43b39 https://github.com/galaxyproject/galaxy/commit/79c75e6e21aa894c949540160d87… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M doc/source/admin/interactive_environments.rst Log Message: ----------- Added docker-on-another-host Commit: 94c61f9f7f31189f3d7d265cf94fab198f5007b8 https://github.com/galaxyproject/galaxy/commit/94c61f9f7f31189f3d7d265cf94f… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M doc/source/admin/interactive_environments.rst Log Message: ----------- Add long tutorial on how-to-GIE Commit: 4b8f9b22a54f828075a7b574762ef0fc19e500dd https://github.com/galaxyproject/galaxy/commit/4b8f9b22a54f828075a7b574762e… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M doc/source/admin/interactive_environments.rst Log Message: ----------- Correct highlighting, and small bugs/typos Commit: 6db64967197b0ee7dff6c4df31d6281c89294720 https://github.com/galaxyproject/galaxy/commit/6db64967197b0ee7dff6c4df31d6… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M doc/source/admin/interactive_environments.rst Log Message: ----------- Correct docker_port/proxy_prefix Commit: ed0fefaa4339d8ec96e60c98befa3fa2e5ff07b4 https://github.com/galaxyproject/galaxy/commit/ed0fefaa4339d8ec96e60c98befa… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M doc/source/admin/interactive_environments.rst Log Message: ----------- Full list of env vars, more doc corrections Commit: 928345fad7aa16bd1c32133e9b571954faddd0f3 https://github.com/galaxyproject/galaxy/commit/928345fad7aa16bd1c32133e9b57… Author: Rémi Marenco <remi.marenco(a)gmail.com> Date: 2015-09-26 (Sat, 26 Sep 2015) Changed paths: M doc/source/admin/interactive_environments.rst Log Message: ----------- Fixed the image to show up The .* did not do the trick, added the .png extension so we could see the image. There is still the "interactive_environments_success.png" missing though! If you want me to take the picture, I can. Just need to know exactly what you want to show :p Commit: 98601084ec7f130f0b7dd27354648afd24cb1e78 https://github.com/galaxyproject/galaxy/commit/98601084ec7f130f0b7dd2735464… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-09-26 (Sat, 26 Sep 2015) Changed paths: M doc/source/admin/interactive_environments.rst Log Message: ----------- Merge pull request #11 from remimarenco/patch-1 Fixed the interactive_environments' image to show up Commit: 771376a742fc1a248cc2223acebb27f5fd24ba43 https://github.com/galaxyproject/galaxy/commit/771376a742fc1a248cc2223acebb… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-26 (Sat, 26 Sep 2015) Changed paths: A doc/source/admin/interactive_environments_success.png Log Message: ----------- Added success picture Commit: e81517bb9cefb7e4ddab991d3da59ae63619fd81 https://github.com/galaxyproject/galaxy/commit/e81517bb9cefb7e4ddab991d3da5… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-26 (Sat, 26 Sep 2015) Changed paths: M doc/source/admin/interactive_environments.rst Log Message: ----------- Merge branch 'gie-docs' of github.com:erasche/galaxy into gie-docs Commit: f5a6e25ebd9d96a709781291cf04bc9e461216c6 https://github.com/galaxyproject/galaxy/commit/f5a6e25ebd9d96a709781291cf04… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-28 (Mon, 28 Sep 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/tool_runner.py Log Message: ----------- Reinsert data_source tool execution into tool runner controller (requires separate PR) Commit: c1faf48d819ded4317995fe5f5ca436f847a4d09 https://github.com/galaxyproject/galaxy/commit/c1faf48d819ded4317995fe5f5ca… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-28 (Mon, 28 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/scripts/mvc/ui/ui-misc.js M static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/ui/ui-misc.js.map M static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/ui/ui-misc.js Log Message: ----------- Add large message style and use for initial tool loading notifications Commit: 7777ea8f91928a9dd2c581eed53ba7e2ed1f3255 https://github.com/galaxyproject/galaxy/commit/7777ea8f91928a9dd2c581eed53b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-28 (Mon, 28 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js M static/maps/mvc/ui/ui-misc.js.map M static/scripts/mvc/ui/ui-misc.js Log Message: ----------- Extend large ui-messages to cover states (info, warning, danger, success) Commit: d3b53544dffd0297f326f67757e11b153b898b3d https://github.com/galaxyproject/galaxy/commit/d3b53544dffd0297f326f67757e1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-28 (Mon, 28 Sep 2015) Changed paths: M lib/galaxy/tools/parser/yaml.py Log Message: ----------- Fix framework test failures. Some other fix caused the yaml example tool to load in the framework and api tests again after a long regression, this in turn caused a more recent regression to pop out in the framework test suite. This fixes that, thanks for the heads up @martenson. Commit: 796f803df0bc139b7ae3d1f7cf6d718da186cef7 https://github.com/galaxyproject/galaxy/commit/796f803df0bc139b7ae3d1f7cf6d… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-28 (Mon, 28 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-model.js M lib/galaxy/managers/folders.py M lib/galaxy/webapps/galaxy/api/folders.py M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-model.js.map M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-model.js Log Message: ----------- provide UI to delete and udelete lib folders; slight refactor Commit: 10c915bb62c69017a6cf7ffc18a90f196899feb9 https://github.com/galaxyproject/galaxy/commit/10c915bb62c69017a6cf7ffc18a9… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-28 (Mon, 28 Sep 2015) Changed paths: M .gitignore M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/scripts/mvc/tools/tools-jobs.js M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/grunt-tasks/scripts.js M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M 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static/scripts/viz/visualization.js A test-data/1.RData M test/api/helpers.py M test/api/test_dataset_collections.py M test/api/test_tools.py M test/api/test_workflows.py M test/base/test_data.py M test/base/twilltestcase.py M test/functional/tools/disambiguate_cond.xml M test/functional/tools/min_repeat.xml M test/functional/tools/samples_tool_conf.xml M test/functional/tools/validation_repeat.xml M test/unit/jobs/test_job_configuration.py R tool-data/shared/ucsc/manual_builds.txt A tool-data/shared/ucsc/manual_builds.txt.sample Log Message: ----------- Merge branch 'dev' into data-lib-work Conflicts: static/maps/mvc/library/library-foldertoolbar-view.js.map static/scripts/mvc/library/library-foldertoolbar-view.js also re-grunted Commit: b77c28cd77fa4ccfb37e2ac8feceba5dc1628ffb https://github.com/galaxyproject/galaxy/commit/b77c28cd77fa4ccfb37e2ac8fece… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-28 (Mon, 28 Sep 2015) Changed paths: M lib/galaxy/managers/folders.py Log Message: ----------- flake8 fix Commit: f778a3864c8d95ea91359de7cc3f44dc78a290d1 https://github.com/galaxyproject/galaxy/commit/f778a3864c8d95ea91359de7cc3f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-28 (Mon, 28 Sep 2015) Changed paths: M lib/galaxy/managers/folders.py M lib/galaxy/webapps/galaxy/api/folders.py Log Message: ----------- :bird::eyes: and some docs Commit: 3e0221c0d092f3512768c24dcb48398398f4bedf https://github.com/galaxyproject/galaxy/commit/3e0221c0d092f3512768c24dcb48… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-28 (Mon, 28 Sep 2015) Changed paths: M lib/galaxy/tools/parser/yaml.py Log Message: ----------- Merge pull request #807 from jmchilton/framework_test_failures Fix framework test failures. Commit: e9f12d3b5b297b52372dbbf23a45955399e6293d https://github.com/galaxyproject/galaxy/commit/e9f12d3b5b297b52372dbbf23a45… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-28 (Mon, 28 Sep 2015) Changed paths: M lib/galaxy/managers/folders.py M lib/galaxy/webapps/galaxy/api/folders.py Log Message: ----------- move dict formatting call from api controller to manager Commit: ac18cbe978c72c90c9659f225a05adad653971c6 https://github.com/galaxyproject/galaxy/commit/ac18cbe978c72c90c9659f225a05… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-29 (Tue, 29 Sep 2015) Changed paths: M lib/galaxy/datatypes/registry.py A lib/galaxy/datatypes/set_metadata_tool.xml M lib/galaxy/tools/imp_exp/__init__.py A lib/galaxy/tools/imp_exp/exp_history_to_archive.xml M lib/galaxy/tools/toolbox/base.py M test/unit/tools/test_parsing.py Log Message: ----------- Improved "special" tool loading. Instead of writing out the tools on startup (a more expensive operation than reading), just read the existing files in. Add new abstraction to the tool panel to reduce some otherwise duplicated code. Testing: The following two API tests should cover the modified behavior, they verify that metadata is still detectable and that history import and export still works. ``` ./run_tests.sh -api test/api/test_histories.py:HistoriesApiTestCase.test_import_export ./run_tests.sh -with_framework_test_tools -api test/api/test_tools.py:ToolsTestCase.test_rdata_not_decompressed ``` Commit: de2bb5771bd86d1f3f95bdce84b0e07536d27cb9 https://github.com/galaxyproject/galaxy/commit/de2bb5771bd86d1f3f95bdce84b0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-29 (Tue, 29 Sep 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Remove unused code. Commit: de03710756c1858b47802bae5b3d3d67fde248b7 https://github.com/galaxyproject/galaxy/commit/de03710756c1858b47802bae5b3d… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-29 (Tue, 29 Sep 2015) Changed paths: M doc/source/admin/interactive_environments.rst Log Message: ----------- Comment out default value Commit: 76db6d5274f7fd527d7e161b4ec21492176096f7 https://github.com/galaxyproject/galaxy/commit/76db6d5274f7fd527d7e161b4ec2… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-29 (Tue, 29 Sep 2015) Changed paths: M doc/source/admin/index.rst Log Message: ----------- Link to the wiki Commit: 90f63a401b0c7c15dfca19f6d9f2c1546216127c https://github.com/galaxyproject/galaxy/commit/90f63a401b0c7c15dfca19f6d9f2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-29 (Tue, 29 Sep 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Tweak password reset email template to truly be plain text. Commit: 86aa3ca22bb820e240642aca64131ff7a5350bd2 https://github.com/galaxyproject/galaxy/commit/86aa3ca22bb820e240642aca6413… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-29 (Tue, 29 Sep 2015) Changed paths: M doc/source/admin/index.rst M doc/source/index.rst Log Message: ----------- Document that this isn't the primary admin docs Commit: 90dc2b1093d631bd312857b3ecb13d46fe1e0cdd https://github.com/galaxyproject/galaxy/commit/90dc2b1093d631bd312857b3ecb1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-29 (Tue, 29 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-form.js M lib/pulsar/client/amqp_exchange.py M static/maps/mvc/tools/tools-form.js.map M static/scripts/mvc/tools/tools-form.js Log Message: ----------- Merge branch 'release_15.07' into dev Commit: 75cc56793c21f991d15b787e0f07e9c6897e1ce4 https://github.com/galaxyproject/galaxy/commit/75cc56793c21f991d15b787e0f07… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-29 (Tue, 29 Sep 2015) Changed paths: M lib/galaxy/datatypes/registry.py A lib/galaxy/datatypes/set_metadata_tool.xml M lib/galaxy/tools/__init__.py M lib/galaxy/tools/imp_exp/__init__.py A lib/galaxy/tools/imp_exp/exp_history_to_archive.xml M lib/galaxy/tools/toolbox/base.py M test/unit/tools/test_parsing.py Log Message: ----------- Merge pull request #813 from jmchilton/tool_loading Small tweaks to tool loading. Commit: 531875753df5158073c4de642ba3d4046810956d https://github.com/galaxyproject/galaxy/commit/531875753df5158073c4de642ba3… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-29 (Tue, 29 Sep 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Merge pull request #812 from dannon/prt_email_tweak Tweak password reset email template to truly be plain text. Commit: 6406276146715ee14a8624a18238ec40ea7c341c https://github.com/galaxyproject/galaxy/commit/6406276146715ee14a8624a18238… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-29 (Tue, 29 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-model.js M lib/galaxy/managers/folders.py M lib/galaxy/managers/libraries.py M lib/galaxy/model/__init__.py M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/api/folders.py M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-model.js.map M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-model.js Log Message: ----------- Merge pull request #806 from martenson/data-lib-work UI and API for data library folders management Commit: 6d00f38f0a08281d5597872616154af0b3d306c2 https://github.com/galaxyproject/galaxy/commit/6d00f38f0a08281d559787261615… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-29 (Tue, 29 Sep 2015) Changed paths: M .gitignore M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-model.js M client/galaxy/scripts/mvc/tools/tools-form.js M client/galaxy/scripts/mvc/tools/tools-jobs.js M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/ipython/templates/ipython.mako M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample M config/plugins/interactive_environments/rstudio/templates/rstudio.mako M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/registry.py A lib/galaxy/datatypes/set_metadata_tool.xml M lib/galaxy/jobs/__init__.py M lib/galaxy/managers/folders.py M lib/galaxy/managers/libraries.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/imp_exp/__init__.py A lib/galaxy/tools/imp_exp/exp_history_to_archive.xml M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/__init__.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/webapps/galaxy/api/folders.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/workflow/run.py M lib/pulsar/client/amqp_exchange.py M scripts/common_startup.sh M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-model.js.map M static/maps/mvc/tools/tools-form.js.map M static/maps/mvc/tools/tools-jobs.js.map M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-model.js M static/scripts/mvc/tools/tools-form.js M static/scripts/mvc/tools/tools-jobs.js A test-data/1.RData M test/api/helpers.py M test/api/test_tools.py M test/api/test_workflows.py M test/base/test_data.py M test/base/twilltestcase.py M test/functional/tools/disambiguate_cond.xml M test/functional/tools/min_repeat.xml M test/functional/tools/samples_tool_conf.xml M test/functional/tools/validation_repeat.xml M test/unit/jobs/test_job_configuration.py M test/unit/tools/test_parsing.py R tool-data/shared/ucsc/manual_builds.txt A tool-data/shared/ucsc/manual_builds.txt.sample Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into tool_form_003 Conflicts: client/galaxy/scripts/mvc/tools/tools-form.js static/maps/mvc/tools/tools-form.js.map static/scripts/mvc/tools/tools-form.js Commit: 082c8952e03d11a44bd0cd354a3560f2471305e0 https://github.com/galaxyproject/galaxy/commit/082c8952e03d11a44bd0cd354a35… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-29 (Tue, 29 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-form.js M static/maps/mvc/tools/tools-form.js.map M static/scripts/mvc/tools/tools-form.js Log Message: ----------- Undo initial errors Commit: f64a23fbe16d2af956840ffef673f6455700249f https://github.com/galaxyproject/galaxy/commit/f64a23fbe16d2af956840ffef673… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-29 (Tue, 29 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/library/library-model.js M static/maps/mvc/library/library-librarylist-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/maps/mvc/library/library-model.js.map M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/library/library-model.js Log Message: ----------- initial implementation of library search Commit: 91ef04a25bdc5962ce650d925db5f8a94c345d06 https://github.com/galaxyproject/galaxy/commit/91ef04a25bdc5962ce650d925db5… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-29 (Tue, 29 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/scripts/mvc/library/library-librarytoolbar-view.js Log Message: ----------- docs, refac and indentation Commit: 56734878e7bce2954933b23d4c3c4bc8fd640a5b https://github.com/galaxyproject/galaxy/commit/56734878e7bce2954933b23d4c3c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-30 (Wed, 30 Sep 2015) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py A lib/galaxy/web/framework/middleware/statsd.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Statsd middleware for request timing. Commit: 9aee2122251cb8e6c5398bbfef147f61a0884f12 https://github.com/galaxyproject/galaxy/commit/9aee2122251cb8e6c5398bbfef14… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-30 (Wed, 30 Sep 2015) Changed paths: M .ci/flake8_blacklist.txt M lib/galaxy/webapps/tool_shed/model/migrate/versions/0001_initial_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0002_add_tool_suite_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0003_review_and_review_association_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0004_repository_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0005_drop_tool_related_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0006_add_email_alerts_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0007_add_long_description_times_downloaded_columns.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0008_add_repository_metadata_table.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0009_add_malicious_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0010_add_new_repo_alert_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0011_add_tool_versions_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0012_add_downloadable_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0013_add_review_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0014_add_deprecated_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0015_add_api_keys_table.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0016_add_do_not_test_tools_functionally_correct_errors_columns.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0017_add_galaxy_utility_columns_to_repository_metadata_table.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0018_add_repository_metadata_flag_columns.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0019_add_skip_tool_test_table_and_test_install_error_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0020_add_repository_type_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0021_change_repository_type_value.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0022_add_repository_admin_roles.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0023_add_repository_url_and_hompeage_url.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0024_password_reset.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0025_session_timeout.py Log Message: ----------- Merge pull request #770 from nsoranzo/dev flake8 lib/galaxy/webapps/tool_shed/model/migrate/versions/ . Commit: 47113bedcabe3c82ad99ea1ef16307f8c3c5512f https://github.com/galaxyproject/galaxy/commit/47113bedcabe3c82ad99ea1ef163… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-30 (Wed, 30 Sep 2015) Changed paths: M .ci/flake8_blacklist.txt M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-model.js M client/galaxy/scripts/mvc/tools/tools-form.js M lib/galaxy/datatypes/registry.py A lib/galaxy/datatypes/set_metadata_tool.xml M lib/galaxy/managers/folders.py M lib/galaxy/managers/libraries.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/imp_exp/__init__.py A lib/galaxy/tools/imp_exp/exp_history_to_archive.xml M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/api/folders.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0001_initial_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0002_add_tool_suite_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0003_review_and_review_association_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0004_repository_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0005_drop_tool_related_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0006_add_email_alerts_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0007_add_long_description_times_downloaded_columns.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0008_add_repository_metadata_table.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0009_add_malicious_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0010_add_new_repo_alert_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0011_add_tool_versions_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0012_add_downloadable_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0013_add_review_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0014_add_deprecated_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0015_add_api_keys_table.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0016_add_do_not_test_tools_functionally_correct_errors_columns.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0017_add_galaxy_utility_columns_to_repository_metadata_table.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0018_add_repository_metadata_flag_columns.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0019_add_skip_tool_test_table_and_test_install_error_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0020_add_repository_type_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0021_change_repository_type_value.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0022_add_repository_admin_roles.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0023_add_repository_url_and_hompeage_url.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0024_password_reset.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0025_session_timeout.py M lib/pulsar/client/amqp_exchange.py M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-model.js.map M static/maps/mvc/tools/tools-form.js.map M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-model.js M static/scripts/mvc/tools/tools-form.js M test/unit/tools/test_parsing.py Log Message: ----------- Merge branch 'dev' of github.com:galaxyproject/galaxy into dev Commit: 1a13efe488037aa30a98c80fdab8287bfdaaf923 https://github.com/galaxyproject/galaxy/commit/1a13efe488037aa30a98c80fdab8… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-09-30 (Wed, 30 Sep 2015) Changed paths: M lib/galaxy/managers/datasets.py M lib/galaxy/managers/hdas.py Log Message: ----------- API, Datasets: fix returned tuple from creating_job; normalize id encoding, parens, naming; move both rerunnable and creating_job into datasets.py to allow (future?) use by lddas and ldas Commit: b1a8aebad680654bb2c9f19fe4b126e7fb3def2f https://github.com/galaxyproject/galaxy/commit/b1a8aebad680654bb2c9f19fe4b1… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-30 (Wed, 30 Sep 2015) Changed paths: M lib/galaxy/managers/datasets.py M lib/galaxy/managers/hdas.py Log Message: ----------- Merge pull request #817 from carlfeberhard/fix.creating_job API, Datasets: fix returned tuple from creating_job Commit: 728c5450906c8b2ba395f06fa4dbe7e7cc5a7aa6 https://github.com/galaxyproject/galaxy/commit/728c5450906c8b2ba395f06fa4db… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-30 (Wed, 30 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-analysis.js M client/galaxy/scripts/mvc/tools.js M static/maps/mvc/app/app-analysis.js.map M static/maps/mvc/tools.js.map M static/scripts/mvc/app/app-analysis.js M static/scripts/mvc/tools.js Log Message: ----------- Hide regular tool form for upload tool Commit: e710c46f2461eee2303f219b3e2c6081f932d7a4 https://github.com/galaxyproject/galaxy/commit/e710c46f2461eee2303f219b3e2c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-30 (Wed, 30 Sep 2015) Changed paths: M lib/galaxy/web/framework/middleware/statsd.py Log Message: ----------- Fix namespacing of events Commit: 1b841a9aa408fbd6e555cbbd8b298cdbd07e4590 https://github.com/galaxyproject/galaxy/commit/1b841a9aa408fbd6e555cbbd8b29… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-30 (Wed, 30 Sep 2015) Changed paths: M lib/galaxy/web/framework/middleware/statsd.py Log Message: ----------- Tweak docstring Commit: 6ee9a08cf2d3624985ceed2cf4f4bfd46ca24563 https://github.com/galaxyproject/galaxy/commit/6ee9a08cf2d3624985ceed2cf4f4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-30 (Wed, 30 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-analysis.js M client/galaxy/scripts/mvc/app/app-view.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/tools.js M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/scripts/mvc/tools/tools-form.js M client/galaxy/scripts/mvc/ui/ui-misc.js M lib/galaxy/tools/__init__.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/controllers/tool_runner.py M static/maps/mvc/app/app-analysis.js.map M static/maps/mvc/app/app-view.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/tools.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/tools/tools-form.js.map M static/maps/mvc/ui/ui-misc.js.map M static/scripts/mvc/app/app-analysis.js M static/scripts/mvc/app/app-view.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/tools.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/tools/tools-form.js M static/scripts/mvc/ui/ui-misc.js R templates/webapps/galaxy/tool_form.mako M test/unit/tools/test_execution.py Log Message: ----------- Merge pull request #786 from guerler/tool_form_003 Remove tool form mako, reduce tool runner, fix job resubmission options Commit: 2c45f356a942a64fb6506358d793bc2c4b4579f9 https://github.com/galaxyproject/galaxy/commit/2c45f356a942a64fb6506358d793… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-09-30 (Wed, 30 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/hdca-li.js M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/history/hdca-li.js.map M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/history/hdca-li.js Log Message: ----------- UI, Collections: correct foldout expansion for collections only re-rendering on 'populated' or 'visible' change; correct foldout expansion in published histories by giving dataset collection elements an api endpoint and moving 'rerunnable' and 'creating_job' fetch into li-edit Commit: c7c269572e618710b87986b3f4b51d187140dd7e https://github.com/galaxyproject/galaxy/commit/c7c269572e618710b87986b3f4b5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-30 (Wed, 30 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/hdca-li.js M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/history/hdca-li.js.map M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/history/hdca-li.js Log Message: ----------- Merge pull request #819 from carlfeberhard/fix.collection-expansion UI, Collections: correct foldout expansion for collections only re-re… Commit: 52a51af4edb7b6488f1823be5e2702438216d96b https://github.com/galaxyproject/galaxy/commit/52a51af4edb7b6488f1823be5e27… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-30 (Wed, 30 Sep 2015) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Fix middleware application message. Commit: d8ce3c25df0e6f0e44278e2dadd771d2030ae087 https://github.com/galaxyproject/galaxy/commit/d8ce3c25df0e6f0e44278e2dadd7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-30 (Wed, 30 Sep 2015) Changed paths: A doc/source/admin/index.rst A doc/source/admin/interactive_environments.png A doc/source/admin/interactive_environments.rst A doc/source/admin/interactive_environments.svg A doc/source/admin/interactive_environments_success.png M doc/source/dev/faq.rst M doc/source/index.rst Log Message: ----------- Merge pull request #803 from erasche/gie-docs Document GIEs Commit: 6592a140899a93a54d0bff1f7944a489e746bf06 https://github.com/galaxyproject/galaxy/commit/6592a140899a93a54d0bff1f7944… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-01 (Thu, 01 Oct 2015) Changed paths: M lib/galaxy/model/orm/scripts.py Log Message: ----------- Fix db initialization when galaxy.ini doesn't exist. Commit: b0b119356b130b82c39c6c811369f002cc571614 https://github.com/galaxyproject/galaxy/commit/b0b119356b130b82c39c6c811369… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-01 (Thu, 01 Oct 2015) Changed paths: M run_tests.sh Log Message: ----------- Normalize test output name. Update toolshed, casperjs, and framework tests to produce reports with the name of run_<type>_tests.html to match functional and API tests. Commit: 49740caaa2cf00e1eeb8bfdef1939638256103a0 https://github.com/galaxyproject/galaxy/commit/49740caaa2cf00e1eeb8bfdef193… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-01 (Thu, 01 Oct 2015) Changed paths: M run_tests.sh M test/casperjs/casperjs_runner.py Log Message: ----------- Add documentation for running casperjs tests through run_tests.sh. Add option to run a specific test. Verified xunit reports work and --dockerize works for casperjs tests. Commit: fc69247d500bda21c6e766b54495179208039e10 https://github.com/galaxyproject/galaxy/commit/fc69247d500bda21c6e766b54495… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-01 (Thu, 01 Oct 2015) Changed paths: M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Fix default statsd port. Commit: c6794e62c594cf7090323cdc154e1587f2491e85 https://github.com/galaxyproject/galaxy/commit/c6794e62c594cf7090323cdc154e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-01 (Thu, 01 Oct 2015) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- In lieu of rolling an egg, just test for statsd when middleware is wrapped. Commit: 72330cc316ede4ef083c2c92b5162e03994df37b https://github.com/galaxyproject/galaxy/commit/72330cc316ede4ef083c2c92b516… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-01 (Thu, 01 Oct 2015) Changed paths: M lib/galaxy/web/framework/middleware/statsd.py Log Message: ----------- 'Fix' for unit tests. Commit: 3fa78449563f1e6c050172268371ceca0f03d95f https://github.com/galaxyproject/galaxy/commit/3fa78449563f1e6c050172268371… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-01 (Thu, 01 Oct 2015) Changed paths: M lib/galaxy/web/framework/middleware/statsd.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Opt for failing instead of continuing to run Galaxy if statsd middleware is configured but module is not available. Commit: c133078b60146450fc9b05db8c5a4ff52af5bc95 https://github.com/galaxyproject/galaxy/commit/c133078b60146450fc9b05db8c5a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-01 (Thu, 01 Oct 2015) Changed paths: M lib/galaxy/model/orm/scripts.py Log Message: ----------- Merge pull request #822 from jmchilton/db_test_fix Fix db initialization when galaxy.ini doesn't exist. Commit: a5e97e6e590c6cc387530e914af4bea8af66fe44 https://github.com/galaxyproject/galaxy/commit/a5e97e6e590c6cc387530e914af4… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-10-01 (Thu, 01 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/history/history-panel-edit-current.js M static/maps/mvc/history/history-panel-edit-current.js.map M static/scripts/mvc/history/history-panel-edit-current.js Log Message: ----------- UI, histories: fix scroll position capture/restore for the current history Commit: de82b1236dcf92137e9002cc9cad6e16125119fe https://github.com/galaxyproject/galaxy/commit/de82b1236dcf92137e9002cc9cad… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-01 (Thu, 01 Oct 2015) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- Merge branch 'master' into dev Commit: 50547177f954377d66b9193e504bdbfb01e04e7d https://github.com/galaxyproject/galaxy/commit/50547177f954377d66b9193e504b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-01 (Thu, 01 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/history/history-panel-edit-current.js M static/maps/mvc/history/history-panel-edit-current.js.map M static/scripts/mvc/history/history-panel-edit-current.js Log Message: ----------- Merge pull request #824 from carlfeberhard/fix.history-scroll-capture UI, histories: fix scroll position capture/restore for the current hi… Commit: bf33c847e03ed0998f493c126c011fb492b07fb0 https://github.com/galaxyproject/galaxy/commit/bf33c847e03ed0998f493c126c01… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-01 (Thu, 01 Oct 2015) Changed paths: M run_tests.sh M test/casperjs/casperjs_runner.py Log Message: ----------- Merge pull request #825 from jmchilton/db_test_fix Various small run_tests.sh fixes/enhancements. Commit: 8cc27b45d04da7d6298a0b63c0a9c820dc6bed03 https://github.com/galaxyproject/galaxy/commit/8cc27b45d04da7d6298a0b63c0a9… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-10-01 (Thu, 01 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M lib/galaxy/tools/parameters/basic.py M static/maps/mvc/ui/ui-options.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/mvc/ui/ui-options.js M static/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Fix default value for optional select fields Commit: df74d2651b32f110137359d4d9b41c7c581846fd https://github.com/galaxyproject/galaxy/commit/df74d2651b32f110137359d4d9b4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-10-01 (Thu, 01 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-default.js M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Fix label text Commit: 5592422d01ea99bb0ba7c688227e38e963e96061 https://github.com/galaxyproject/galaxy/commit/5592422d01ea99bb0ba7c688227e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-01 (Thu, 01 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M lib/galaxy/tools/parameters/basic.py M static/maps/mvc/ui/ui-options.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/mvc/ui/ui-options.js M static/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Merge pull request #826 from guerler/fix_select_000 Fix default value for optional select fields Commit: 8af833cb347a02212403e058cd7f8cc9d263499d https://github.com/galaxyproject/galaxy/commit/8af833cb347a02212403e058cd7f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-02 (Fri, 02 Oct 2015) Changed paths: M lib/galaxy/jobs/runners/local.py Log Message: ----------- Fix a potentially problematic file operation. It might be causing intermittent test failures when running this code in Docker containers, we are unsure. Commit: a8bc87473672bf3def3dc101bd515cc608664a72 https://github.com/galaxyproject/galaxy/commit/a8bc87473672bf3def3dc101bd51… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-10-02 (Fri, 02 Oct 2015) Changed paths: M test/tool_shed/functional/test_1140_tool_help_images.py Log Message: ----------- Remove test broken after #786. Commit: e9961d3dfec0b349aba7b8fad899cc923cd3fde2 https://github.com/galaxyproject/galaxy/commit/e9961d3dfec0b349aba7b8fad899… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-02 (Fri, 02 Oct 2015) Changed paths: M test/tool_shed/functional/test_1140_tool_help_images.py Log Message: ----------- Merge pull request #828 from nsoranzo/dev Remove test broken after #786. Commit: b3a37564247623181422e68766e7ccd878b01be0 https://github.com/galaxyproject/galaxy/commit/b3a37564247623181422e68766e7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-02 (Fri, 02 Oct 2015) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py A lib/galaxy/web/framework/middleware/statsd.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Merge pull request #821 from dannon/statsd Request timing middleware via statsd Commit: 02962ae646805816f83a649c39d4c9336baf7056 https://github.com/galaxyproject/galaxy/commit/02962ae646805816f83a649c39d4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-02 (Fri, 02 Oct 2015) Changed paths: M lib/galaxy/jobs/runners/local.py Log Message: ----------- Merge pull request #830 from jmchilton/local_close Improved file handling in local runner. Commit: 4e3fe5012f295e9f64c81b914332068a8a04d8fb https://github.com/galaxyproject/galaxy/commit/4e3fe5012f295e9f64c81b914332… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-10-02 (Fri, 02 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/history/history-panel-edit-current.js M static/maps/mvc/history/history-panel-edit-current.js.map M static/scripts/mvc/history/history-panel-edit-current.js Log Message: ----------- Fix to a5e97e6: correctly pass in dom fragment to setUpBehaviors (fixes multiselect btn and name editing Commit: a47f9defe32211b8b589794a7a761889b053326c https://github.com/galaxyproject/galaxy/commit/a47f9defe32211b8b589794a7a76… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-02 (Fri, 02 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/history/history-panel-edit-current.js M static/maps/mvc/history/history-panel-edit-current.js.map M static/scripts/mvc/history/history-panel-edit-current.js Log Message: ----------- Merge pull request #834 from carlfeberhard/fix.multiselect Fix to a5e97e6: correctly pass in dom fragment to setUpBehaviors (fix… Commit: 4e35ff04a116a4a9ca1d96e9b3c5842be9fa9f7f https://github.com/galaxyproject/galaxy/commit/4e35ff04a116a4a9ca1d96e9b3c5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M lib/galaxy/jobs/command_factory.py Log Message: ----------- More improved file handling for job code. Another stab in the dark that won't actually fix the testing issues with Docker. Commit: b75175f18d15000a2dc5826f49424eba6dc7d489 https://github.com/galaxyproject/galaxy/commit/b75175f18d15000a2dc5826f4942… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/cli.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/pbs.py Log Message: ----------- Centralize logic for writing job scripts. Runners were using various permissions, some didn't close file handles, etc.... In addition, run sync after script is written to avoid "Text file busy" problems in all job script scenerios. Commit: 54410d7d70c13c76ac370e83c12db7810192fc71 https://github.com/galaxyproject/galaxy/commit/54410d7d70c13c76ac370e83c12d… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M lib/galaxy/datatypes/converters/bgzip.py M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py M lib/galaxy/datatypes/converters/interval_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/interval_to_fli.py M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py M lib/galaxy/datatypes/converters/maf_to_fasta_converter.py M lib/galaxy/datatypes/converters/maf_to_interval_converter.py M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/datatypes/display_applications/util.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/util/gff_util.py Log Message: ----------- Use eggs.require() instead of pkg_resources in lib/galaxy/datatypes/ . Fix https://github.com/galaxyproject/galaxy/issues/809#issuecomment-145107037 . Commit: ea28282b59e286570d6a4fb2c93259f99db0d1df https://github.com/galaxyproject/galaxy/commit/ea28282b59e286570d6a4fb2c932… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M run_tests.sh Log Message: ----------- Add new run_tests.sh command to mount the external tmp directory. This is an attempt to potentially end these "Text file busy" problems on test: https://jenkins.galaxyproject.org/job/docker-api/170/testReport/junit/api.t…. Commit: 2210f83da95b702ea10f7809b29ee77d54fc1529 https://github.com/galaxyproject/galaxy/commit/2210f83da95b702ea10f7809b29e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: R run_functional_tests.sh Log Message: ----------- Remove run_functional_tests.sh. It has been deprecated who a while and removed once already - hopefully now we can kill it. Commit: 596f9116f25f384899f9c7acb5517d57b88ca358 https://github.com/galaxyproject/galaxy/commit/596f9116f25f384899f9c7acb551… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M run_tests.sh Log Message: ----------- Use framework test tools for --api and --casperjs tests. These tests are explicitly designed to test the framework and use a tool panel. ``sh run_tests.sh`` and ``sh run_tests.sh -id`` are meant to test Galaxy's configuration to some degree, and other tests qunit, unit, and toolshed do not depend on the toolbox. Commit: 1564dc665be8e2a44cb3298f22e0d70811205c15 https://github.com/galaxyproject/galaxy/commit/1564dc665be8e2a44cb3298f22e0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Swap debug mode to be off by default in galaxy.ini.sample. Commit: a92ed830ee66719708b062b39f64092741a83975 https://github.com/galaxyproject/galaxy/commit/a92ed830ee66719708b062b39f64… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Merge pull request #840 from dannon/default_debug_off Swap debug mode to be off by default in galaxy.ini.sample. Commit: e3364d6db428d0695ce978dfa0604e775da11f67 https://github.com/galaxyproject/galaxy/commit/e3364d6db428d0695ce978dfa060… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Update comment in sample. Commit: 51a3f5414064d0b927023cb9e0096995e0470b8d https://github.com/galaxyproject/galaxy/commit/51a3f5414064d0b927023cb9e009… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Merge pull request #841 from dannon/default_debug_off Update comment in sample. Commit: 591519009b0ead989ddf5a87fee9d5c69216b97c https://github.com/galaxyproject/galaxy/commit/591519009b0ead989ddf5a87fee9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M tools/sr_mapping/srma_wrapper.xml M tools/visualization/LAJ.xml Log Message: ----------- Add citations to a few more tools. Commit: 88239abf5c2473af841eea139edc0164b3a4856c https://github.com/galaxyproject/galaxy/commit/88239abf5c2473af841eea139edc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M tools/data_source/biomart.xml M tools/data_source/biomart_test.xml M tools/sr_mapping/bfast_wrapper.xml M tools/sr_mapping/fastq_statistics.xml M tools/sr_mapping/mosaik.xml Log Message: ----------- Add more distribution tool citations. xref #361. Commit: f50702f96253d1d4a6ad1dbe088b1d04c6e1506a https://github.com/galaxyproject/galaxy/commit/f50702f96253d1d4a6ad1dbe088b… Author: Eric Rasche <rasche.eric(a)yandex.ru> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: R tools/data_source/echo.py R tools/data_source/echo.xml Log Message: ----------- Remove unused echo tool Commit: 7dcd2636fd83dc935306cbd405091c60c1d54bdf https://github.com/galaxyproject/galaxy/commit/7dcd2636fd83dc935306cbd40509… Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/library/library-model.js M static/maps/mvc/library/library-librarylist-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/maps/mvc/library/library-model.js.map M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/library/library-model.js Log Message: ----------- Merge pull request #820 from martenson/lib-search Initial implementation of data library search Commit: 1aebbc3f68ad5a82834edb82ef52e3840fec697b https://github.com/galaxyproject/galaxy/commit/1aebbc3f68ad5a82834edb82ef52… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: R lib/galaxy/webapps/galaxy/controllers/ucsc_proxy.py R tools/data_source/ucsc_archaea.xml R tools/data_source/ucsc_filter.py R tools/data_source/ucsc_proxy.py R tools/data_source/ucsc_proxy.xml R tools/data_source/ucsc_testproxy.xml Log Message: ----------- Remove likely broken UCSC proxy and associated tools. Unused for many, many years and likely no longer works. Commit: a6f9e62c1a4048d3f7669d5783a836d38d6f8f96 https://github.com/galaxyproject/galaxy/commit/a6f9e62c1a4048d3f7669d5783a8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M tools/data_source/ucsc_tablebrowser.xml M tools/data_source/ucsc_tablebrowser_archaea.xml M tools/data_source/ucsc_tablebrowser_test.xml Log Message: ----------- Add citations to ucsc browser tools. Commit: 6430b9c4e834161910c23438f9fd779b78846de7 https://github.com/galaxyproject/galaxy/commit/6430b9c4e834161910c23438f9fd… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M tools/filters/gff/gff_filter_by_attribute.xml Log Message: ----------- Update documentation for the gff_filter_by_attribute tool Commit: 0a83a244f170226ec02f41a9972bd9bfcb261449 https://github.com/galaxyproject/galaxy/commit/0a83a244f170226ec02f41a9972b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: R run_functional_tests.sh M run_tests.sh Log Message: ----------- Merge pull request #844 from jmchilton/run_test_adjustments More small adjustments to test script. Commit: 3687d45a037166e2fffcdfe7fda4cfd6d2b08346 https://github.com/galaxyproject/galaxy/commit/3687d45a037166e2fffcdfe7fda4… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M lib/galaxy/datatypes/converters/bgzip.py M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py M lib/galaxy/datatypes/converters/interval_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/interval_to_fli.py M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py M lib/galaxy/datatypes/converters/maf_to_fasta_converter.py M lib/galaxy/datatypes/converters/maf_to_interval_converter.py M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/datatypes/display_applications/util.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/util/gff_util.py Log Message: ----------- Merge pull request #838 from nsoranzo/pkg_resources Use eggs.require() instead of pkg_resources in lib/galaxy/datatypes/ . Commit: bb43ace5092799e49875589f6da7404806e27137 https://github.com/galaxyproject/galaxy/commit/bb43ace5092799e49875589f6da7… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M tools/filters/gff/gff_filter_by_attribute.xml Log Message: ----------- Merge pull request #842 from bgruening/filter_by_attribute Update documentation for the gff_filter_by_attribute tool Commit: 753bb9de0fa031720b8c7881ff1d52cbf6a522d3 https://github.com/galaxyproject/galaxy/commit/753bb9de0fa031720b8c7881ff1d… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/cli.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/pbs.py Log Message: ----------- Merge pull request #839 from jmchilton/text_file_busy Attempt to fix "Text file busy" errors (testing and production) Commit: 4cd4dac0a088b3d040766853fee8b179d94f144a https://github.com/galaxyproject/galaxy/commit/4cd4dac0a088b3d040766853fee8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: R tools/data_source/echo.py R tools/data_source/echo.xml Log Message: ----------- Merge pull request #848 from jmchilton/echo_remove Remove unused echo tool Commit: 5f4502b6500ca0aae57d6d76da12804d5d2fb9d1 https://github.com/galaxyproject/galaxy/commit/5f4502b6500ca0aae57d6d76da12… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample Log Message: ----------- Pin images for next release of Galaxy Commit: e9a3ec95b9485ea3b5b15bce4f8a96751f225b53 https://github.com/galaxyproject/galaxy/commit/e9a3ec95b9485ea3b5b15bce4f8a… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M doc/source/dev/faq.rst Log Message: ----------- Update faq.rst Commit: 053f51eb537a4624bc0751c0ae39efb59eb996ea https://github.com/galaxyproject/galaxy/commit/053f51eb537a4624bc0751c0ae39… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M static/maps/mvc/form/form-view.js.map M static/scripts/mvc/form/form-view.js Log Message: ----------- forgoten minification and map Commit: 3201005739ab5071399a55b0aa99682ffb539c26 https://github.com/galaxyproject/galaxy/commit/3201005739ab5071399a55b0aa99… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M static/maps/mvc/form/form-view.js.map M static/scripts/mvc/form/form-view.js Log Message: ----------- Merge pull request #850 from martenson/forgotten-minification forgoten minification and map Commit: f90c49e2705ed66bfa668de96568ea53126edc94 https://github.com/galaxyproject/galaxy/commit/f90c49e2705ed66bfa668de96568… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M tools/data_source/biomart.xml M tools/data_source/biomart_test.xml M tools/sr_mapping/bfast_wrapper.xml M tools/sr_mapping/fastq_statistics.xml M tools/sr_mapping/mosaik.xml M tools/sr_mapping/srma_wrapper.xml M tools/visualization/LAJ.xml Log Message: ----------- Merge pull request #847 from jmchilton/citations_5 Add more distribution tool citations. Commit: 092fc17ec008f092f016014f30317bdf68b9c567 https://github.com/galaxyproject/galaxy/commit/092fc17ec008f092f016014f3031… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: R lib/galaxy/webapps/galaxy/controllers/ucsc_proxy.py R tools/data_source/ucsc_archaea.xml R tools/data_source/ucsc_filter.py R tools/data_source/ucsc_proxy.py R tools/data_source/ucsc_proxy.xml M tools/data_source/ucsc_tablebrowser.xml M tools/data_source/ucsc_tablebrowser_archaea.xml M tools/data_source/ucsc_tablebrowser_test.xml R tools/data_source/ucsc_testproxy.xml Log Message: ----------- Merge pull request #846 from jmchilton/ucsc_cleanup UCSC Tool Cleanup Commit: b5b36c0ab184d38b611fe0b293424bedd687cb28 https://github.com/galaxyproject/galaxy/commit/b5b36c0ab184d38b611fe0b29342… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-06 (Tue, 06 Oct 2015) Changed paths: M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample Log Message: ----------- Merge pull request #849 from erasche/gie-pinning-15.10 GIE pinning 15.10 Commit: cc23adb0a962f1c9780b838604718319a0a71888 https://github.com/galaxyproject/galaxy/commit/cc23adb0a962f1c9780b83860471… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-06 (Tue, 06 Oct 2015) Changed paths: M run_tests.sh Log Message: ----------- Merge pull request #843 from jmchilton/text_file_busy_2 Allow reuse of parent /tmp directory in dockerized testing. Commit: 31c89ea29c2c504878f336d90dfcf320b873b2ee https://github.com/galaxyproject/galaxy/commit/31c89ea29c2c504878f336d90dfc… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-10-06 (Tue, 06 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/collection/collection-li-edit.js M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/history/hda-li-edit.js M static/maps/mvc/collection/collection-li-edit.js.map M static/maps/mvc/collection/collection-li.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/history/hda-li-edit.js.map M static/scripts/mvc/collection/collection-li-edit.js M static/scripts/mvc/collection/collection-li.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/history/hda-li-edit.js Log Message: ----------- UI, Collections: allow expansion to fetch details for DatasetDCEs (assuming they're HDAs); move rerunnable and creating_job fetch to HDAs Commit: 69cd5a98dcda30771ce78118ebd3a934dfb09c65 https://github.com/galaxyproject/galaxy/commit/69cd5a98dcda30771ce78118ebd3… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-10-06 (Tue, 06 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/collection/collection-li-edit.js M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/history/hda-li-edit.js M static/maps/mvc/collection/collection-li-edit.js.map M static/maps/mvc/collection/collection-li.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/history/hda-li-edit.js.map M static/scripts/mvc/collection/collection-li-edit.js M static/scripts/mvc/collection/collection-li.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/history/hda-li-edit.js Log Message: ----------- Merge pull request #854 from carlfeberhard/release_15.10 [15.10] UI, Collections: allow expansion to fetch details for DatasetDCEs (as… Commit: 4705409d386f6cabe1874ac044617d6ed226a80e https://github.com/galaxyproject/galaxy/commit/4705409d386f6cabe1874ac04461… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-10-08 (Thu, 08 Oct 2015) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Expose all API keys to admins under REMOTE_USER This is the default setting for non-remote-user setups, this commit adjusts the middleware to behave as expected. Issue raised in http://dev.list.galaxyproject.org/User-API-keys-with-External-LDAP-authenti… Commit: a0ad2b75c29eca2c33ccfcdd4aa4a834c06c5265 https://github.com/galaxyproject/galaxy/commit/a0ad2b75c29eca2c33ccfcdd4aa4… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-10-08 (Thu, 08 Oct 2015) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Merge pull request #873 from erasche/api-key-backpatch [release_15.10] Expose all API keys to admins under REMOTE_USER Commit: 60a1b45704c4794e6fcac2e9ab6001484a801ca6 https://github.com/galaxyproject/galaxy/commit/60a1b45704c4794e6fcac2e9ab60… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-08 (Thu, 08 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-model.js M static/maps/mvc/library/library-model.js.map M static/scripts/mvc/library/library-model.js Log Message: ----------- make lib search case insensitive Commit: 2d4bd2e6f5c64162ab2c1de6d6b1e338bafb4b16 https://github.com/galaxyproject/galaxy/commit/2d4bd2e6f5c64162ab2c1de6d6b1… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-08 (Thu, 08 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/style/less/library.less M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/scripts/mvc/library/library-librarytoolbar-view.js M static/style/blue/base.css M static/style/blue/library.css Log Message: ----------- fix the ordering and margins of lib toolbar items Commit: 39f5b7adf1cb835eed7b450806b249200c2a9cbe https://github.com/galaxyproject/galaxy/commit/39f5b7adf1cb835eed7b450806b2… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-08 (Thu, 08 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M static/maps/mvc/library/library-librarylist-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js Log Message: ----------- show proper message when search has no results Commit: 775ee33d4dbf7cb763e9f25430aae645d2df4c65 https://github.com/galaxyproject/galaxy/commit/775ee33d4dbf7cb763e9f25430aa… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-08 (Thu, 08 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M static/maps/mvc/library/library-librarylist-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js Log Message: ----------- fix options default order to fix bug with improper page being rendered also add missing comma for previous commit Commit: fe8dbd8183fe5706e041686ee57a683d1fd63c9e https://github.com/galaxyproject/galaxy/commit/fe8dbd8183fe5706e041686ee57a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-08 (Thu, 08 Oct 2015) Changed paths: M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M static/maps/galaxy.library.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-librarylist-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/scripts/galaxy.library.js M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js Log Message: ----------- fix problems with multiple bindings of view events; drop attempts at caching the libraries - need to study more for that Commit: 251f390f7c45f5d02af90f01f7b892b207950cb6 https://github.com/galaxyproject/galaxy/commit/251f390f7c45f5d02af90f01f7b8… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-08 (Thu, 08 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- fix the ordering of folder controls to match library's also fix the active area of 'include deleted' checkbox Commit: 90506ba1c6b83731cf5e11badabfde1f8d3e34c4 https://github.com/galaxyproject/galaxy/commit/90506ba1c6b83731cf5e11badabf… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-10-08 (Thu, 08 Oct 2015) Changed paths: M templates/webapps/galaxy/data_manager/index.mako M templates/webapps/galaxy/data_manager/view_job.mako Log Message: ----------- Fix for no longer being able to access data managers. Have datamanager links point to root with tool_id provided while targeting a new window. Commit: 38b9ca3400eaf482c50c6224438d3341241453c1 https://github.com/galaxyproject/galaxy/commit/38b9ca3400eaf482c50c6224438d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-08 (Thu, 08 Oct 2015) Changed paths: M templates/webapps/galaxy/data_manager/index.mako M templates/webapps/galaxy/data_manager/view_job.mako Log Message: ----------- Merge pull request #879 from blankenberg/datamanager-fix [15.10] Fix for no longer being able to access data managers. Commit: 6c5f6e3f692c2b151afab39126a068f56971708d https://github.com/galaxyproject/galaxy/commit/6c5f6e3f692c2b151afab39126a0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-12 (Mon, 12 Oct 2015) Changed paths: M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/library/library-model.js M client/galaxy/style/less/library.less M static/maps/galaxy.library.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-librarylist-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/maps/mvc/library/library-model.js.map M static/scripts/galaxy.library.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/library/library-model.js M static/style/blue/base.css M static/style/blue/library.css Log Message: ----------- Merge pull request #878 from martenson/datalib-fixes-release [15.10] Release Fixes for Data Libraries Commit: b470843c89af119b9800d6fb68323338c7020fb6 https://github.com/galaxyproject/galaxy/commit/b470843c89af119b9800d6fb6832… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-10-13 (Tue, 13 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-analysis.js M static/maps/mvc/app/app-analysis.js.map M static/scripts/mvc/app/app-analysis.js Log Message: ----------- UI, histories: fix multiview button to be logged-in users only Commit: 99fab6f342f6f50536b1a5544b8b07f769805497 https://github.com/galaxyproject/galaxy/commit/99fab6f342f6f50536b1a5544b8b… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-10-13 (Tue, 13 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/history/history-panel.js M client/galaxy/scripts/mvc/list/list-panel.js M static/maps/mvc/history/history-panel.js.map M static/maps/mvc/list/list-panel.js.map M static/scripts/mvc/history/history-panel.js M static/scripts/mvc/list/list-panel.js Log Message: ----------- UI, histories: on first history search, use current searchFor value at callback and not value when ajax began Commit: 34a11d1187127face6dd0c780051458b2b5d7430 https://github.com/galaxyproject/galaxy/commit/34a11d1187127face6dd0c780051… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-10-13 (Tue, 13 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/history/multi-panel.js M static/maps/mvc/history/multi-panel.js.map M static/scripts/mvc/history/multi-panel.js Log Message: ----------- UI, histories: fix default empty message for lazy loaded panels in multi-view Commit: 41069e8ba6dcd6328864eabb104e36a2a70e6140 https://github.com/galaxyproject/galaxy/commit/41069e8ba6dcd6328864eabb104e… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-10-13 (Tue, 13 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/history/multi-panel.js M static/maps/mvc/history/multi-panel.js.map M static/scripts/mvc/history/multi-panel.js Log Message: ----------- UI, histories: fix/reverse order for drag and drop dataset copy Commit: 03c7aae512d010a3100a547af3c194e6f8957e35 https://github.com/galaxyproject/galaxy/commit/03c7aae512d010a3100a547af3c1… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-10-13 (Tue, 13 Oct 2015) Changed paths: M client/galaxy/style/less/list-item.less M static/style/blue/base.css Log Message: ----------- UI, histories: disable user-select on dataset selectors to prevent text select/highlight when using shift to select a range Commit: ee42fd05319171a79791803d5c0adc168ef2cced https://github.com/galaxyproject/galaxy/commit/ee42fd05319171a79791803d5c0a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-analysis.js M client/galaxy/scripts/mvc/history/history-panel.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/list/list-panel.js M client/galaxy/style/less/list-item.less M static/maps/mvc/app/app-analysis.js.map M static/maps/mvc/history/history-panel.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/list/list-panel.js.map M static/scripts/mvc/app/app-analysis.js M static/scripts/mvc/history/history-panel.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/list/list-panel.js M static/style/blue/base.css Log Message: ----------- Merge pull request #910 from carlfeberhard/release_15.10 [15.10] Some minor fixes to the history UI Commit: 120ec61264dadb90b0386e46bd4c33a2f6481c52 https://github.com/galaxyproject/galaxy/commit/120ec61264dadb90b0386e46bd4c… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M tools/filters/cutWrapper.xml Log Message: ----------- Fix command quoting and remove size from text input for Cut tool. Commit: cf59e8bd3c52f52ae717ca9755e6b10f48382b07 https://github.com/galaxyproject/galaxy/commit/cf59e8bd3c52f52ae717ca9755e6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M tools/filters/cutWrapper.xml Log Message: ----------- Merge pull request #913 from blankenberg/cut_15.10 [15.10] Fix command quoting and remove size from text input for Cut tool. Commit: a742198a36d700f299019ef8929a9dc55d58c17a https://github.com/galaxyproject/galaxy/commit/a742198a36d700f299019ef8929a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Fixes for switching history (standard as well as multiview) when using IE11. Intentionally minimal fix for 15.10, more comprehensive refactoring+solution forthcoming for dev. Commit: 11d17b3e7b305a28aaa0fb8392424dbb650e70d6 https://github.com/galaxyproject/galaxy/commit/11d17b3e7b305a28aaa0fb839242… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-15 (Thu, 15 Oct 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Merge pull request #920 from dannon/release_15.10 [15.10] IE11 history-stuck fix Commit: 15a8c594bd8041c17512a719eab6185c6b478f19 https://github.com/galaxyproject/galaxy/commit/15a8c594bd8041c17512a719eab6… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-16 (Fri, 16 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-librarylist-view.js M static/maps/mvc/library/library-librarylist-view.js.map M static/scripts/mvc/library/library-librarylist-view.js Log Message: ----------- fix the filter on deleted libraries to not show the public deleted libs by default Commit: 47ce939322111da71b914976170dd9ad41c0fe7d https://github.com/galaxyproject/galaxy/commit/47ce939322111da71b914976170d… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-16 (Fri, 16 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-librarylist-view.js M static/maps/mvc/library/library-librarylist-view.js.map M static/scripts/mvc/library/library-librarylist-view.js Log Message: ----------- remove log Commit: b7dfeb4174183135f8ac7c858d6ce33ba69286c0 https://github.com/galaxyproject/galaxy/commit/b7dfeb4174183135f8ac7c858d6c… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-10-19 (Mon, 19 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-librarylist-view.js M static/maps/mvc/library/library-librarylist-view.js.map M static/scripts/mvc/library/library-librarylist-view.js Log Message: ----------- Merge pull request #934 from martenson/fix-showing-deleted-libs [15.10] fix the filter on search results to not show the public deleted libs Commit: dd2d6960db3cd14238a9b10595cc0f5840e8f92b https://github.com/galaxyproject/galaxy/commit/dd2d6960db3cd14238a9b10595cc… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-10-20 (Tue, 20 Oct 2015) Changed paths: M client/galaxy/style/less/base.less M static/style/blue/base.css Log Message: ----------- Fixed missing trackster navigation pane (issue #946) Please enter the commit message for your changes. Lines starting Commit: 0f9067d2444575760f138e7fe9c4b6302b172ace https://github.com/galaxyproject/galaxy/commit/0f9067d2444575760f138e7fe9c4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-20 (Tue, 20 Oct 2015) Changed paths: M client/galaxy/style/less/base.less M static/style/blue/base.css Log Message: ----------- Merge pull request #957 from guerler/fix_trackster_001 [15.10] Fixed missing trackster navigation pane (issue #946) Commit: 732b4f5b1f45a6e676ff70590944f3b6dcf8a77f https://github.com/galaxyproject/galaxy/commit/732b4f5b1f45a6e676ff70590944… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-20 (Tue, 20 Oct 2015) Changed paths: M templates/webapps/galaxy/root/index.mako Log Message: ----------- fix missing analytics on the analysis page we abandoned base_panels for this page so the script was missing Commit: d53e13a4a997beec3cef5532ce39558296f54977 https://github.com/galaxyproject/galaxy/commit/d53e13a4a997beec3cef5532ce39… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-20 (Tue, 20 Oct 2015) Changed paths: M templates/webapps/galaxy/root/index.mako Log Message: ----------- Merge pull request #958 from martenson/fix-google-analytics [15.10] Fix google analytics on the analysis page Commit: 6f5aafe6279337b318149058e90b749e94838eaa https://github.com/galaxyproject/galaxy/commit/6f5aafe6279337b318149058e90b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-21 (Wed, 21 Oct 2015) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- For require_login=True, redirect directly to login without showing empty (and broken) looking panels, and potentially hitting an endless reload cycle. Commit: 92666cdf66914e98535567cd46946b745d02673e https://github.com/galaxyproject/galaxy/commit/92666cdf66914e98535567cd4694… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-10-21 (Wed, 21 Oct 2015) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- Merge pull request #965 from dannon/login_req [15.10] Fix endless redirect cycle when login is required Compare: https://github.com/galaxyproject/galaxy/compare/43ed7d556a4d...92666cdf6691

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