Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
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: 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: 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: 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 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/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/collection-model.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/dataset/dataset-li-edit.js.map
M static/maps/mvc/dataset/dataset-li.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/hdca-li.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-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/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
A static/maps/mvc/upload/upload-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/collection-model.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/dataset/dataset-li-edit.js
M static/scripts/mvc/dataset/dataset-li.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/hdca-li.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-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/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
A static/scripts/mvc/upload/upload-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
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: 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: 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
Compare: https://github.com/galaxyproject/galaxy/compare/531875753df5...640627614671
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
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: 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.
Compare: https://github.com/galaxyproject/galaxy/compare/90dc2b1093d6...75cc56793c21
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: e52b9ac2552ea19c6e534968661382e23cc362fa
https://github.com/galaxyproject/galaxy/commit/e52b9ac2552ea19c6e5349686613…
Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com>
Date: 2015-09-25 (Fri, 25 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:
-----------
Show tool parameter errors on initial tool form load. Needed for e.g. proper rerun display behavoir.
Commit: 394c3726d6ff6d515b99361465c743d7cd9651d9
https://github.com/galaxyproject/galaxy/commit/394c3726d6ff6d515b99361465c7…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2015-09-28 (Mon, 28 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:
-----------
Merge pull request #802 from blankenberg/tool_error_fixes
[15.07] Show tool parameter errors on initial tool form load.
Commit: 6fef4465ae3f8875a1aa6153d957941dd3fd737e
https://github.com/galaxyproject/galaxy/commit/6fef4465ae3f8875a1aa6153d957…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2015-09-28 (Mon, 28 Sep 2015)
Changed paths:
M lib/pulsar/client/amqp_exchange.py
Log Message:
-----------
[Pulsar] Resubmit AMQP acknowledgement messages to the correct queue
when consuming more than one. Also, only start one acknowledgement
manager thread rather than one per consumer.
Commit: 8c9e8686a159ec9fbee65457a8042fdcefd632f2
https://github.com/galaxyproject/galaxy/commit/8c9e8686a159ec9fbee65457a804…
Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com>
Date: 2015-09-29 (Tue, 29 Sep 2015)
Changed paths:
M lib/pulsar/client/amqp_exchange.py
Log Message:
-----------
Merge pull request #808 from natefoo/amqp_ack
[15.07] [Pulsar] Resubmit AMQP acknowledgement messages to the correct queue
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
Compare: https://github.com/galaxyproject/galaxy/compare/3e0221c0d092...90dc2b1093d6
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
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: 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.
Compare: https://github.com/galaxyproject/galaxy/compare/bd3e86c046bf...3e0221c0d092
Branch: refs/heads/release_15.07
Home: https://github.com/galaxyproject/galaxy
Commit: e52b9ac2552ea19c6e534968661382e23cc362fa
https://github.com/galaxyproject/galaxy/commit/e52b9ac2552ea19c6e5349686613…
Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com>
Date: 2015-09-25 (Fri, 25 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:
-----------
Show tool parameter errors on initial tool form load. Needed for e.g. proper rerun display behavoir.
Commit: 394c3726d6ff6d515b99361465c743d7cd9651d9
https://github.com/galaxyproject/galaxy/commit/394c3726d6ff6d515b99361465c7…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2015-09-28 (Mon, 28 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:
-----------
Merge pull request #802 from blankenberg/tool_error_fixes
[15.07] Show tool parameter errors on initial tool form load.
Compare: https://github.com/galaxyproject/galaxy/compare/1a17dbb68d23...394c3726d6ff