Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 293726c57933cb2465a650d005332241eac0f912
https://github.com/galaxyproject/galaxy/commit/293726c57933cb2465a650d00533…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-03-03 (Fri, 03 Mar 2017)
Changed paths:
M config/galaxy.ini.sample
M config/plugins/interactive_environments/bam_iobio/config/bam_iobio.ini.sample
M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample
M config/plugins/interactive_environments/neo/config/neo.ini.sample
M config/plugins/interactive_environments/phinch/config/phinch.ini.sample
M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample
A cron/clean_docker_swarm_mode_services.sh
M doc/source/admin/interactive_environments.rst
M lib/galaxy/config.py
M lib/galaxy/web/base/interactive_environments.py
Log Message:
-----------
Support Docker Engine swarm mode
Commit: 4aec70cae28f336212a6bc8f5d24a325cb851bab
https://github.com/galaxyproject/galaxy/commit/4aec70cae28f336212a6bc8f5d24…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-03-03 (Fri, 03 Mar 2017)
Changed paths:
M config/galaxy.ini.sample
M config/plugins/interactive_environments/bam_iobio/config/bam_iobio.ini.sample
M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample
M config/plugins/interactive_environments/neo/config/neo.ini.sample
M config/plugins/interactive_environments/phinch/config/phinch.ini.sample
M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample
A cron/clean_docker_swarm_mode_services.sh
M doc/source/admin/interactive_environments.rst
M lib/galaxy/config.py
M lib/galaxy/web/base/interactive_environments.py
Log Message:
-----------
Merge pull request #3666 from natefoo/docker-swarm-mode
Support Docker Engine swarm mode for Interactive Environments
Compare: https://github.com/galaxyproject/galaxy/compare/bb604e65ee0f...4aec70cae28f
Branch: refs/heads/master
Home: https://github.com/galaxyproject/usegalaxy-playbook
Commit: dbaff915e1bd2c4ddf4d66c84959a2f45d3e3ee7
https://github.com/galaxyproject/usegalaxy-playbook/commit/dbaff915e1bd2c4d…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-03-02 (Thu, 02 Mar 2017)
Changed paths:
M stage/group_vars/galaxyservers.yml
Log Message:
-----------
Set conda_prefix so conda uses /cvmfs for shebangs and whatnot, instead of /galaxy/test/deps, which is a symlink to /cvmfs/test.galaxyproject.org/deps
Branch: refs/heads/release_17.01
Home: https://github.com/galaxyproject/galaxy
Commit: dda11d21c2e88f6b935f9f90f270a7aeccd929da
https://github.com/galaxyproject/galaxy/commit/dda11d21c2e88f6b935f9f90f270…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-03-01 (Wed, 01 Mar 2017)
Changed paths:
M lib/galaxy/tools/deps/container_resolvers/__init__.py
M lib/galaxy/tools/deps/container_resolvers/mulled.py
M lib/galaxy/tools/deps/requirements.py
Log Message:
-----------
[17.01] Fix container resolver log statements exposing pointers.
These log statements:
```
2017-02-27 12:11:50,959 INFO [galaxy.tools.deps.containers] Checking with container resolver [<galaxy.tools.deps.container_resolvers.explicit.ExplicitContainerResolver object at 0x10b211590>] found description [None]
2017-02-27 12:11:51,062 INFO [galaxy.tools.deps.containers] Checking with container resolver [<galaxy.tools.deps.container_resolvers.mulled.CachedMulledContainerResolver object at 0x10b2115d0>] found description [None]
2017-02-27 12:11:51,490 INFO [galaxy.tools.deps.containers] Checking with container resolver [<galaxy.tools.deps.container_resolvers.mulled.MulledContainerResolver object at 0x10b211610>] found description [<galaxy.tools.deps.requirements.ContainerDescription object at 0x10d6f1550>]
```
Become:
```
2017-02-27 13:19:06,201 INFO [galaxy.tools.deps.containers] Checking with container resolver [ExplicitContainerResolver[]] found description [None]
2017-02-27 13:19:06,251 INFO [galaxy.tools.deps.containers] Checking with container resolver [CachedMulledContainerResolver[namespace=None]] found description [None]
2017-02-27 13:19:06,679 INFO [galaxy.tools.deps.containers] Checking with container resolver [MulledContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/seqtk:1.2--0,type=docker]]
```
Rebased with suggestion from @nsoranzo :eagle::eyes:
Commit: ca5bb99ee043587fe37cc9354885d3de6fbd5ce3
https://github.com/galaxyproject/galaxy/commit/ca5bb99ee043587fe37cc9354885…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2017-03-01 (Wed, 01 Mar 2017)
Changed paths:
M lib/galaxy/tools/deps/container_resolvers/__init__.py
M lib/galaxy/tools/deps/container_resolvers/mulled.py
M lib/galaxy/tools/deps/requirements.py
Log Message:
-----------
Merge pull request #3679 from jmchilton/fix_logs
[17.01] Fix container resolver log statements exposing pointers.
Compare: https://github.com/galaxyproject/galaxy/compare/7824cd31fd7b...ca5bb99ee043
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: fd082663866c06afb35a179327b1df6efd9c77c7
https://github.com/galaxyproject/galaxy/commit/fd082663866c06afb35a179327b1…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-21 (Tue, 21 Feb 2017)
Changed paths:
M lib/galaxy/workflow/modules.py
Log Message:
-----------
Parse name to label on module initialization
Commit: 8a4c0eb7e3ea096ed56471a010003e6717f31957
https://github.com/galaxyproject/galaxy/commit/8a4c0eb7e3ea096ed56471a01000…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-21 (Tue, 21 Feb 2017)
Changed paths:
M lib/galaxy/workflow/modules.py
Log Message:
-----------
Use shared initialization procedure for subworkflows
Commit: fc1e0702542af846c28e2910d77cbd07f0913769
https://github.com/galaxyproject/galaxy/commit/fc1e0702542af846c28e2910d77c…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-21 (Tue, 21 Feb 2017)
Changed paths:
M lib/galaxy/workflow/modules.py
Log Message:
-----------
Hide name input fields for data input modules
Commit: b91680a5b2dfc83b8ee974fdc9ed6f2ab405829c
https://github.com/galaxyproject/galaxy/commit/b91680a5b2dfc83b8ee974fdc9ed…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-21 (Tue, 21 Feb 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M static/maps/mvc/workflow/workflow-view.js.map
M static/scripts/mvc/workflow/workflow-view.js
Log Message:
-----------
Use shared label/annotation input parameter building process
Commit: e13958ffcd14f2eb62b29f446a535487dd344904
https://github.com/galaxyproject/galaxy/commit/e13958ffcd14f2eb62b29f446a53…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-21 (Tue, 21 Feb 2017)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-workflow.js
M static/maps/mvc/tool/tool-form-workflow.js.map
M static/scripts/mvc/tool/tool-form-workflow.js
Log Message:
-----------
Remove tool module related annotation input parameter
Commit: 92bd559c11e62ef1ab704b967621966a31f71e39
https://github.com/galaxyproject/galaxy/commit/92bd559c11e62ef1ab704b967621…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-21 (Tue, 21 Feb 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M static/maps/mvc/workflow/workflow-view.js.map
M static/scripts/mvc/workflow/workflow-view.js
Log Message:
-----------
Move label/annotation input parameters at top for all modules
Commit: 0f742a6d8380af15ac87a9e654e1119a177bd426
https://github.com/galaxyproject/galaxy/commit/0f742a6d8380af15ac87a9e654e1…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-21 (Tue, 21 Feb 2017)
Changed paths:
R client/galaxy/scripts/mvc/tool/tool-form-workflow.js
A client/galaxy/scripts/mvc/workflow/workflow-view-form.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
R static/maps/mvc/tool/tool-form-workflow.js.map
A static/maps/mvc/workflow/workflow-view-form.js.map
M static/maps/mvc/workflow/workflow-view.js.map
R static/scripts/mvc/tool/tool-form-workflow.js
A static/scripts/mvc/workflow/workflow-view-form.js
M static/scripts/mvc/workflow/workflow-view.js
Log Message:
-----------
Move workflow related tool form to workflow directory
Commit: 3a7e6b0b744b9331ec175d8104a17519687fa464
https://github.com/galaxyproject/galaxy/commit/3a7e6b0b744b9331ec175d8104a1…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-21 (Tue, 21 Feb 2017)
Changed paths:
A client/galaxy/scripts/mvc/workflow/workflow-forms.js
R client/galaxy/scripts/mvc/workflow/workflow-view-form.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
R static/maps/mvc/workflow/workflow-view-form.js.map
M static/maps/mvc/workflow/workflow-view.js.map
R static/scripts/mvc/workflow/workflow-view-form.js
M static/scripts/mvc/workflow/workflow-view.js
Log Message:
-----------
Enable labels for all modules, used shared building process
Commit: ff7ab0853d6ea901253ba6175aa343fd9ef3a108
https://github.com/galaxyproject/galaxy/commit/ff7ab0853d6ea901253ba6175aa3…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-21 (Tue, 21 Feb 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-forms.js
Log Message:
-----------
Fix comments, show default wrapper first in code file
Commit: b03904b52c6064e77a378347d9213ec0b270ebb9
https://github.com/galaxyproject/galaxy/commit/b03904b52c6064e77a378347d921…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-21 (Tue, 21 Feb 2017)
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/workflow/workflow-forms.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M static/maps/mvc/form/form-input.js.map
M static/maps/mvc/form/form-section.js.map
M static/maps/mvc/workflow/workflow-view.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/form/form-input.js
M static/scripts/mvc/form/form-section.js
M static/scripts/mvc/workflow/workflow-view.js
Log Message:
-----------
Allow input specific error handling, fix input parameter configuration
Commit: c9b765794bb14adbaee13a44290e9df242778ffe
https://github.com/galaxyproject/galaxy/commit/c9b765794bb14adbaee13a44290e…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-21 (Tue, 21 Feb 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M static/maps/mvc/workflow/workflow-view.js.map
M static/scripts/mvc/workflow/workflow-view.js
Log Message:
-----------
Fix form handler
Commit: a967c088f78e39819d4cc0bd349166501e00d74e
https://github.com/galaxyproject/galaxy/commit/a967c088f78e39819d4cc0bd3491…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-21 (Tue, 21 Feb 2017)
Changed paths:
M lib/galaxy/workflow/modules.py
Log Message:
-----------
Avoid parsing default names of inputs to labels
Commit: f652e9c778af3835de929cfa7823cf1f0a0aed8a
https://github.com/galaxyproject/galaxy/commit/f652e9c778af3835de929cfa7823…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-21 (Tue, 21 Feb 2017)
Changed paths:
M lib/galaxy/workflow/modules.py
Log Message:
-----------
Remove hidden input parameters, attempt to identify label directly from previous state
Commit: a3de5b042e8edae2f7beee6554ae78e18f5f115b
https://github.com/galaxyproject/galaxy/commit/a3de5b042e8edae2f7beee6554ae…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-21 (Tue, 21 Feb 2017)
Changed paths:
M lib/galaxy/managers/workflows.py
M lib/galaxy/workflow/modules.py
Log Message:
-----------
Move backward compatibility handling of former names out of modules to the workflow manager
Commit: 81f799c01f38bab0c584e9b39872d2a1dd7f0348
https://github.com/galaxyproject/galaxy/commit/81f799c01f38bab0c584e9b39872…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-21 (Tue, 21 Feb 2017)
Changed paths:
M lib/galaxy/managers/workflows.py
Log Message:
-----------
Revise comment
Commit: afe2a6116a450fa69ae87705c14a4e43a7ef5830
https://github.com/galaxyproject/galaxy/commit/afe2a6116a450fa69ae87705c14a…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-21 (Tue, 21 Feb 2017)
Changed paths:
M lib/galaxy/workflow/modules.py
Log Message:
-----------
Use label to connect workflow steps
Commit: ae751adac8ae46d7f0eb2831666258143724bc0f
https://github.com/galaxyproject/galaxy/commit/ae751adac8ae46d7f0eb28316662…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-22 (Wed, 22 Feb 2017)
Changed paths:
M lib/galaxy/workflow/modules.py
M test/unit/workflows/test_modules.py
Log Message:
-----------
Adjust unit test to use labels instead of name through state
Commit: 488c42aa4c3e3e903e0234804d3cd90277d9a930
https://github.com/galaxyproject/galaxy/commit/488c42aa4c3e3e903e0234804d3c…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-22 (Wed, 22 Feb 2017)
Changed paths:
M lib/galaxy/managers/workflows.py
Log Message:
-----------
Use constants to filter default naming of input modules
Commit: dde9ba83acfbedd50a59ccb211cf9d352c86de97
https://github.com/galaxyproject/galaxy/commit/dde9ba83acfbedd50a59ccb211cf…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-22 (Wed, 22 Feb 2017)
Changed paths:
M client/galaxy/scripts/mvc/history/history-model.js
M client/galaxy/scripts/mvc/history/history-view.js
M client/galaxy/scripts/mvc/history/options-menu.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M lib/galaxy/datatypes/data.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/web/framework/middleware/remoteuser.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M static/maps/mvc/history/history-model.js.map
M static/maps/mvc/history/history-view.js.map
M static/maps/mvc/history/options-menu.js.map
M static/maps/mvc/tool/tool-form-composite.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/history/history-model.js
M static/scripts/mvc/history/history-view.js
M static/scripts/mvc/history/options-menu.js
M static/scripts/mvc/tool/tool-form-composite.js
A test/functional/tools/mulled_example_multi_incomplete.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Merge branch 'dev' into unify_label_name_000
Commit: 528b00667d4a053b3b8db4790323b0f655b18f9b
https://github.com/galaxyproject/galaxy/commit/528b00667d4a053b3b8db4790323…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-22 (Wed, 22 Feb 2017)
Changed paths:
M lib/galaxy/workflow/modules.py
Log Message:
-----------
Fix comment
Commit: 619bfeffd503681ab7d6072426f621fde7485fd5
https://github.com/galaxyproject/galaxy/commit/619bfeffd503681ab7d6072426f6…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-22 (Wed, 22 Feb 2017)
Changed paths:
M lib/galaxy/workflow/modules.py
Log Message:
-----------
Attempt to use fixed default name for unlabeled subworkflow inputs
Commit: 007b6599c21a4927d58629210f103829e947011f
https://github.com/galaxyproject/galaxy/commit/007b6599c21a4927d58629210f10…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-22 (Wed, 22 Feb 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/workflows.py
Log Message:
-----------
Fix name handling in build module
Commit: 198d36f77bb444572f03a34aec7c695d0adc52e1
https://github.com/galaxyproject/galaxy/commit/198d36f77bb444572f03a34aec7c…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-22 (Wed, 22 Feb 2017)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M static/maps/mvc/tool/tool-form-composite.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tool-form-composite.js
Log Message:
-----------
Fix step title in composite tool form
Commit: 05687b8a19785c89772db499d6ede5a097ba47ce
https://github.com/galaxyproject/galaxy/commit/05687b8a19785c89772db499d6ed…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-22 (Wed, 22 Feb 2017)
Changed paths:
M test/unit/workflows/test_modules.py
Log Message:
-----------
Strip debug output
Commit: 820c46cf63602b788ed282f4277a19129d4b3dd8
https://github.com/galaxyproject/galaxy/commit/820c46cf63602b788ed282f4277a…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-24 (Fri, 24 Feb 2017)
Changed paths:
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Repack scripts
Commit: 2f53b1d6d12457e0eaba5ca5da8b95321c69ff54
https://github.com/galaxyproject/galaxy/commit/2f53b1d6d12457e0eaba5ca5da8b…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-24 (Fri, 24 Feb 2017)
Changed paths:
M config/datatypes_conf.xml.sample
M lib/galaxy/datatypes/proteomics.py
M lib/galaxy/exceptions/error_codes.py
M lib/galaxy/jobs/dynamic_tool_destination.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/mulled/invfile.lua
M lib/galaxy/tools/deps/mulled/mulled_build.py
M lib/galaxy/tools/linters/general.py
M lib/galaxy/tools/linters/outputs.py
M lib/galaxy/tools/linters/stdio.py
M lib/galaxy/tools/linters/tests.py
M lib/galaxy/tools/toolbox/base.py
M scripts/bootstrap_history.py
M static/maps/mvc/tool/tool-form-composite.js.map
M static/scripts/mvc/tool/tool-form-composite.js
Log Message:
-----------
Merge branch 'dev' into unify_label_name_000
Commit: b9ba754ce6eb2d4b23c54aa557cb6c0a512c4082
https://github.com/galaxyproject/galaxy/commit/b9ba754ce6eb2d4b23c54aa557cb…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-24 (Fri, 24 Feb 2017)
Changed paths:
M static/maps/mvc/tool/tool-form-composite.js.map
A static/maps/mvc/workflow/workflow-forms.js.map
R static/maps/mvc/workflow/workflow.js.map
M static/scripts/mvc/tool/tool-form-composite.js
A static/scripts/mvc/workflow/workflow-forms.js
Log Message:
-----------
Fix repacked files
Commit: c80380dc57305be36e615ec13d1d17aecd285114
https://github.com/galaxyproject/galaxy/commit/c80380dc57305be36e615ec13d1d…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-28 (Tue, 28 Feb 2017)
Changed paths:
M .ci/flake8_blacklist.txt
M client/galaxy/scripts/mvc/grid/grid-view.js
M config/plugins/interactive_environments/jupyter/config/allowed_images.yml.sample
M lib/galaxy/auth/providers/ldap_ad.py
M lib/galaxy/visualization/plugins/plugin.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M scripts/bootstrap_history.py
M static/maps/mvc/grid/grid-view.js.map
M static/scripts/mvc/grid/grid-view.js
M templates/grid_base.mako
M tools/data_source/upload.py
Log Message:
-----------
Merge branch 'dev' into unify_label_name_000
Commit: d3840c5c4140807297b22ad1e9b7da97eb1a6570
https://github.com/galaxyproject/galaxy/commit/d3840c5c4140807297b22ad1e9b7…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-03-01 (Wed, 01 Mar 2017)
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/tool/tool-form-composite.js
R client/galaxy/scripts/mvc/tool/tool-form-workflow.js
A client/galaxy/scripts/mvc/workflow/workflow-forms.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M lib/galaxy/managers/workflows.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/workflow/modules.py
M static/maps/mvc/form/form-input.js.map
M static/maps/mvc/form/form-section.js.map
M static/maps/mvc/tool/tool-form-composite.js.map
R static/maps/mvc/tool/tool-form-workflow.js.map
A static/maps/mvc/workflow/workflow-forms.js.map
M static/maps/mvc/workflow/workflow-view.js.map
R static/maps/mvc/workflow/workflow.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/form/form-input.js
M static/scripts/mvc/form/form-section.js
M static/scripts/mvc/tool/tool-form-composite.js
R static/scripts/mvc/tool/tool-form-workflow.js
A static/scripts/mvc/workflow/workflow-forms.js
M static/scripts/mvc/workflow/workflow-view.js
M test/unit/workflows/test_modules.py
Log Message:
-----------
Merge pull request #3644 from guerler/unify_label_name_000
Introduce labels for all modules, remove name handling field for data inputs
Compare: https://github.com/galaxyproject/galaxy/compare/0b4e52c8e93a...d3840c5c4140
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: d10f740cff8e3520383c004a16830700b2789c9f
https://github.com/galaxyproject/galaxy/commit/d10f740cff8e3520383c004a1683…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-02-23 (Thu, 23 Feb 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/user.py
A templates/webapps/galaxy/user/manage_info.mako
Log Message:
-----------
The user controller functions for changing information were ripped out before providing a way for admin functionality to use the new javascript stuff. Seems nontrivial, so this puts the endpoint back temporarily until the adminjs rewrite which can include the new functionality.
Commit: 6f3c8c7447e9a71c580ef9307395cd5dcd314915
https://github.com/galaxyproject/galaxy/commit/6f3c8c7447e9a71c580ef9307395…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-02-23 (Thu, 23 Feb 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/user.py
Log Message:
-----------
This template inherited field never worked apparently, but nobody noticed. This correctly sets the is_admin flag here.
Commit: 4be00d3058396ed30da4f6f0958ad6fa989249cb
https://github.com/galaxyproject/galaxy/commit/4be00d3058396ed30da4f6f0958a…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-02-23 (Thu, 23 Feb 2017)
Changed paths:
M templates/webapps/galaxy/user/manage_info.mako
Log Message:
-----------
Strip out unnecessary user address editing.
Commit: 456acf0b84004c85c94d3129f0a89af9be2d5452
https://github.com/galaxyproject/galaxy/commit/456acf0b84004c85c94d3129f0a8…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-02-23 (Thu, 23 Feb 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/user.py
Log Message:
-----------
Update docstring to explicitly mention this as a temporary endpoint.
Commit: b46ac475a93fbf0da71272861677a00a3877b91b
https://github.com/galaxyproject/galaxy/commit/b46ac475a93fbf0da71272861677…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-02-23 (Thu, 23 Feb 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/user.py
Log Message:
-----------
Fix verbiage in temporary method.
Commit: 64036a441284151e1b1a3e9305537d526005ff3a
https://github.com/galaxyproject/galaxy/commit/64036a441284151e1b1a3e930553…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-02-23 (Thu, 23 Feb 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/user.py
A templates/webapps/galaxy/user/manage_info.mako
Log Message:
-----------
Merge pull request #3656 from dannon/admin-userinfo-edit-fix
[17.01] Admin user information editing
Commit: 0636053901545a26662ed8f42a15bb67407f2231
https://github.com/galaxyproject/galaxy/commit/0636053901545a26662ed8f42a15…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-02-24 (Fri, 24 Feb 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/user.py
Log Message:
-----------
Use pgcalc when possible
Commit: 895351cdf8e8867452d28dffb89a2067eabfadb3
https://github.com/galaxyproject/galaxy/commit/895351cdf8e8867452d28dffb89a…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-02-24 (Fri, 24 Feb 2017)
Changed paths:
M lib/galaxy/queue_worker.py
M lib/galaxy/webapps/galaxy/controllers/user.py
Log Message:
-----------
initial working async recalc
Commit: 45d75e3da55e43a4444c1a7982e1ea31e1aa5cb7
https://github.com/galaxyproject/galaxy/commit/45d75e3da55e43a4444c1a7982e1…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-02-24 (Fri, 24 Feb 2017)
Changed paths:
M lib/galaxy/queue_worker.py
M lib/galaxy/webapps/galaxy/controllers/user.py
Log Message:
-----------
Encode userid in messages.
Commit: c373bf27e79e48bc2e8ba983e9f08abde16db4df
https://github.com/galaxyproject/galaxy/commit/c373bf27e79e48bc2e8ba983e9f0…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-02-24 (Fri, 24 Feb 2017)
Changed paths:
M lib/galaxy/queue_worker.py
Log Message:
-----------
Change handling of declare in queue_async_task
Commit: 00b1591f05af4743d8b16b7d1bbbbc99a3974adb
https://github.com/galaxyproject/galaxy/commit/00b1591f05af4743d8b16b7d1bbb…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-02-24 (Fri, 24 Feb 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/user.py
Log Message:
-----------
Fix inline doc
Commit: 5a5dbb97f1e04dfe15fbf71c441eb50ae4b70b11
https://github.com/galaxyproject/galaxy/commit/5a5dbb97f1e04dfe15fbf71c441e…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-02-25 (Sat, 25 Feb 2017)
Changed paths:
M doc/source/releases/17.01_announce.rst
Log Message:
-----------
improve 17.01 get galaxy release notes
Commit: 53c00df805e7ae7e509c08374bc941d31d20000d
https://github.com/galaxyproject/galaxy/commit/53c00df805e7ae7e509c08374bc9…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-02-25 (Sat, 25 Feb 2017)
Changed paths:
M lib/galaxy/queue_worker.py
M lib/galaxy/webapps/galaxy/controllers/user.py
Log Message:
-----------
Rename send_local_controL_task, add at least a tiny bit of documentation.
Commit: d4b677bc38b221678bc991e0fddc43622accb928
https://github.com/galaxyproject/galaxy/commit/d4b677bc38b221678bc991e0fddc…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2017-02-27 (Mon, 27 Feb 2017)
Changed paths:
M lib/galaxy/queue_worker.py
M lib/galaxy/webapps/galaxy/controllers/user.py
Log Message:
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Merge pull request #3669 from dannon/logout-recalc-improvements
[17.01] Logout recalc improvements
Commit: 28875de584ac1967a8f2c0cdc8f5fa7b37e70f21
https://github.com/galaxyproject/galaxy/commit/28875de584ac1967a8f2c0cdc8f5…
Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com>
Date: 2017-02-28 (Tue, 28 Feb 2017)
Changed paths:
M doc/source/releases/17.01_announce.rst
Log Message:
-----------
Merge pull request #3670 from martenson/fix-RN1701
[17.01] improve 17.01 get galaxy release notes
Commit: 0997348a1c0a450986d376a96af024c73d4c7f37
https://github.com/galaxyproject/galaxy/commit/0997348a1c0a450986d376a96af0…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-02-28 (Tue, 28 Feb 2017)
Changed paths:
M lib/galaxy/tools/search/__init__.py
Log Message:
-----------
fix tool search idnex building for tools with / in id and not from TS
Commit: c11cb3dd4572e7a4f1f814a31a45477f9ecd5ae9
https://github.com/galaxyproject/galaxy/commit/c11cb3dd4572e7a4f1f814a31a45…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-02-28 (Tue, 28 Feb 2017)
Changed paths:
M lib/galaxy/tools/search/__init__.py
Log Message:
-----------
fix typo spotted by :beer: :eyes:
Commit: 169b45b138685164010043be95cefe8148c6f713
https://github.com/galaxyproject/galaxy/commit/169b45b138685164010043be95ce…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-28 (Tue, 28 Feb 2017)
Changed paths:
M lib/galaxy/managers/workflows.py
Log Message:
-----------
Fix step name display for 17.01
Commit: e23facb966c9962bb5bd1fdd07bf6ee28d7d5930
https://github.com/galaxyproject/galaxy/commit/e23facb966c9962bb5bd1fdd07bf…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-02-28 (Tue, 28 Feb 2017)
Changed paths:
M lib/galaxy/tools/search/__init__.py
Log Message:
-----------
Merge pull request #3680 from martenson/fix-id-indexing
[17.01] fix tool search index building for tools with slash in id and not from TS
Commit: 7824cd31fd7b9351efa1cf8274b89b2b9a0d811d
https://github.com/galaxyproject/galaxy/commit/7824cd31fd7b9351efa1cf8274b8…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2017-03-01 (Wed, 01 Mar 2017)
Changed paths:
M lib/galaxy/managers/workflows.py
Log Message:
-----------
Merge pull request #3681 from guerler/fix_name_display
[17.01] Fix step name display for 17.01
Commit: 0b4e52c8e93aa5693f97ff1fc5d0a4c272f58b18
https://github.com/galaxyproject/galaxy/commit/0b4e52c8e93aa5693f97ff1fc5d0…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-03-01 (Wed, 01 Mar 2017)
Changed paths:
M doc/source/releases/17.01_announce.rst
M lib/galaxy/queue_worker.py
M lib/galaxy/tools/search/__init__.py
M lib/galaxy/webapps/galaxy/controllers/user.py
A templates/webapps/galaxy/user/manage_info.mako
Log Message:
-----------
Merge branch 'release_17.01' into dev
Conflicts:
lib/galaxy/managers/workflows.py
Discarded all changes made to
lib/galaxy/managers/workflows.py
in https://github.com/galaxyproject/galaxy/pull/3681
Compare: https://github.com/galaxyproject/galaxy/compare/f0a26f309dd3...0b4e52c8e93a