Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 5f1b7d5a5060c3c45601b499a953113e0b1b3125
https://github.com/galaxyproject/galaxy/commit/5f1b7d5a5060c3c45601b499a953…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-13 (Sun, 13 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/workflow/workflow-forms.js
M client/galaxy/scripts/mvc/workflow/workflow-manager.js
M client/galaxy/scripts/mvc/workflow/workflow-node.js
Log Message:
-----------
Show verison button in workflow editor and trigger on_change
Commit: 25e05b62c7b529b0379e3ff50fc75ccb5b8c28b6
https://github.com/galaxyproject/galaxy/commit/25e05b62c7b529b0379e3ff50fc7…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-13 (Sun, 13 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-base.js
Log Message:
-----------
Do postchange action only when modifiying tool versions in the workflow editor
Commit: 5afe490822325d4aa6c9be726183175743dc88f6
https://github.com/galaxyproject/galaxy/commit/5afe490822325d4aa6c9be726183…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-13 (Sun, 13 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-node.js
Log Message:
-----------
Fix qunit test
Commit: 36ce9113f7ccb6372bc2d1f8e92e95a8aafdd066
https://github.com/galaxyproject/galaxy/commit/36ce9113f7ccb6372bc2d1f8e92e…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-13 (Sun, 13 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-manager.js
Log Message:
-----------
Keep spacing consistent (thx @nsoranzo)
Commit: 526e98e372e61747b1e3cd4b86a04603ca08959b
https://github.com/galaxyproject/galaxy/commit/526e98e372e61747b1e3cd4b86a0…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-13 (Sun, 13 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/workflow/workflow-forms.js
M client/galaxy/scripts/mvc/workflow/workflow-node.js
Log Message:
-----------
Reset outputs when changing tool versions in wf-editor
Commit: db2ea853f699bf6b55b67cf7199ab355196910bc
https://github.com/galaxyproject/galaxy/commit/db2ea853f699bf6b55b67cf7199a…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-13 (Sun, 13 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-forms.js
M client/galaxy/scripts/mvc/workflow/workflow-node.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
Log Message:
-----------
Now thing are mostly working -- input and output connections are correctly altered ... but saving the workflow and reloading occasionally loads the wrong workflow
Commit: ea1f4f866658e77465d1272b4d7f37bb85ee488b
https://github.com/galaxyproject/galaxy/commit/ea1f4f866658e77465d1272b4d7f…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-13 (Sun, 13 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-manager.js
Log Message:
-----------
Fix the occasional loading of the wrong workflow. Turns out that sometimes the tool_version is undefined (i.e) if the exact node had not been manipulated, but config_form.version is always up to date
Commit: bc95f5e81b46a0bee54f6ffdd5c3a6615258af20
https://github.com/galaxyproject/galaxy/commit/bc95f5e81b46a0bee54f6ffdd5c3…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-13 (Sun, 13 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-node.js
Log Message:
-----------
Now adding/removing datasets and multiple version switches work fine, but PJA parameters are still problematic
Commit: 92fedc0ae86127d670f3ff8e829d07ee657f30d7
https://github.com/galaxyproject/galaxy/commit/92fedc0ae86127d670f3ff8e829d…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-13 (Sun, 13 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-forms.js
M client/galaxy/scripts/mvc/workflow/workflow-manager.js
M client/galaxy/scripts/mvc/workflow/workflow-node.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
Log Message:
-----------
Fix logic for adding and removing outputs
Commit: 1c286b158a8304380f499709b2f14c958b6fe203
https://github.com/galaxyproject/galaxy/commit/1c286b158a8304380f499709b2f1…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-13 (Sun, 13 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-forms.js
M client/galaxy/scripts/mvc/workflow/workflow-node.js
Log Message:
-----------
Remove extra newlines
Commit: 2e95026317e2e781163cf8bd4449bfd5ddfb894f
https://github.com/galaxyproject/galaxy/commit/2e95026317e2e781163cf8bd4449…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-13 (Sun, 13 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-base.js
Log Message:
-----------
Remove unused old_version variable
Commit: 31c423a45a4186c41981f71d41a590177bad033d
https://github.com/galaxyproject/galaxy/commit/31c423a45a4186c41981f71d41a5…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-13 (Sun, 13 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-node.js
Log Message:
-----------
Fix typo and remove leftover comment (thanks @nsoranzo)
Commit: df91881c1f4dba06a9fb6a1720db68d059664041
https://github.com/galaxyproject/galaxy/commit/df91881c1f4dba06a9fb6a1720db…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-13 (Sun, 13 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-node.js
Log Message:
-----------
Remove unused workflow outputs
Commit: 73f4141d96ad54c25fdf7a3ffb458f2b1933e14e
https://github.com/galaxyproject/galaxy/commit/73f4141d96ad54c25fdf7a3ffb45…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-08-14 (Mon, 14 Aug 2017)
Changed paths:
M static/maps/mvc/tool/tool-form-base.js.map
M static/maps/mvc/workflow/workflow-forms.js.map
M static/maps/mvc/workflow/workflow-manager.js.map
M static/maps/mvc/workflow/workflow-node.js.map
M static/maps/mvc/workflow/workflow-view.js.map
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js.map
M static/scripts/mvc/tool/tool-form-base.js
M static/scripts/mvc/workflow/workflow-forms.js
M static/scripts/mvc/workflow/workflow-manager.js
M static/scripts/mvc/workflow/workflow-node.js
M static/scripts/mvc/workflow/workflow-view.js
Log Message:
-----------
Add static JS
Commit: aa7be28960a43802bd476be1d7d996c85134c055
https://github.com/galaxyproject/galaxy/commit/aa7be28960a43802bd476be1d7d9…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-08-15 (Tue, 15 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M config/datatypes_conf.xml.sample
M config/galaxy.ini.sample
M doc/source/admin/dependency_resolvers.rst
M lib/galaxy/config.py
M lib/galaxy/datatypes/molecules.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/util/checkers.py
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js.map
M static/scripts/mvc/library/library-foldertoolbar-view.js
A test-data/1.sam.gz
A test-data/bad.html.gz
A test-data/random-file
M test/api/test_tools.py
M test/base/api.py
M test/base/interactor.py
M test/base/populators.py
M test/functional/tools/sample_datatypes_conf.xml
A test/integration/test_upload_configuration_options.py
M tools/data_source/upload.py
M tools/data_source/upload.xml
Log Message:
-----------
Merge branch 'dev' into switch_versions_in_workflows
Commit: 27be24963837354af6cac1f429c1bc06e95626e1
https://github.com/galaxyproject/galaxy/commit/27be24963837354af6cac1f429c1…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-08-15 (Tue, 15 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/workflow/workflow-forms.js
M client/galaxy/scripts/mvc/workflow/workflow-manager.js
M client/galaxy/scripts/mvc/workflow/workflow-node.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M static/maps/mvc/tool/tool-form-base.js.map
M static/maps/mvc/workflow/workflow-forms.js.map
M static/maps/mvc/workflow/workflow-manager.js.map
M static/maps/mvc/workflow/workflow-node.js.map
M static/maps/mvc/workflow/workflow-view.js.map
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js.map
M static/scripts/mvc/tool/tool-form-base.js
M static/scripts/mvc/workflow/workflow-forms.js
M static/scripts/mvc/workflow/workflow-manager.js
M static/scripts/mvc/workflow/workflow-node.js
M static/scripts/mvc/workflow/workflow-view.js
Log Message:
-----------
Merge pull request #4373 from mvdbeek/switch_versions_in_workflows
Allow switching tool versions in workflow editor
Compare: https://github.com/galaxyproject/galaxy/compare/44548f8f2fe2...27be24963837
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 4dd503046f59b13e925a76f88862882747dc6ad7
https://github.com/galaxyproject/galaxy/commit/4dd503046f59b13e925a76f88862…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-08-14 (Mon, 14 Aug 2017)
Changed paths:
M config/galaxy.ini.sample
M doc/source/admin/dependency_resolvers.rst
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
Update conda channel order to sync with Bioconda
Commit: 420e7a4f3408ec064403a4283ba22a134b65ece5
https://github.com/galaxyproject/galaxy/commit/420e7a4f3408ec064403a4283ba2…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-08-14 (Mon, 14 Aug 2017)
Changed paths:
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
Remove _ensure_conda_context() function
and make conda_context argument mandatory in functions/methods.
This should help making sure the correct context (e.g. channels)
is used for all Conda operations.
Also remove unused is_target_available() function.
Commit: cdbac056cb664e4c51f84c41c2519993d0412d74
https://github.com/galaxyproject/galaxy/commit/cdbac056cb664e4c51f84c41c251…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-08-14 (Mon, 14 Aug 2017)
Changed paths:
M lib/galaxy/tools/deps/conda_util.py
Log Message:
-----------
Override channel list on the command line instead of modifying condarc
The way we were modifying condarc in the ensure_channels_configured()
method was broken because we were appending the missing channels at the
end, so the final order may not be the one specified in
conda_ensure_channels .
Also:
- not modifying the user condarc is a much better approach
- overriding the channel list on the command line will make debugging
easier
Commit: 44548f8f2fe258051ad2df45b153642586b85e00
https://github.com/galaxyproject/galaxy/commit/44548f8f2fe258051ad2df45b153…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-15 (Tue, 15 Aug 2017)
Changed paths:
M config/galaxy.ini.sample
M doc/source/admin/dependency_resolvers.rst
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
Merge pull request #4409 from nsoranzo/fix_conda_channel_order
Update conda channel order to sync with Bioconda
Compare: https://github.com/galaxyproject/galaxy/compare/8721da8ca2e1...44548f8f2fe2
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 6c6c804ab63866c6239299f4221fa436dd4a9591
https://github.com/galaxyproject/galaxy/commit/6c6c804ab63866c6239299f4221f…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-07-28 (Fri, 28 Jul 2017)
Changed paths:
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
Log Message:
-----------
When a page is involved, the ID will be wrong
Commit: 33a0c7fac3a0624d26efd8d08dabbca5f7e8c226
https://github.com/galaxyproject/galaxy/commit/33a0c7fac3a0624d26efd8d08dab…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-07-28 (Fri, 28 Jul 2017)
Changed paths:
A static/maps/mvc/job/job-params.js.map
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
A static/scripts/mvc/job/job-params.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
Log Message:
-----------
Make client
Commit: a2229783177b76786f581cc78040b059cbd2aab5
https://github.com/galaxyproject/galaxy/commit/a2229783177b76786f581cc78040…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-07-28 (Fri, 28 Jul 2017)
Changed paths:
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
A static/maps/mvc/job/job-params.js.map
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
A static/scripts/mvc/job/job-params.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
Log Message:
-----------
Merge pull request #4355 from erasche/patch-wrong-folder-id
[release_17.05] Patch bug preventing creation of dataset library folders
Commit: ecfb90ef9f8037575db2e62ae49d8bbb7e4e427b
https://github.com/galaxyproject/galaxy/commit/ecfb90ef9f8037575db2e62ae49d…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-07-28 (Fri, 28 Jul 2017)
Changed paths:
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
R static/maps/mvc/job/job-params.js.map
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
R static/scripts/mvc/job/job-params.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
Log Message:
-----------
Revert "[release_17.05] Patch bug preventing creation of dataset library folders"
Commit: 163e4ebbe1fbfc5f1f97b5aabc804621fdd426c9
https://github.com/galaxyproject/galaxy/commit/163e4ebbe1fbfc5f1f97b5aabc80…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-07-28 (Fri, 28 Jul 2017)
Changed paths:
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
R static/maps/mvc/job/job-params.js.map
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
R static/scripts/mvc/job/job-params.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
Log Message:
-----------
Merge pull request #4356 from galaxyproject/revert-4355-patch-wrong-folder-id
Revert "[release_17.05] Patch bug preventing creation of dataset library folders"
Commit: 12f0acba1dc1b81bb621ea130a75ec7dfac0fdaa
https://github.com/galaxyproject/galaxy/commit/12f0acba1dc1b81bb621ea130a75…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-07-28 (Fri, 28 Jul 2017)
Changed paths:
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
A static/maps/mvc/job/job-params.js.map
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
A static/scripts/mvc/job/job-params.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
Log Message:
-----------
Revert "Revert "[release_17.05] Patch bug preventing creation of dataset library folders""
Commit: 10efd7fac6e38c5ca07d94c351d10473811c7d6c
https://github.com/galaxyproject/galaxy/commit/10efd7fac6e38c5ca07d94c351d1…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2017-07-31 (Mon, 31 Jul 2017)
Changed paths:
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
A static/maps/mvc/job/job-params.js.map
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
A static/scripts/mvc/job/job-params.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
Log Message:
-----------
Merge pull request #4357 from galaxyproject/revert-4356-revert-4355-patch-wrong-folder-id
[release_17.05] Patch bug preventing creation of dataset library folders
Commit: ba3249acf07ca1a44a813e2c68a9d6074d2b7c4c
https://github.com/galaxyproject/galaxy/commit/ba3249acf07ca1a44a813e2c68a9…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M config/datatypes_conf.xml.sample
M lib/galaxy/datatypes/molecules.py
Log Message:
-----------
Add missing chemical formats to datatypes_conf.xml.sample
Commit: 61d172f18d8f7740585b038dd786e81178ca1831
https://github.com/galaxyproject/galaxy/commit/61d172f18d8f7740585b038dd786…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-08-11 (Fri, 11 Aug 2017)
Changed paths:
M setup.cfg
M tox.ini
Log Message:
-----------
Update pin for flake8-docstrings
Similar to commit 2586df45637d794c63252838573b2d1e6d692243 .
Commit: a249dc01a5d0afa42474a6e4075ed2a3ad80400f
https://github.com/galaxyproject/galaxy/commit/a249dc01a5d0afa42474a6e4075e…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-08-11 (Fri, 11 Aug 2017)
Changed paths:
M .travis.yml
Log Message:
-----------
Use container-based infrastructure (sudo: false) in TravisCI
Commit: 0f5ad34eaf6b65a2d258f308aa6fea8b4f39a52a
https://github.com/galaxyproject/galaxy/commit/0f5ad34eaf6b65a2d258f308aa6f…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2017-08-14 (Mon, 14 Aug 2017)
Changed paths:
M .travis.yml
M config/datatypes_conf.xml.sample
M lib/galaxy/datatypes/molecules.py
M setup.cfg
M tox.ini
Log Message:
-----------
Merge pull request #4413 from nsoranzo/release_17.01_really_add_datatypes
[17.01] Add missing chemical formats to datatypes_conf.xml.sample
Commit: 4faf496c9898786e8f504bd36b28dc70df4e3e26
https://github.com/galaxyproject/galaxy/commit/4faf496c9898786e8f504bd36b28…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-08-14 (Mon, 14 Aug 2017)
Changed paths:
M config/datatypes_conf.xml.sample
M lib/galaxy/datatypes/molecules.py
Log Message:
-----------
Merge branch 'release_17.01' into release_17.05
Conflicts:
tox.ini
Commit: 9cbabef17e9afb4953324516d0883976edd51e87
https://github.com/galaxyproject/galaxy/commit/9cbabef17e9afb4953324516d088…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-08-14 (Mon, 14 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M config/datatypes_conf.xml.sample
M lib/galaxy/datatypes/molecules.py
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js.map
M static/scripts/mvc/library/library-foldertoolbar-view.js
Log Message:
-----------
Merge branch 'release_17.05' into dev
Conflicts:
static/maps/mvc/library/library-foldertoolbar-view.js.map
static/scripts/bundled/analysis.bundled.js.map
static/scripts/bundled/libs.bundled.js.map
static/scripts/mvc/library/library-foldertoolbar-view.js
Compare: https://github.com/galaxyproject/galaxy/compare/e594152de2dd...9cbabef17e9a
Branch: refs/heads/release_17.01
Home: https://github.com/galaxyproject/galaxy
Commit: ba3249acf07ca1a44a813e2c68a9d6074d2b7c4c
https://github.com/galaxyproject/galaxy/commit/ba3249acf07ca1a44a813e2c68a9…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths:
M config/datatypes_conf.xml.sample
M lib/galaxy/datatypes/molecules.py
Log Message:
-----------
Add missing chemical formats to datatypes_conf.xml.sample
Commit: 61d172f18d8f7740585b038dd786e81178ca1831
https://github.com/galaxyproject/galaxy/commit/61d172f18d8f7740585b038dd786…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-08-11 (Fri, 11 Aug 2017)
Changed paths:
M setup.cfg
M tox.ini
Log Message:
-----------
Update pin for flake8-docstrings
Similar to commit 2586df45637d794c63252838573b2d1e6d692243 .
Commit: a249dc01a5d0afa42474a6e4075ed2a3ad80400f
https://github.com/galaxyproject/galaxy/commit/a249dc01a5d0afa42474a6e4075e…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-08-11 (Fri, 11 Aug 2017)
Changed paths:
M .travis.yml
Log Message:
-----------
Use container-based infrastructure (sudo: false) in TravisCI
Commit: 0f5ad34eaf6b65a2d258f308aa6fea8b4f39a52a
https://github.com/galaxyproject/galaxy/commit/0f5ad34eaf6b65a2d258f308aa6f…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2017-08-14 (Mon, 14 Aug 2017)
Changed paths:
M .travis.yml
M config/datatypes_conf.xml.sample
M lib/galaxy/datatypes/molecules.py
M setup.cfg
M tox.ini
Log Message:
-----------
Merge pull request #4413 from nsoranzo/release_17.01_really_add_datatypes
[17.01] Add missing chemical formats to datatypes_conf.xml.sample
Compare: https://github.com/galaxyproject/galaxy/compare/bfb3ce6e7907...0f5ad34eaf6b
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 7a1fbd37e9fb262432daed6eefc4e9c54ceff406
https://github.com/galaxyproject/galaxy/commit/7a1fbd37e9fb262432daed6eefc4…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-12 (Sat, 12 Aug 2017)
Changed paths:
M lib/galaxy/util/checkers.py
Log Message:
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Fix bug in upload HTML checker.
If a chunk was passed into the check_html function - e.g. it was read from a compressed file - it would search through each character in the string for certain HTML content instead of each line in the string.
Commit: 59aa11864a795861484133dfc85212bf9150cf4a
https://github.com/galaxyproject/galaxy/commit/59aa11864a795861484133dfc852…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-12 (Sat, 12 Aug 2017)
Changed paths:
M lib/galaxy/config.py
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/util/checkers.py
M tools/data_source/upload.py
Log Message:
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Add configuration option to disable upload content checking.
Commit: 53b0b25456c170990ad3345021aab16f68e6e185
https://github.com/galaxyproject/galaxy/commit/53b0b25456c170990ad3345021aa…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-12 (Sat, 12 Aug 2017)
Changed paths:
M test/base/populators.py
Log Message:
-----------
Better error reporting in test/base/populators.py.
Commit: bee6af1e4117e7ff6f7caac0d9c84253ec1c4882
https://github.com/galaxyproject/galaxy/commit/bee6af1e4117e7ff6f7caac0d9c8…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-12 (Sat, 12 Aug 2017)
Changed paths:
M test/base/api.py
Log Message:
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Allow API tests to work with admin users (not just admin keys).
Commit: fec1eab82dc6dea2d03711127ed08b3038ad5bf1
https://github.com/galaxyproject/galaxy/commit/fec1eab82dc6dea2d03711127ed0…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-12 (Sat, 12 Aug 2017)
Changed paths:
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/tools/parameters/grouping.py
M test/base/populators.py
M tools/data_source/upload.py
M tools/data_source/upload.xml
Log Message:
-----------
Add ability to arbitrarily not decompress files on upload via API.
Commit: 06ca789f92ad2f4dfaffc36d3fa0bafb3c74920d
https://github.com/galaxyproject/galaxy/commit/06ca789f92ad2f4dfaffc36d3fa0…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-12 (Sat, 12 Aug 2017)
Changed paths:
A test-data/1.sam.gz
A test-data/bad.html.gz
A test-data/random-file
M test/functional/tools/sample_datatypes_conf.xml
A test/integration/test_upload_configuration_options.py
Log Message:
-----------
Configuration tests for the last few upload enhancements.
Commit: f849c7e6feafabf905653bd008fde23dc1413a85
https://github.com/galaxyproject/galaxy/commit/f849c7e6feafabf905653bd008fd…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2017-08-14 (Mon, 14 Aug 2017)
Changed paths:
M lib/galaxy/config.py
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/util/checkers.py
A test-data/1.sam.gz
A test-data/bad.html.gz
A test-data/random-file
M test/base/api.py
M test/base/populators.py
M test/functional/tools/sample_datatypes_conf.xml
A test/integration/test_upload_configuration_options.py
M tools/data_source/upload.py
M tools/data_source/upload.xml
Log Message:
-----------
Merge pull request #4417 from jmchilton/upload_enhance
Fixes and enhancements for the upload API
Compare: https://github.com/galaxyproject/galaxy/compare/fc861cdf38d1...f849c7e6feaf