Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: e50e7239b58ef80f62c537096bdf642198aaa9cb
https://github.com/galaxyproject/galaxy/commit/e50e7239b58ef80f62c537096bdf…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-09-07 (Thu, 07 Sep 2017)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/config.py
M lib/galaxy/tools/actions/upload.py
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
Log Message:
-----------
Implement IP address whitelisting
Commit: 569bd6bedf17b1b1f73c964345dd41b3d29cf104
https://github.com/galaxyproject/galaxy/commit/569bd6bedf17b1b1f73c964345dd…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-09-07 (Thu, 07 Sep 2017)
Changed paths:
M client/galaxy/scripts/utils/uploadbox.js
M static/maps/utils/uploadbox.js.map
M static/scripts/utils/uploadbox.js
Log Message:
-----------
Show a more useful error when one is available
Commit: d1892fc4446474b14da33b6862002a7d54fd9fd2
https://github.com/galaxyproject/galaxy/commit/d1892fc4446474b14da33b686200…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-09-07 (Thu, 07 Sep 2017)
Changed paths:
M lib/galaxy/config.py
M lib/galaxy/tools/actions/upload_common.py
Log Message:
-----------
the library prefers unicode stuff
Commit: 36758478d590664615f7fe8e32ef9f7879eb2284
https://github.com/galaxyproject/galaxy/commit/36758478d590664615f7fe8e32ef…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-09-07 (Thu, 07 Sep 2017)
Changed paths:
M lib/galaxy/tools/actions/upload_common.py
Log Message:
-----------
non-URL things get passed to this function
Commit: b620536dc25af3b68a28aade5682b6b7a92af15d
https://github.com/galaxyproject/galaxy/commit/b620536dc25af3b68a28aade5682…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-09-07 (Thu, 07 Sep 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:
-----------
rebuild client
Commit: cb416390781e546ce77b94f56cca73e48faed070
https://github.com/galaxyproject/galaxy/commit/cb416390781e546ce77b94f56cca…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-09-07 (Thu, 07 Sep 2017)
Changed paths:
M lib/galaxy/config.py
Log Message:
-----------
flake8
Commit: e8ea1104a7ec1775350d881d3f5eed9fb420b38e
https://github.com/galaxyproject/galaxy/commit/e8ea1104a7ec1775350d881d3f5e…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-09-07 (Thu, 07 Sep 2017)
Changed paths:
M test/integration/test_upload_configuration_options.py
Log Message:
-----------
add a test expecting failure
Commit: 618d89b972258db5d2dafcb127ed3a6b473402ae
https://github.com/galaxyproject/galaxy/commit/618d89b972258db5d2dafcb127ed…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-09-07 (Thu, 07 Sep 2017)
Changed paths:
M lib/galaxy/config.py
Log Message:
-----------
lint-import-order
Commit: 4e2cd5fea628884d1dddd305e28f3ec81b509982
https://github.com/galaxyproject/galaxy/commit/4e2cd5fea628884d1dddd305e28f…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-09-07 (Thu, 07 Sep 2017)
Changed paths:
M static/maps/mvc/library/library-foldertoolbar-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/library/library-foldertoolbar-view.js
Log Message:
-----------
rebuild client
Commit: 2aeb4590d1c9c7bb86bb21b42d6fe20ffc8d59f8
https://github.com/galaxyproject/galaxy/commit/2aeb4590d1c9c7bb86bb21b42d6f…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-09-07 (Thu, 07 Sep 2017)
Changed paths:
M client/galaxy/scripts/utils/uploadbox.js
M config/galaxy.ini.sample
M lib/galaxy/config.py
M lib/galaxy/tools/actions/upload.py
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/maps/utils/uploadbox.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/library/library-foldertoolbar-view.js
M static/scripts/utils/uploadbox.js
M test/integration/test_upload_configuration_options.py
Log Message:
-----------
Merge pull request #4289 from erasche/local-network
Local network access restrictions
Compare: https://github.com/galaxyproject/galaxy/compare/74f7181eafa9...2aeb4590d1c9
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 14497719ba6d3a9727563d15dbeacf2b537551f3
https://github.com/galaxyproject/galaxy/commit/14497719ba6d3a9727563d15dbea…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-09-03 (Sun, 03 Sep 2017)
Changed paths:
M lib/galaxy/tools/actions/upload_common.py
M tools/data_source/upload.py
Log Message:
-----------
Prevent in-place editing if purge_source is false
When importing files from the FTP folder the admin can choose to prevent
purging of imported files. In this case the source file should not be
modified in-place by galaxy.
This also modifies relevant bare `except:` statements and modifies
the meaning of `in_place` in upload.py from no external chown script to
do not edit files in place if we keep the source file.
This fixes https://github.com/galaxyproject/galaxy/issues/4527.
Commit: 62ef8b52aedb9b9b34403db83703083a0cddbaf9
https://github.com/galaxyproject/galaxy/commit/62ef8b52aedb9b9b34403db83703…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-09-03 (Sun, 03 Sep 2017)
Changed paths:
M tools/data_source/upload.py
Log Message:
-----------
Fix sniffing for non-binary files
Commit: 06db29413e838fd88a2ec84ede347f097be161e2
https://github.com/galaxyproject/galaxy/commit/06db29413e838fd88a2ec84ede34…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-09-03 (Sun, 03 Sep 2017)
Changed paths:
M tools/data_source/upload.py
Log Message:
-----------
Move instead of copying converted datasets when possible
shutil.move tries to move files by renaming them. If that fails with
OSError (due to permission or cross-filesystem rename) it falls back to
copying files followed by removing them
(https://github.com/python/cpython/blob/2.7/Lib/shutil.py#L279). By
using shutil.move and catching permission problems we avoid an
unnecessary copy if source and destination are on the same filesystem.
Also avoids shutil.move if the upload tool is run as real-user which
should fix https://github.com/galaxyproject/galaxy/issues/4300.
Commit: 57ff68edd0627a58c1bdce645d666ad3243df8d2
https://github.com/galaxyproject/galaxy/commit/57ff68edd0627a58c1bdce645d66…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-09-07 (Thu, 07 Sep 2017)
Changed paths:
M lib/galaxy/tools/actions/upload_common.py
M tools/data_source/upload.py
Log Message:
-----------
Merge pull request #4539 from mvdbeek/purge_source
Prevent in-place editing of uploaded files if files are imported from the FTP folder
Compare: https://github.com/galaxyproject/galaxy/compare/696a1eda3ca5...57ff68edd062
Branch: refs/heads/master
Home: https://github.com/galaxyproject/usegalaxy-playbook
Commit: f3257f3677ece1445559d1c517876c5455a6776d
https://github.com/galaxyproject/usegalaxy-playbook/commit/f3257f3677ece144…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-09-06 (Wed, 06 Sep 2017)
Changed paths:
M CHANGELOG.md
M env/test/files/galaxy/galaxy_version.yml
M env/test/group_vars/galaxyservers/vars.yml
M env/test/templates/galaxy/config/build_sites.yml.j2
Log Message:
-----------
Update Test and switch it to use UCSC builds and chrom lengths in CVMFS.
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 13ab2fd1a499d64f695e75ce4f6a96449fd8a75c
https://github.com/galaxyproject/galaxy/commit/13ab2fd1a499d64f695e75ce4f6a…
Author: lecorguille <lecorguille(a)users.noreply.github.com>
Date: 2017-06-26 (Mon, 26 Jun 2017)
Changed paths:
A test-data/joiner_out1.bed
A test-data/joiner_out2.bed
A test-data/joiner_out3.bed
A test-data/joiner_out4.bed
Log Message:
-----------
join with header: add test-data output files
Commit: 5cf405902bd86fd3f57d8b8ed12a1e06f3c89662
https://github.com/galaxyproject/galaxy/commit/5cf405902bd86fd3f57d8b8ed12a…
Author: lecorguille <lecorguille(a)users.noreply.github.com>
Date: 2017-06-26 (Mon, 26 Jun 2017)
Changed paths:
A test-data/joiner_header_in1.tab
A test-data/joiner_header_in2.tab
A test-data/joiner_out5.tab
M tools/filters/joiner.xml
Log Message:
-----------
join with header: add test
Commit: 406c71acab0b0fea03dfa31712c06d066cb2a5c6
https://github.com/galaxyproject/galaxy/commit/406c71acab0b0fea03dfa31712c0…
Author: lecorguille <lecorguille(a)users.noreply.github.com>
Date: 2017-06-26 (Mon, 26 Jun 2017)
Changed paths:
M tools/filters/join.py
M tools/filters/joiner.xml
Log Message:
-----------
join with header: test passed
Commit: 712a7045e5a4b092d7ecb4de0e6f11544d10a956
https://github.com/galaxyproject/galaxy/commit/712a7045e5a4b092d7ecb4de0e6f…
Author: lecorguille <lecorguille(a)users.noreply.github.com>
Date: 2017-06-26 (Mon, 26 Jun 2017)
Changed paths:
A test-data/joiner_out7.tab
M tools/filters/joiner.xml
Log Message:
-----------
join with header: add a regression test
Commit: f8bc4076177d56c7b6beed9c975795b6c3a80dd0
https://github.com/galaxyproject/galaxy/commit/f8bc4076177d56c7b6beed9c9757…
Author: lecorguille <lecorguille(a)users.noreply.github.com>
Date: 2017-06-26 (Mon, 26 Jun 2017)
Changed paths:
A test-data/joiner_out6.tab
M tools/filters/joiner.xml
Log Message:
-----------
join with header: add a use case with a fill value
Commit: 222a7502e7672be3d433611269735e449daa0101
https://github.com/galaxyproject/galaxy/commit/222a7502e7672be3d43361126973…
Author: lecorguille <lecorguille(a)users.noreply.github.com>
Date: 2017-06-26 (Mon, 26 Jun 2017)
Changed paths:
M tools/filters/joiner.xml
Log Message:
-----------
join header: fix tool syntax
Commit: 530827f6548e5b4360ac7d6a2e1569395ec8ec68
https://github.com/galaxyproject/galaxy/commit/530827f6548e5b4360ac7d6a2e15…
Author: lecorguille <lecorguille(a)users.noreply.github.com>
Date: 2017-06-26 (Mon, 26 Jun 2017)
Changed paths:
M tools/filters/join.py
Log Message:
-----------
join with header: flake import order fix
Commit: d887cb17f0e330bed43d80073801568165746454
https://github.com/galaxyproject/galaxy/commit/d887cb17f0e330bed43d80073801…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-09-06 (Wed, 06 Sep 2017)
Changed paths:
A test-data/joiner_header_in1.tab
A test-data/joiner_header_in2.tab
A test-data/joiner_out1.bed
A test-data/joiner_out2.bed
A test-data/joiner_out3.bed
A test-data/joiner_out4.bed
A test-data/joiner_out5.tab
A test-data/joiner_out6.tab
A test-data/joiner_out7.tab
M tools/filters/join.py
M tools/filters/joiner.xml
Log Message:
-----------
Merge join_header into dev.
Commit: 696a1eda3ca5695f9c0631c3f2f357c83b4a8995
https://github.com/galaxyproject/galaxy/commit/696a1eda3ca5695f9c0631c3f2f3…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-09-06 (Wed, 06 Sep 2017)
Changed paths:
A test-data/joiner_header_in1.tab
A test-data/joiner_header_in2.tab
A test-data/joiner_out1.bed
A test-data/joiner_out2.bed
A test-data/joiner_out3.bed
A test-data/joiner_out4.bed
A test-data/joiner_out5.tab
A test-data/joiner_out6.tab
A test-data/joiner_out7.tab
M tools/filters/join.py
M tools/filters/joiner.xml
Log Message:
-----------
Merge integration branch of 'header_join' into dev
Compare: https://github.com/galaxyproject/galaxy/compare/20b935639670...696a1eda3ca5
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 30b97f1f1ea9987f967e9774f65ed2e3d8450a3b
https://github.com/galaxyproject/galaxy/commit/30b97f1f1ea9987f967e9774f65e…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-09-06 (Wed, 06 Sep 2017)
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:
-----------
refactor callback hell to use promises
Commit: cf09a25fdc742998d5bd71deca32527a947c6812
https://github.com/galaxyproject/galaxy/commit/cf09a25fdc742998d5bd71deca32…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-09-06 (Wed, 06 Sep 2017)
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:
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fix import of collections to datalibs
I swear I fixed this before
Commit: 20b935639670d171eadb96b3406d00174d978ae6
https://github.com/galaxyproject/galaxy/commit/20b935639670d171eadb96b3406d…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-09-06 (Wed, 06 Sep 2017)
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:
-----------
Merge pull request #4568 from martenson/fix-collection-import
Fix datalib collection import
Compare: https://github.com/galaxyproject/galaxy/compare/8f7d2374cac0...20b935639670