Branch: refs/heads/release_18.05
Home: https://github.com/galaxyproject/galaxy
Commit: fe37996de35ccf675f07dd5c7efbaa28b7d89da7
https://github.com/galaxyproject/galaxy/commit/fe37996de35ccf675f07dd5c7efb…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2018-05-16 (Wed, 16 May 2018)
Changed paths:
M config/galaxy.yml.sample
M config/reports.yml.sample
M config/tool_shed.yml.sample
M doc/source/admin/galaxy_options.rst
M doc/source/admin/reports_options.rst
M doc/source/releases/18.05_announce.rst
M lib/galaxy/config.py
M lib/galaxy/webapps/galaxy/config_schema.yml
M lib/galaxy/webapps/reports/config.py
M lib/galaxy/webapps/reports/config_schema.yml
M lib/galaxy/webapps/tool_shed/config.py
M lib/galaxy/webapps/tool_shed/config_schema.yml
M test/unit/unittest_utils/galaxy_mock.py
Log Message:
-----------
rename the config option to enable_gdpr_beta
to reflect the information that we do not guarantee compliance
Commit: 10a2e68b82a3e175afe33f4686b9b015e7ac4ec4
https://github.com/galaxyproject/galaxy/commit/10a2e68b82a3e175afe33f4686b9…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-05-17 (Thu, 17 May 2018)
Changed paths:
M config/galaxy.yml.sample
M config/reports.yml.sample
M config/tool_shed.yml.sample
M doc/source/admin/galaxy_options.rst
M doc/source/admin/reports_options.rst
M doc/source/releases/18.05_announce.rst
M lib/galaxy/config.py
M lib/galaxy/webapps/galaxy/config_schema.yml
M lib/galaxy/webapps/reports/config.py
M lib/galaxy/webapps/reports/config_schema.yml
M lib/galaxy/webapps/tool_shed/config.py
M lib/galaxy/webapps/tool_shed/config_schema.yml
M test/unit/unittest_utils/galaxy_mock.py
Log Message:
-----------
Merge pull request #6152 from martenson/compliance-rename
[18.05] rename the config option to enable_beta_gdpr
Compare: https://github.com/galaxyproject/galaxy/compare/b488c1d12b77...10a2e68b82a3
**NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.
Branch: refs/heads/release_18.05
Home: https://github.com/galaxyproject/galaxy
Commit: a6df95508d5c9ea3bcd3be67d31cf91cc4bc281a
https://github.com/galaxyproject/galaxy/commit/a6df95508d5c9ea3bcd3be67d31c…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-05-16 (Wed, 16 May 2018)
Changed paths:
M client/galaxy/scripts/mvc/history/history-content-model.js
M client/galaxy/scripts/mvc/history/history-contents.js
M client/galaxy/scripts/mvc/history/history-model.js
Log Message:
-----------
Backbone model url fixes (urlRoot isn't necessary in many of these situations, and only complicates (and breaks) some things
Commit: 680948b1a5351b3819f6b7c55720f2bd2e68cadc
https://github.com/galaxyproject/galaxy/commit/680948b1a5351b3819f6b7c55720…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-05-16 (Wed, 16 May 2018)
Changed paths:
M client/galaxy/scripts/mvc/history/history-content-model.js
M client/galaxy/scripts/mvc/history/history-contents.js
M client/galaxy/scripts/mvc/history/history-model.js
Log Message:
-----------
Previous changes overstepped; this should be enough to fix the prefix
serving at least in the multiview, and I'm not seeing errors elsewhere
(yet). We should look at other urlRoot usage though; it likely has
issues.
This reverts commit 62811d0a40aafe5db8c5121ff857788c59880b56.
Commit: b488c1d12b7742e64d95fba434bdb15aef57dd2c
https://github.com/galaxyproject/galaxy/commit/b488c1d12b7742e64d95fba434bd…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-05-17 (Thu, 17 May 2018)
Changed paths:
M client/galaxy/scripts/mvc/history/history-model.js
Log Message:
-----------
Merge pull request #6151 from dannon/urlroot_fixes
[18.05] Backbone model url handling
Compare: https://github.com/galaxyproject/galaxy/compare/7029cb936a9f...b488c1d12b77
**NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.
Branch: refs/heads/release_18.05
Home: https://github.com/galaxyproject/galaxy
Commit: d2dc22d97f35ff1c4cc780ce03c3a6e41ded86cb
https://github.com/galaxyproject/galaxy/commit/d2dc22d97f35ff1c4cc780ce03c3…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-05-16 (Wed, 16 May 2018)
Changed paths:
M lib/galaxy/jobs/runners/util/cli/shell/rsh.py
Log Message:
-----------
Use RetryActionExecutor when executing commands via paramiko
This should work around issues like
```
galaxy.jobs.runners ERROR 2018-05-16 10:15:55,522 [p:13768,w:0,m:1] [ShellRunner.work_thread-3] (34130) Unhandled exception calling queue_job
Traceback (most recent call last):
File "lib/galaxy/jobs/runners/__init__.py", line 112, in run_next
method(arg)
File "lib/galaxy/jobs/runners/cli.py", line 94, in queue_job
chmod_out = shell.execute("chmod +x %s" % tool_script)
File "lib/galaxy/jobs/runners/util/cli/shell/rsh.py", line 77, in execute
self.connect()
File "lib/galaxy/jobs/runners/util/cli/shell/rsh.py", line 69, in connect
timeout=self.timeout)
File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/paramiko/client.py", line 424, in connect
passphrase,
File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/paramiko/client.py", line 714, in _auth
raise saved_exception
SSHException: not a valid OPENSSH private key file
```
that can intermittently occur with rapid submission of many small jobs.
Commit: 7029cb936a9f016a7f714dcbdc88709231ee8d5a
https://github.com/galaxyproject/galaxy/commit/7029cb936a9f016a7f714dcbdc88…
Author: Dannon <dannon.baker(a)gmail.com>
Date: 2018-05-16 (Wed, 16 May 2018)
Changed paths:
M lib/galaxy/jobs/runners/util/cli/shell/rsh.py
Log Message:
-----------
Merge pull request #6149 from mvdbeek/fix_stuck_jobs_when_paramiko_fails
[18.05] Use RetryActionExecutor when executing commands via paramiko
Compare: https://github.com/galaxyproject/galaxy/compare/5c455c4472f8...7029cb936a9f
**NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.
Branch: refs/heads/release_18.05
Home: https://github.com/galaxyproject/galaxy
Commit: 0c9fd0e6de6d884dc5324288d74bdf049bc57e3d
https://github.com/galaxyproject/galaxy/commit/0c9fd0e6de6d884dc5324288d74b…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-04-27 (Fri, 27 Apr 2018)
Changed paths:
A doc/source/releases/18.05.rst
M doc/source/releases/18.05_announce.rst
A doc/source/releases/18.05_new_viz.png
A doc/source/releases/18.09_announce.rst
M doc/source/releases/index.rst
Log Message:
-----------
Release notes for 18.05.
Commit: 276858e38e8126332c0952b581c09a2034b6a8d8
https://github.com/galaxyproject/galaxy/commit/276858e38e8126332c0952b581c0…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-04-30 (Mon, 30 Apr 2018)
Changed paths:
M doc/source/releases/18.05.rst
M doc/source/releases/18.05_announce.rst
Log Message:
-----------
Fixes to the 18.05 release thanks to @nsoranzo's review.
Commit: f3e49fb1e16ea063bd64de9f59914bf1ba2ada5c
https://github.com/galaxyproject/galaxy/commit/f3e49fb1e16ea063bd64de9f5991…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2018-04-30 (Mon, 30 Apr 2018)
Changed paths:
M doc/source/releases/18.05_announce.rst
Log Message:
-----------
One more typo
Commit: 63d4ea900b0fe8f1c3e653ebff33d7d9c3c25d05
https://github.com/galaxyproject/galaxy/commit/63d4ea900b0fe8f1c3e653ebff33…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2018-05-15 (Tue, 15 May 2018)
Changed paths:
M doc/source/releases/18.05.rst
M doc/source/releases/18.05_announce.rst
R doc/source/releases/18.05_new_viz.png
Log Message:
-----------
add most important PRs added
Commit: 5d6249ec6fb45db681ad727c63612d20cb40a013
https://github.com/galaxyproject/galaxy/commit/5d6249ec6fb45db681ad727c6361…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2018-05-15 (Tue, 15 May 2018)
Changed paths:
M doc/source/releases/18.05_announce.rst
Log Message:
-----------
add security and breaking changes to release notes
Commit: 77e187ddd1d6571de72f4a67a4fc7eeb148ae14c
https://github.com/galaxyproject/galaxy/commit/77e187ddd1d6571de72f4a67a4fc…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2018-05-15 (Tue, 15 May 2018)
Changed paths:
M doc/source/releases/18.05_announce.rst
Log Message:
-----------
match styling with older RN
Commit: d70aadd6d10337e0cc43df325f52a8ce2ec31376
https://github.com/galaxyproject/galaxy/commit/d70aadd6d10337e0cc43df325f52…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2018-05-15 (Tue, 15 May 2018)
Changed paths:
M doc/source/releases/18.05_announce.rst
Log Message:
-----------
add minor tinies
Commit: c4f74c19f3d5b3f550fe384a94bd524d1e93acfc
https://github.com/galaxyproject/galaxy/commit/c4f74c19f3d5b3f550fe384a94bd…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2018-05-15 (Tue, 15 May 2018)
Changed paths:
M doc/source/releases/18.05_announce.rst
Log Message:
-----------
add more breaking changes
Commit: 04d1536edff9d9d467a8158ca536fdffecf097bb
https://github.com/galaxyproject/galaxy/commit/04d1536edff9d9d467a8158ca536…
Author: Nicola Soranzo <nicola.soranzo(a)gmail.com>
Date: 2018-05-16 (Wed, 16 May 2018)
Changed paths:
M doc/source/releases/18.05.rst
Log Message:
-----------
Fix typos
Commit: 82dce758f1ad7b6d9d517531eea5497e9ac5ed3f
https://github.com/galaxyproject/galaxy/commit/82dce758f1ad7b6d9d517531eea5…
Author: Nicola Soranzo <nicola.soranzo(a)gmail.com>
Date: 2018-05-16 (Wed, 16 May 2018)
Changed paths:
M doc/source/releases/18.05_announce.rst
Log Message:
-----------
Small fixes
Commit: 206daec262d974bb8e50a091da91a102cb35c022
https://github.com/galaxyproject/galaxy/commit/206daec262d974bb8e50a091da91…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-05-16 (Wed, 16 May 2018)
Changed paths:
A doc/source/releases/18.05.rst
M doc/source/releases/18.05_announce.rst
A doc/source/releases/18.09_announce.rst
M doc/source/releases/index.rst
Log Message:
-----------
Merge pull request #6006 from jmchilton/release_18.05_release_notes
[18.05] Release notes for 18.05.
Compare: https://github.com/galaxyproject/galaxy/compare/b114b1d6bafc...206daec262d9
**NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.