Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 78d290c9fbf26adc0a4621174502e50047bbd843
https://github.com/galaxyproject/galaxy/commit/78d290c9fbf26adc0a4621174502…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-06-03 (Sun, 03 Jun 2018)
Changed paths:
M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
M lib/galaxy/dependencies/pipfiles/update.sh
Log Message:
-----------
Do not install py2-ipaddress under Python 3
Commit: 662682c14818dfbc52579e96ff4aae4a8e047070
https://github.com/galaxyproject/galaxy/commit/662682c14818dfbc52579e96ff4a…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-06-03 (Sun, 03 Jun 2018)
Changed paths:
M lib/galaxy/util/path/__init__.py
M lib/galaxy/web/stack/__init__.py
Log Message:
-----------
unicodify bytestrings from uwsgi.opt
Fix the 2 following tracebacks:
```
added lib/ to pythonpath.
Traceback (most recent call last):
File "lib/galaxy/webapps/galaxy/buildapp.py", line 180, in uwsgi_app
return galaxy.web.framework.webapp.build_native_uwsgi_app(app_factory, "galaxy")
File "lib/galaxy/web/framework/webapp.py", line 968, in build_native_uwsgi_app
app_kwds = get_app_kwds(config_section)
File "lib/galaxy/web/stack/__init__.py", line 434, in get_app_kwds
return application_stack_class().get_app_kwds(config_section, app_name=app_name)
File "lib/galaxy/web/stack/__init__.py", line 260, in get_app_kwds
has_ini_config = has_ini_config or (config_file and has_ext(config_file, "ini", aliases=True, ignore="sample"))
File "lib/galaxy/util/path/__init__.py", line 290, in has_ext
root, _ext = __splitext_ignore(path, ignore=ignore)
File "lib/galaxy/util/path/__init__.py", line 387, in __splitext_ignore
root, ext = __splitext_no_sep(path)
File "lib/galaxy/util/path/__init__.py", line 381, in __splitext_no_sep
return (path.rsplit(extsep, 1) + [''])[0:2]
TypeError: a bytes-like object is required, not 'str'
unable to load app 0 (mountpoint='') (callable not found or import error)
```
```
galaxy.queue_worker INFO 2018-06-03 02:12:51,186 [p:2150,w:1,m:0] [MainThread] Binding and starting galaxy control worker for main.web.1
Traceback (most recent call last):
File "lib/galaxy/web/stack/__init__.py", line 456, in _do_uwsgi_postfork
f(*args, **kwargs)
File "lib/galaxy/webapps/galaxy/buildapp.py", line 190, in postfork_setup
app.application_stack.log_startup()
File "lib/galaxy/web/stack/__init__.py", line 351, in log_startup
for s in UWSGIApplicationStack._serving_on():
File "lib/galaxy/web/stack/__init__.py", line 237, in _serving_on
yield UWSGIApplicationStack._socket_opt_to_str(opt, val)
File "lib/galaxy/web/stack/__init__.py", line 208, in _socket_opt_to_str
if val.startswith('='):
TypeError: startswith first arg must be bytes or a tuple of bytes, not str
```
Commit: e81931cd753e4c85e624d80e3901c97d6064f9e1
https://github.com/galaxyproject/galaxy/commit/e81931cd753e4c85e624d80e3901…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-06-03 (Sun, 03 Jun 2018)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Fix loading of tools under Python 3
Tools containing a text parameter fail with a traceback like:
```
[pid: 2433|app: 0|req: 15/28] 127.0.0.1 () {42 vars in 905 bytes} [Sun Jun 3 02:24:59 2018] GET /api/tools/addValue/build?version=1.0.0&__identifer=nv6x1qdhzxo&tool_version=1.0.0 => generated 71 bytes in 58 msecs (HTTP/1.1 500) 3 headers in 143 bytes (1 switches on core 1)
galaxy.web.framework.decorators ERROR 2018-06-03 02:25:01,999 [p:2433,w:1,m:0] [uWSGIWorker1Core0] Uncaught exception in exposed API method:
Traceback (most recent call last):
File "lib/galaxy/web/framework/decorators.py", line 281, in decorator
rval = func(self, trans, *args, **kwargs)
File "lib/galaxy/webapps/galaxy/api/tools.py", line 113, in build
return tool.to_json(trans, kwd.get('inputs', kwd))
File "lib/galaxy/tools/__init__.py", line 1913, in to_json
'state_inputs' : params_to_strings(self.inputs, state_inputs, self.app),
File "lib/galaxy/tools/parameters/__init__.py", line 207, in params_to_strings
rval[key] = value if nested else str(dumps(value))
File "/usr/lib/python3.5/json/__init__.py", line 230, in dumps
return _default_encoder.encode(obj)
File "/usr/lib/python3.5/json/encoder.py", line 198, in encode
chunks = self.iterencode(o, _one_shot=True)
File "/usr/lib/python3.5/json/encoder.py", line 256, in iterencode
return _iterencode(o, 0)
File "/usr/lib/python3.5/json/encoder.py", line 179, in default
raise TypeError(repr(o) + " is not JSON serializable")
TypeError: b'c1,c2' is not JSON serializable
```
Commit: b08455ecab5fa068b7f8b93fe08c9c552c8c25a0
https://github.com/galaxyproject/galaxy/commit/b08455ecab5fa068b7f8b93fe08c…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-06-04 (Mon, 04 Jun 2018)
Changed paths:
M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
M lib/galaxy/dependencies/pipfiles/update.sh
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/util/path/__init__.py
M lib/galaxy/web/stack/__init__.py
Log Message:
-----------
Merge pull request #6265 from nsoranzo/python3
Python3 fixes
Compare: https://github.com/galaxyproject/galaxy/compare/2f6c184e6f5c...b08455ecab5f
**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/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 825d7f6fa74384d195739fe7ac0bf4e1d5b9c1cf
https://github.com/galaxyproject/galaxy/commit/825d7f6fa74384d195739fe7ac0b…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-05-31 (Thu, 31 May 2018)
Changed paths:
M lib/galaxy/tools/parser/output_actions.py
Log Message:
-----------
Allow from_param to reference a child collection
This is necessary when mapping over a collection over an input
that is referenced in the output section, like so:
```
...
<when value="paired_collection">
<action type="format">
<option type="from_param" name="library.input_1" param_attribute="reverse.ext" />
</action>
</when>
...
```
Commit: 50c98701b7682d8878cbc2fa1acdc3f28abdad0e
https://github.com/galaxyproject/galaxy/commit/50c98701b7682d8878cbc2fa1acd…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-05-31 (Thu, 31 May 2018)
Changed paths:
M lib/galaxy/dataset_collections/subcollections.py
Log Message:
-----------
Do not adapt target collection to child collection type
Otherwise mapping over list:list:pair to a pair input breaks
at https://github.com/galaxyproject/galaxy/blob/21b44bf348ae10d170ab96a3b6f30b….
This and the previous commit should fix
https://github.com/galaxyproject/tools-iuc/issues/1563.
Commit: 99889af1d52a263737dca3c7461baa5ce4fe8ad7
https://github.com/galaxyproject/galaxy/commit/99889af1d52a263737dca3c7461b…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-05-31 (Thu, 31 May 2018)
Changed paths:
M test/api/test_tools.py
A test/functional/tools/output_action_change_format_paired.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Test case for mapping over inputs with output ftype determined via input extension
Commit: f690386f0b88fa4f5f94b83e4dea8c97f60747fd
https://github.com/galaxyproject/galaxy/commit/f690386f0b88fa4f5f94b83e4dea…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-06-01 (Fri, 01 Jun 2018)
Changed paths:
M lib/galaxy/tools/parser/output_actions.py
Log Message:
-----------
Drop unused COLLECTION_ATTRIBUTES
Commit: 2f6c184e6f5c614e36f8100648b1a5f5a8f6ac94
https://github.com/galaxyproject/galaxy/commit/2f6c184e6f5c614e36f8100648b1…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-06-04 (Mon, 04 Jun 2018)
Changed paths:
M lib/galaxy/dataset_collections/subcollections.py
M lib/galaxy/tools/parser/output_actions.py
M test/api/test_tools.py
A test/functional/tools/output_action_change_format_paired.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Merge pull request #6253 from mvdbeek/mapping_over_from_param_fixes
Mapping over from_param fixes
Compare: https://github.com/galaxyproject/galaxy/compare/9cf66df7a7af...2f6c184e6f5c
**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/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 30b5e50ba0079a7dd24d3334cacbde2e4b9c07dc
https://github.com/galaxyproject/galaxy/commit/30b5e50ba0079a7dd24d3334cacb…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2018-05-24 (Thu, 24 May 2018)
Changed paths:
M config/galaxy.yml.sample
M doc/source/admin/galaxy_options.rst
M lib/galaxy/config.py
M lib/galaxy/queue_worker.py
A lib/galaxy/util/watcher.py
M lib/galaxy/webapps/galaxy/config_schema.yml
M lib/galaxy/webapps/galaxy/config_watchers.py
Log Message:
-----------
Enable dynamic reload of dynamic job rules when configured, using
watchdog notifications.
Commit: 91dbeebf5f4ea2fd94586a883616e6fc148940ae
https://github.com/galaxyproject/galaxy/commit/91dbeebf5f4ea2fd94586a883616…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2018-05-24 (Thu, 24 May 2018)
Changed paths:
M lib/galaxy/webapps/galaxy/config_watchers.py
Log Message:
-----------
Fix non-Galaxy webapp unit tests
Commit: 41a601d5375669bfb612b6a98e289fccd4eac8a9
https://github.com/galaxyproject/galaxy/commit/41a601d5375669bfb612b6a98e28…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2018-05-24 (Thu, 24 May 2018)
Changed paths:
M lib/galaxy/util/watcher.py
M lib/galaxy/webapps/galaxy/config_watchers.py
Log Message:
-----------
Watch any objects in job rule directories that are not python bytecode,
rather than only watching python source.
Commit: 8bd856da5120eb15053e1d32f1964aaa851626ad
https://github.com/galaxyproject/galaxy/commit/8bd856da5120eb15053e1d32f196…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2018-05-25 (Fri, 25 May 2018)
Changed paths:
M lib/galaxy/util/watcher.py
Log Message:
-----------
Ignore change events for dot files. This could be configurable if it's
needed but I can't imagine when it would be. Prevents reloading on vim
swapfile writes.
Commit: 73ea1189e9fae103e367955fc62916e497074b38
https://github.com/galaxyproject/galaxy/commit/73ea1189e9fae103e367955fc629…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-06-01 (Fri, 01 Jun 2018)
Changed paths:
M lib/galaxy/util/watcher.py
Log Message:
-----------
Avoid using builtins for variable names. file->file_path, dir->dir_path in generic watcher functions
Commit: 1652c4221eacfac2a04955ee6fd4004c84f97ae6
https://github.com/galaxyproject/galaxy/commit/1652c4221eacfac2a04955ee6fd4…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2018-06-01 (Fri, 01 Jun 2018)
Changed paths:
M lib/galaxy/util/watcher.py
Log Message:
-----------
Merge pull request #8 from dannon/dynamic-rule-dynamic-reload
Avoid using builtins for variable names.
Commit: 5ba71f580fc861be9c924991a762f0917811b720
https://github.com/galaxyproject/galaxy/commit/5ba71f580fc861be9c924991a762…
Author: Dannon <dannon.baker(a)gmail.com>
Date: 2018-06-01 (Fri, 01 Jun 2018)
Changed paths:
M config/galaxy.yml.sample
M doc/source/admin/galaxy_options.rst
M lib/galaxy/config.py
M lib/galaxy/queue_worker.py
A lib/galaxy/util/watcher.py
M lib/galaxy/webapps/galaxy/config_schema.yml
M lib/galaxy/webapps/galaxy/config_watchers.py
Log Message:
-----------
Merge pull request #6215 from natefoo/dynamic-rule-dynamic-reload
Enable automatic reload of dynamic job rules on change
Compare: https://github.com/galaxyproject/galaxy/compare/a5594551c092...5ba71f580fc8
**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/dev
Home: https://github.com/galaxyproject/galaxy
Commit: c1614be1ef5abaab241bf9739fb99390a8954343
https://github.com/galaxyproject/galaxy/commit/c1614be1ef5abaab241bf9739fb9…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-05-31 (Thu, 31 May 2018)
Changed paths:
M lib/galaxy/jobs/handler.py
Log Message:
-----------
Pause jobs with invalid inputs
Otherwise these jobs may hang around forever/until the admin
does a cleanup. This is probably preferable for users as well,
as the pause message gives a hint of why their job didn't start
running. Fixes https://github.com/galaxyproject/galaxy/issues/6022
and would minimize maintenance as outlined in https://github.com/galaxyproject/galaxy/issues/5944.
I'm working on tests, but one easy way to test this is create a collection
through the list builder interface, then delete the source HDAs.
Then run a workflow on the collection and without this commit
the outputs get created but the job just hangs around indefinetely.
With the PR the steps consuming the collection and the subsequent jobs
will be paused.
Set to paused
Commit: 0e31f97269586b061ce58a9eac75743590e310a3
https://github.com/galaxyproject/galaxy/commit/0e31f97269586b061ce58a9eac75…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-05-31 (Thu, 31 May 2018)
Changed paths:
M test/api/test_workflows.py
Log Message:
-----------
Add a testcase for pausing jobs with deleted input
Fix test
Commit: ed0b087926c53f4c2c4293ff6443f997fafa9526
https://github.com/galaxyproject/galaxy/commit/ed0b087926c53f4c2c4293ff6443…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-05-31 (Thu, 31 May 2018)
Changed paths:
M lib/galaxy/jobs/handler.py
M lib/galaxy/model/__init__.py
M test/api/test_workflows.py
Log Message:
-----------
Fail jobs with purged inputs
We can't resume these jobs anyway, so better to set them to failed.
Also resets the info field for datasets produced by resumed jobs.
Commit: f9a65a10eb10fd2942ca3306b461ba7dbae4aa09
https://github.com/galaxyproject/galaxy/commit/f9a65a10eb10fd2942ca3306b461…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-05-31 (Thu, 31 May 2018)
Changed paths:
M client/galaxy/scripts/mvc/dataset/dataset-li.js
Log Message:
-----------
Display the info field for paused jobs
Commit: f8cc653b3051b93cea446317194fcdd88d1aa674
https://github.com/galaxyproject/galaxy/commit/f8cc653b3051b93cea446317194f…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-05-31 (Thu, 31 May 2018)
Changed paths:
M lib/galaxy/jobs/handler.py
M test/api/test_workflows.py
Log Message:
-----------
Pause job if input dataset state is paused
Commit: ca31222cf87a471648876575f068f4e5ac3cba92
https://github.com/galaxyproject/galaxy/commit/ca31222cf87a471648876575f068…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-05-31 (Thu, 31 May 2018)
Changed paths:
M lib/galaxy/model/__init__.py
Log Message:
-----------
Optimize job resume function
Commit: c401f5a713c1774e2dd8d817de04d48e2864e40f
https://github.com/galaxyproject/galaxy/commit/c401f5a713c1774e2dd8d817de04…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-06-01 (Fri, 01 Jun 2018)
Changed paths:
M client/galaxy/scripts/mvc/dataset/dataset-li.js
Log Message:
-----------
Use info style when displaying the reason for pausing a dataset
Commit: a5594551c09250db0dac799711a0d5676817038c
https://github.com/galaxyproject/galaxy/commit/a5594551c09250db0dac799711a0…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2018-06-01 (Fri, 01 Jun 2018)
Changed paths:
M client/galaxy/scripts/mvc/dataset/dataset-li.js
M lib/galaxy/jobs/handler.py
M lib/galaxy/model/__init__.py
M test/api/test_workflows.py
Log Message:
-----------
Merge pull request #6036 from mvdbeek/kill_jobs_with_invalid_input
Pause jobs with invalid inputs
Compare: https://github.com/galaxyproject/galaxy/compare/f19f09b30f60...a5594551c092
**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.