Dannon Baker
c18887c0d1
Clean up pam auth helper.
2015-07-17 08:06:04 -04:00
Dannon Baker
7019e32305
Merge with dev
2015-07-17 07:54:25 -04:00
Nate Coraor
cb8f6354de
Merge pull request #458 from pvanheus/auth_pam
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AuthProvider for PAM (Pluggable Authentication Modules)
2015-07-14 22:12:17 -04:00
Peter van Heusden
b9c9f11ce1
* New PAM AuthProvider for interfacing with the Pluggable Authentication Module system ( http://www.linux-pam.org/ )
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* Helper script to allow authenticating against modules as root
2015-07-15 00:47:13 +02:00
Nicola Soranzo
cc9b0bed85
Fix all E712 errors. Standardize sqlalchemy imports.
2015-07-14 20:49:34 +01:00
Nicola Soranzo
34d9388456
Use os.pardir everywhere instead of '..' .
2015-07-14 16:20:29 +01:00
Nicola Soranzo
6569c2dcc3
Partially lint scripts/ .
2015-07-13 20:13:28 +01:00
Martin Cech
eb54b1d854
expose searching full TS toolset over a separate index
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the index is created by the same script (build_ts_whoosh_index.py)
2015-06-19 16:24:27 -04:00
John Chilton
4e82c80293
Fix for 38679a0d32.
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Reported by @golharam.
2015-06-18 15:57:49 -04:00
Martin Cech
508b685c70
fix common API scripts so they dont fail when response has no url param
2015-06-15 16:12:21 -04:00
John Chilton
374795f631
Only cleanup successful jobs when testing.
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As per the recommendation of Ryan G. at http://dev.list.galaxyproject.org/keep-job-output-and-scripts-on-failed-tests-td4667327.html .
I considered making this 'never' - since those files will get cleaned up at the end anyway. This would actually reduce our test coverage related to job cleanup logic - so I have decided this is a fine a middle ground.
2015-06-15 09:53:59 -04:00
John Chilton
584f673f8d
Merge remote-tracking branch 'jmchilton/dev' into ts-search-expansion
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Conflicts:
lib/galaxy/webapps/tool_shed/buildapp.py
2015-06-15 09:43:59 -04:00
John Chilton
732abcc0db
Merge remote-tracking branch 'jmchilton/release_15.05' into dev
2015-06-08 14:04:28 -04:00
Nicola Soranzo
292d16a593
Mark also HDAs as purged when purging datasets via cleanup script.
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This will make purged datasets be shown as purged in histories,
preventing them to be undeleted through the UI.
This will not fix datasets previously purged through this script,
scripts/cleanup_datasets/pgcleanup.py may be used for that.
2015-06-04 18:06:01 +01:00
Dannon Baker
e56b2a3433
Merge pull request #274 from dpryan79/dev
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Add usage information to python cleanup scripts
2015-06-02 07:57:02 -04:00
John Chilton
3946ff50bb
Merge pull request #80 from erasche/jbrowse-ie
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Add EDAM IDs to datatypes
2015-05-22 09:42:59 -05:00
dpryan79
00eb96923f
Add a missing period in populate_uuid.py
2015-05-20 13:01:40 +02:00
dpryan79
0ff5a050d5
Indentation fix
2015-05-19 21:55:36 +02:00
dpryan79
0763cab37a
Update the remainder of the python cleanup scripts
2015-05-19 21:53:45 +02:00
John Chilton
98d8c2cc2e
Allow config of shed tool conf used with `run_tests.sh -installed`.
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Set with GALAXY_TEST_SHED_TOOL_CONF.
This is required to implement galaxyproject/planemo#176 .
2015-05-18 02:07:36 -04:00
John Chilton
08e2c351d9
Add edam formats to most Galaxy datatypes and a script for producing a mapping.
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See notes in scripts/edam_mapping.py for more information on mapping.
This is based on mapping of terms done by Eric Rasche (@erasche) (in galaxyproject/galaxy#80 ) and by the team at Pasteur including @hmenager, @fmareuil, and @odoppelt (in https://docs.google.com/spreadsheets/d/1vptTpJvQfb5FOtRJOajjftUkL9aZ0eeVdhUPvd9h5wY/edit#gid=0 ).
Current mapping at time of commit is https://gist.github.com/jmchilton/73cd540d7a08488843d7 .
2015-05-16 16:47:39 -04:00
Nate Coraor
656d9bef50
Merge remote-tracking branch 'upstream/release_15.05' into dev
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Conflicts:
lib/galaxy/version.py
2015-05-14 11:11:46 -04:00
dpryan79
4c20494011
Make python scripts executable. Tweak remove_renamed_datasets_from_disk.py.
2015-05-12 18:25:32 +02:00
John Chilton
4e1324e432
Add PR7 to release notes (caught by @bgruening).
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... small updates to bootstrap history script for reuse in planemo.
2015-05-12 12:15:56 -04:00
dpryan79
a092aa2f59
Start providing usage information for the various cleanup scripts
2015-05-12 17:53:18 +02:00
John Chilton
bb7fb089fe
First crack at release notes for 15.05.
2015-05-11 23:05:56 -04:00
Martin Cech
e0c7e02e40
do not require option that is actualy in the config
2015-05-07 16:50:27 -04:00
John Chilton
0aabdd4048
Merge remote-tracking branch 'jmchilton/release_15.05' into dev
2015-05-06 20:56:43 -04:00
John Chilton
5d31ce641a
Fix problem with twill's custom subprocess module.
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There has been for some time a scary warning when testing (http://dev.list.galaxyproject.org/run-test-sh-ImportError-cannot-import-name-args-from-interpreter-flags-td4666277.html ) that I now understand is the result of Twill being packaged with its own custom subprocess module that conflicts with modules using multiprocessing (e.g. kombu).
After the #198 this scary warning has become an exception that prevents exception of tests (see https://travis-ci.org/galaxyproject/planemo/jobs/61547827 for instance). Importing subprocess seems to force Python to use the system module instead of twills - which seems to prevent these problems.
There have been other reports of this problem with Twill in other projects and removing the subprocess module didn't seem to break anything for them either.
2015-05-06 20:24:50 -04:00
John Chilton
6e71a90cdd
Merge pull request #151 from natefoo/runtime_stats
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A command line script for collecting stats on job runtimes
2015-04-28 13:11:33 -05:00
Marek Vavrusa
43cd2083f6
runners/drmaa: set 'workingDirectory' correctly
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this fixes an issue with when the Galaxy lib (and therefore working
directory) is not shared with the compute nodes
2015-04-24 16:12:33 +02:00
Nate Coraor
73dd0b1a6f
Add some additional documentation/usage in the doc string
2015-04-23 16:03:58 -04:00
Nate Coraor
bdbc98c47c
Fix the connection string when a database username is provided (reported
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by @afgane in #151 ).
2015-04-23 15:46:46 -04:00
Nate Coraor
fd5c41e902
Pull runtime stats from metrics by default (job state history remains an
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option), a couple other minor improvements to the script.
2015-04-23 15:42:46 -04:00
Nate Coraor
ef69881e56
Added a command line script for collecting stats on job runtimes to help
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admins make decisions about how/where to run jobs.
2015-04-23 12:56:06 -04:00
Martin Cech
16ee7fa74c
add default config for TS search; rename to match TS playbook
2015-04-21 11:59:01 -04:00
Martin Cech
dc736c73f2
remove another abspath; use optparse;
2015-04-14 11:31:44 -04:00
Martin Cech
66e61271b1
add comments and example; add consistency checks; remove bash script
2015-04-14 10:55:34 -04:00
Martin Cech
c12b8063e3
remove abspath
2015-04-13 14:39:31 -04:00
Martin Cech
a9bc7dc5ca
generate separate index for tools in repositories
2015-04-13 13:45:32 -04:00
John Chilton
a357e2b613
Workflow scaling test infrastructure.
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- Add script to hit the API with workflows requests.
- Update testing Dockerfile to allow just booting up with a fixed master API key for this test to leverage.
- WIP: on updating test Dockerfile to work with slurm, multiple handlers, uwsgi, etc...
2015-03-25 14:54:48 -04:00
Carl Eberhard
9a7f5fc17b
Remove scripts/packed, packing infrastructure, and pack_scripts config options
2015-03-17 10:31:35 -04:00
Nicola Soranzo
b4acf247df
Uniform configuration of "From" field of sent emails.
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Subsume activation_email in email_from (used also in tool_shed.ini).
Try also getfqdn in PJA.
Default to 'galaxy-no-reply@' instead of 'galaxy-noreply@' in PJA.
2015-03-13 01:07:57 +00:00
Dannon Baker
8c476931f9
Cleanup related to PR#7 and affected files.
2015-03-05 09:47:14 -05:00
Dannon Baker
fe226e1a9b
Refactoring of set_user_disk_usage and admin controller disk usage to use the same pgcalc
2015-02-25 12:52:47 -05:00
Dannon Baker
9f01d275ef
Add all the necessary dependency requires. Note to self: fix the egg dependency resolution bug so we don't have to dot his.
2015-02-14 10:35:42 -05:00
Nate Coraor
e64ab4c85c
There's no reliable way to use the Galaxy config file to control egg use/fetching since so many things use galaxy.eggs from outside of Galaxy, so drop the support for the config file options and rely on the environment variables only. Reverse the defaults so that eggs and fetching are enabled by default. I'll make sure that they properly get passed to the tool execution environments in the next commit.
2015-02-12 15:10:19 -05:00
Nate Coraor
1e07117791
Place the new egg config options into the environment at Galaxy startup since
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eggs.require() has no access to the config file.
2015-02-12 14:27:37 -05:00
Nate Coraor
92f6ace47f
Ensure the correct default Galaxy config file is found in common_startup.sh, it
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makes a difference for egg fetching since some eggs are conditional based on
config.
2015-02-12 11:47:58 -05:00
Dannon Baker
c733ce370b
Fix path insertion vs appending of <galaxy>/lib for all scripts.
2015-02-12 10:34:51 -05:00
Dannon Baker