Dannon Baker
e7d3cceb5e
Another sqla comparison in the user controller.
2015-07-21 08:28:29 -04:00
Dannon Baker
ed616f5575
sqlalchemy fixes in toolshed repository controller
2015-07-21 08:21:33 -04:00
Dannon Baker
01010d3a69
Another job handler comparison fix.
2015-07-21 08:19:11 -04:00
Nicola Soranzo
4ba3cf2a13
Fix last SQLAlchemy comparison broken in 9805294f97 .
2015-07-21 02:48:43 +02:00
Dannon Baker
fed3bddc30
Import null, oops.
2015-07-20 15:38:36 -04:00
Dannon Baker
b0c6512c5b
Fix more sqlalchemy comparisons broken during flake8'ing.
2015-07-20 15:36:59 -04:00
Martin Cech
6d9ac63681
Merge pull request #370 from Airistotal/Reports_Paginate
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Reports pagination
2015-07-20 13:31:26 +02:00
Dannon Baker
209ff0f6e6
Fix for egg building broken in flake8'ing
2015-07-18 08:49:18 -04:00
Airistotal
5710ee1458
Removed unused import
2015-07-17 14:43:33 -05:00
Airistotal
3811c43eb9
Fixed duplicate imports
2015-07-17 14:42:29 -05:00
Airistotal
e7eb7686ac
Fix imports
2015-07-17 14:30:43 -05:00
Airistotal
7e6198a8f7
Merge branch 'dev' of https://github.com/galaxyproject/galaxy into Reports_Paginate
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Conflicts:
lib/galaxy/webapps/reports/controllers/jobs.py
2015-07-17 14:28:23 -05:00
John Chilton
be3bd7a296
Merge pull request #419 from kaktus42/error_specification
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add error message for bad dependency declaration
2015-07-17 14:56:52 +01:00
Dannon Baker
345c86d8ef
More fixes for toolshed step handler post-merge.
2015-07-17 08:04:19 -04:00
Dannon Baker
7019e32305
Merge with dev
2015-07-17 07:54:25 -04:00
Nate Coraor
37cf1af4df
lint fixes for #458
2015-07-14 22:15:08 -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
John Chilton
23209d5497
Merge pull request #441 from Christian-B/unlinked_dependencies
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Added unlinked dependency resolver
2015-07-14 12:54:16 -04:00
John Chilton
141980451c
Merge pull request #444 from yhoogstrate/dev
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Fix md5sum/sha256 in toolshed action
2015-07-14 12:48:02 -04:00
Nicola Soranzo
34d9388456
Use os.pardir everywhere instead of '..' .
2015-07-14 16:20:29 +01:00
John Chilton
163b0e37ca
Implement <filter> tag for output collections.
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Closes #445 .
2015-07-14 10:18:24 +01:00
Dannon Baker
29c4f1ae85
Clean up model.mapping. TODO: this made it compliant, still needs a pass to make it consistent.
2015-07-13 15:12:04 -04:00
Dannon Baker
1f62be4e1a
Fix lped converters and remove from flake8 blacklist
2015-07-13 14:44:47 -04:00
Nate Coraor
37b231cb3d
Verify MD5 and SHA256 sums on other types of actions. For all types of
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actions other than download_by_url, these must be specified as
attributes on the <action> tag, the old `#hash#` method in the URL is
not supported.
2015-07-13 14:43:05 -04:00
Dannon Baker
e1bbbe5ae8
Merge branch 'dev' into lint-additions
2015-07-13 14:20:24 -04:00
Dannon Baker
e0d38ae662
noqa removal in api/histories
2015-07-13 13:59:14 -04:00
Dannon Baker
b8b34cef60
noqa removal in api/groups
2015-07-13 13:59:01 -04:00
Dannon Baker
589dad6205
pep8'd and noqa removal of framework/webapp
2015-07-13 13:53:20 -04:00
Dannon Baker
e68e81dc67
sqlalchemy expressions in grids helper
2015-07-13 13:03:04 -04:00
Dannon Baker
8a031fb290
sqlalchemy expressions in admin controller
2015-07-13 12:54:27 -04:00
Dannon Baker
cb5593f840
Noqa sqlalchemy fix in base controller.
2015-07-13 12:50:25 -04:00
Dannon Baker
3df6daa52c
Various fixes and removal of noqas in security module
2015-07-13 12:47:12 -04:00
Dannon Baker
f623e28ae9
Fix alignment in model
2015-07-13 12:37:51 -04:00
Dannon Baker
2c100d715b
Remove noqas from model
2015-07-13 12:37:29 -04:00
Dannon Baker
db6786e413
Remove noqas from sharable manager
2015-07-13 12:32:44 -04:00
Dannon Baker
a34c5460a4
Remove noqas in library manager
2015-07-13 12:27:27 -04:00
Nate Coraor
72b7381fc2
Improvements to @erasche's download hash changes suggested by
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@yhoogstrate.
2015-07-13 11:36:16 -04:00
carlfeberhard
4792825924
Merge pull request #446 from jgoecks/trackster-close-files
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Trackster fixes: (a) close data provider files after reading from the…
2015-07-13 11:36:02 -04:00
Dannon Baker
97ac587fed
One more sqlalchemy identity/value comparison fix.
2015-07-13 11:32:21 -04:00
Nate Coraor
d5b28bea6d
Merge pull request #443 from Christian-B/config_file_not_found
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Added log error for config file not found
2015-07-13 16:13:59 +01:00
Dannon Baker
ab45efaba9
Fix broken sqlalchemy identity logic. Example:
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```
In [3]:
sa_session.query(galaxy.model.User).filter(galaxy.model.User.deleted is
False).all()
Out[3]: []
In [4]:
sa_session.query(galaxy.model.User).filter(galaxy.model.User.deleted ==
False).all()
Out[4]: [<galaxy.model.User at 0x1094e1610>]
```
2015-07-13 11:00:57 -04:00
Martin Cech
e9aa6e843d
Merge pull request #426 from ericenns/feature/library_folder_export_to_history
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Feature/library folder export to history
2015-07-13 16:29:01 +02:00
Nicola Soranzo
43aa5fa482
Lint various Python files.
2015-07-13 00:13:21 +01:00
Nicola Soranzo
626871c2b4
Fix for 6135cb5764 "linting lib/galaxy/webapps" .
2015-07-12 21:33:12 +01:00
Bjoern Gruening
cdf089e322
remove unsued import
2015-07-12 21:31:47 +01:00
Bjoern Gruening
f1fa2ab316
additional linting of datatypes to make it more strict
2015-07-12 21:31:12 +01:00
Bjoern Gruening
1dab5f9384
revert changes to model/migrate/versions/
2015-07-12 21:30:43 +01:00
Nicola Soranzo
9805294f97
Revert "Revert "[WIP] Mega flake8 linting""
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This reverts commit 37f1976d38
2015-07-12 21:25:44 +01:00
Dannon Baker