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e4924942825c6ea2d472d8ccff45222f165fa6bf
Commit Graph
15180 Commits
Author SHA1 Message Date
John Chilton e492494282 Merge pull request #4456 from nsoranzo/logging_fixes 
Logging fixes
 2017-08-18 09:51:57 -04:00
Marius van den Beek dd89a9c65f Merge pull request #4437 from jmchilton/galaxy_json_rev 
Enhanced tool options for dataset discovery
 2017-08-18 14:18:50 +02:00
Eric Rasche b459399ede Merge pull request #4454 from xgaia/interactive_environment 
Interactive Environment: possibility to don't uppercase env variables
 2017-08-18 13:48:25 +02:00
Nicola Soranzo bd88524a10 Fix import order and Python3 compatibility 2017-08-18 12:35:04 +01:00
Nicola Soranzo e32ad2864f Remove container config log message from cleanup scripts logs 2017-08-18 12:35:04 +01:00
Nicola Soranzo 4e75635d62 Use log.warning() instead of deprecated warn() 2017-08-18 12:35:04 +01:00
Nicola Soranzo 784e6f5fd3 Merge pull request #4396 from jmchilton/workflow_warnings 
Slightly improve workflow warnings/errors logging.
 2017-08-18 12:34:14 +01:00
xgaia 2489499fb6 possibility to don't uppercase env variables 2017-08-18 11:47:00 +02:00
John Chilton 1e1df6786a Variety of fixes for #4437. 2017-08-17 15:43:34 -04:00
John Chilton a8bec7a275 Allow override of provided metadata location. 
Eliminates that terrible circular dependency between tools and jobs.
 2017-08-17 15:41:11 -04:00
John Chilton 39d4411f8c Move determining tool provided metadata style to tool parser. 
Allow override by specifying "provided_metadata_style=" attribute on outputs in tool XML - this should allow newer profile tools to use the older style JSON providing a clear path for upgrades.
 2017-08-17 15:41:11 -04:00
John Chilton 6563e387a5 Allow discovering dataset collections in galaxy.json in a nested fashion. 
Fixes #2658.
 2017-08-17 15:41:11 -04:00
John Chilton 72e361bcf1 Allow discovering datasets directly from galaxy.json... 
without needing to specify a discovered dataset pattern. If the ``discovered_datasets`` tag includes ``from_tool_provided_metadata="true"`` the datsets listed in galaxy.json will just be used directly without needing to be "discovered" using a dataset pattern. Metadata and such can continue to be specified either in that file or on the discovered_dataset element except things like pattern (which is not used) and sort_by (since the json should describe the order I suppose).
 2017-08-17 15:41:10 -04:00
John Chilton 517f248ac4 Overhaul of tool provided job metadata. 
- Add another test to demonstrate referencing entries in galaxy.json for datasets by dataset path basename instead of ID.
- Add a bit more documentation to test tools.
- Redo the structure of galaxy.json for profile >= 17.09 tools with two new test tools to demonstrate the new structure - for both output dataset metadata and discovered dataset metadata.
- Improved abstractions for interaction between tools and jobs to enable different tool provided metadata collection depending on tool profile version.
 2017-08-17 15:41:10 -04:00
John Chilton 0fa287f76a Add autopep8 script to help rebasing branches after #4440. 
Fixes a few more PEP8 issues as part of the autopep8'ing as well.
 2017-08-17 13:47:03 -04:00
Dannon Baker df442ea51a Fix E201 errors (spaces in parens) in new memepsp datatype 2017-08-17 09:44:08 -04:00
Dannon Baker cca1f9e9bc Merge pull request #4430 from gregvonkuster/psp_format 
Add support for the MEME psp format
 2017-08-17 09:41:25 -04:00
John Chilton 7bf7f39963 Cleanup a couple things in #4396 caught by @nsoranzo. 2017-08-17 09:16:02 -04:00
John Chilton 2131370281 Print warning if any input connections are unused during workflow execution. 2017-08-17 09:16:02 -04:00
John Chilton b8f11dfee4 Improve error message for unknown module types when encountered. 2017-08-17 09:12:29 -04:00
Nicola Soranzo a8d7b2df8b Fix more indentation errors 2017-08-17 11:35:39 +01:00
Nicola Soranzo a353b2e88f Fix E127 errors introduced by previous commit 
using:
```
autopep8 -i -r --exclude $(sed -e 's|^|./|' -e 's|/$||' .ci/flake8_blacklist.txt | paste -sd,) --select E127 .
```
 2017-08-17 11:35:39 +01:00
Nicola Soranzo 21b44bf348 Fix all E201 and E202 style errors 
using the following command:
```
autopep8 -i -r --exclude $(sed -e 's|^|./|' -e 's|/$||' .ci/flake8_blacklist.txt | paste -sd,) --select E201,E202 .
```
 2017-08-17 11:35:39 +01:00
Björn Grüning 5799fbc3d1 change file_ext to be inline with memexml and co 2017-08-17 08:49:04 +02:00
Björn Grüning 008a1d849c Merge pull request #4434 from chambm/patch-1 
Avoid adding `(imported from API)` to workflows
 2017-08-17 08:44:39 +02:00
Martin Cech 2c4cf686f8 Merge branch 'dev' into admin_grid_toolversion 
and repack
 2017-08-16 15:18:39 -04:00
guerler fdcd46918d Remove unfilterable columns from group and quota search grids 2017-08-16 15:04:08 -04:00
Matt Chambers c72f43dc5f Avoid adding (imported from API) to workflows 
This should fail a few tests which I will fix with additional commits. Doing this from GitHub...
 2017-08-16 10:01:51 -05:00
Greg Von Kuster 3026bf56c9 Remove strange import - no idea from where it originated 2017-08-16 10:31:02 -04:00
Max Schaefer 43ddd47320 Add missing var declarations. 
In all these cases, a variable was not declared to be a local using `var` (and hence was implicitly interpreted as a global variable), but all uses of that variable were preceded by a definition within the same function, suggesting that the variable was, in fact, meant to be local, not global.
 2017-08-16 15:22:42 +01:00
Greg Von Kuster 7dae650fdb Change Psp to MemePsp and misc fixes per initial review 2017-08-16 09:58:41 -04:00
Dannon Baker c5a91491c6 Merge pull request #4432 from guerler/fix_role_association_check 
Fix private role validation
 2017-08-16 09:27:50 -04:00
Björn Grüning b6f0600e98 Merge pull request #4387 from jmchilton/tool_unit_test_cleanup 
Cleanup of Unit Test Code for Loading Tools
 2017-08-16 14:55:14 +02:00
guerler 522ca9e5c2 Fix private role validation 2017-08-15 17:22:41 -04:00
guerler 86cdaaf610 Add validation messages if resource ids are not correct 2017-08-15 17:14:59 -04:00
guerler f1e13cef05 More messages to validate inputs 2017-08-15 17:02:04 -04:00
guerler bebc5ff56a Move decode id to correct location 2017-08-15 16:46:42 -04:00
guerler f9e8892150 Catch user input error for auto created roles and groups 2017-08-15 16:26:25 -04:00
guerler 246489a7aa Fix messages 2017-08-15 16:06:25 -04:00
guerler 96cad03980 Fix label for default quotas 2017-08-15 15:37:00 -04:00
guerler 4688eef2a4 Fix user id decoding, fix optional array handling 2017-08-15 15:34:40 -04:00
guerler a1897bd32a Hide select all for role and group selectors 2017-08-15 15:12:54 -04:00
Greg Von Kuster 5cebb086b2 Add support for the MEME psp format 2017-08-15 14:03:47 -04:00
guerler b726c33c80 Merge branch 'admin_grid_groups' into admin_grid_toolversion 2017-08-15 12:15:33 -04:00
guerler e72948cb74 Merge branch 'dev' into admin_grid_groups 2017-08-15 12:12:53 -04:00
Nicola Soranzo 07a3049999 Merge branch 'release_17.05' into dev 
Conflicts:
	lib/galaxy/model/tool_shed_install/__init__.py
 2017-08-15 16:24:32 +01:00
John Chilton 44548f8f2f Merge pull request #4409 from nsoranzo/fix_conda_channel_order 
Update conda channel order to sync with Bioconda
 2017-08-15 09:32:54 -04:00
John Chilton 8721da8ca2 Merge pull request #4426 from erasche/local-runner-unicode 
some unicoding for local runner
 2017-08-15 09:27:38 -04:00
John Chilton 7f78ee7b18 Merge pull request #4420 from mvdbeek/fix_wrong_tool_version_cast 
[17.05] Don't cast tool_version to string if tool_version is None-type
 2017-08-15 09:26:58 -04:00
E Rasche 68555f5571 some unicoding 2017-08-15 14:04:05 +02:00