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Commit Graph
15356 Commits
Author SHA1 Message Date
mvdbeek 912da2f3b9 Fix checking WorkflowInvocation for published workflows 2017-08-19 14:45:58 +02:00
Nuwan Goonasekera 52b26f45a2 Registered genomespace_importer as a tool needing Galaxy's python env 2017-08-19 00:38:08 +05:30
Nuwan Goonasekera b73e21b584 Formatting and linting fixes for GenomeSpace tool 2017-08-19 00:38:07 +05:30
Nuwan Goonasekera ae6ae8ffe2 Added new config setting for GenomeSpace UI URL 2017-08-19 00:38:07 +05:30
Nuwan Goonasekera cb1b086324 Fixed pylint errors 2017-08-19 00:38:07 +05:30
Nuwan Goonasekera e39901ef06 Moved back some code to wrapper and added back data type sniffing. 2017-08-19 00:38:06 +05:30
Nuwan Goonasekera 1342c2bd70 Integrated File Browsing and Workflow support for GenomeSpace 2017-08-19 00:38:06 +05:30
Martin Cech d883fc162e add ommitted conflict resolution 2017-08-18 13:44:34 -04:00
John Chilton cd22de114c Merge pull request #4457 from erasche/sentry-extra-info 
More detailed sentry reports
 2017-08-18 13:02:28 -04:00
Dannon Baker 9c6fd670cf Merge pull request #4455 from nsoranzo/multiline_if_conditionals 
Uniform indentation of multiline if conditionals
 2017-08-18 10:13:05 -04:00
John Chilton e492494282 Merge pull request #4456 from nsoranzo/logging_fixes 
Logging fixes
 2017-08-18 09:51:57 -04:00
xgaia 30562c09c5 don't uppercase envoverride 2017-08-18 15:13:57 +02:00
E Rasche e987b9b9e4 swap id to username 2017-08-18 14:25:44 +02:00
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
E Rasche 8d132b2bca More detailed sentry reports 2017-08-18 14:18:23 +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
Nicola Soranzo d2d1f857bb Fix import order and Python3 compatibility for lib/galaxy/util/pastescript/serve.py 2017-08-18 12:18:42 +01:00
Nicola Soranzo cff9292f07 Uniform indentation of multiline if conditionals 
Use 8-spaces indentation for the conditional continuation lines of an
`if`-statement where the conditional part spans multiple lines.

According to PEP-8, using 4-spaces "can produce a visual conflict with
the indented suite of code nested inside the `if`-statement", but the PEP
"takes no explicit position".

There were only 2 places in the whole codebase where 8 spaces were not
used, this will make it uniform.
 2017-08-18 12:18:42 +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
Martin Cech 50ebc19afd rename lda_datasets to library_datasets 2017-08-17 15:36:08 -04:00
Martin Cech cd09d1327a refactor the rest of the module to use new manager 2017-08-17 15:30:57 -04:00
Martin Cech e17ab411e3 refactor show method to use new manager 2017-08-17 15:23:32 -04:00
Martin Cech dc834a52c1 fix copypasta error 2017-08-17 15:18:36 -04:00
Martin Cech 61eb011403 refactor decode_id method to use base manager 2017-08-17 15:18:28 -04:00
Martin Cech 042386ff87 wip on improving libraries 2017-08-17 15:14:10 -04:00
mvdbeek 685b9de09b Merge remote-tracking branch 'origin/release_17.01' into release_17.05 2017-08-17 20:18:56 +02:00
Matthias Bernt a76547281f Set timeout for aquiring lock to 5min 2017-08-17 20:02:47 +02:00
Matthias Bernt 349c9c8f10 version with no repetition at all 2017-08-17 20:02:41 +02:00
Matthias Bernt a1b8a54ef8 ensure_installed is now iterative instead of recursive 2017-08-17 20:02:36 +02:00
Matthias Bernt 1e1c549e69 added missing parameter to function ensure_installed 2017-08-17 20:02:29 +02:00
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