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Author SHA1 Message Date
Martin Cech d72eee3d4a wrap bare str raises with generic Exception() 
as Pyton 2.7 does not support bare str
 2016-05-26 13:14:22 -04:00
John Chilton 4eeb73ec8c Merge pull request #2418 from nsoranzo/toolbox_watcher 
Raise Exception if watch_tools has an unrecognized value
 2016-05-26 08:17:06 -04:00
Nicola Soranzo 4bfcce0d56 Raise Exception if watch_tools has an unrecognized value 
Also do not log message "Watchdog library unavailable" if watch_tools is
False
 2016-05-26 11:59:08 +01:00
Björn Grüning 27b70ca984 Merge pull request #2396 from guerler/scratchbook_slider_000 
Add history navigation options for dataset frames to scratch book
 2016-05-26 02:10:52 +02:00
Dannon Baker 50359e1633 Merge remote-tracking branch 'upstream/release_16.04' into dev 2016-05-25 17:06:25 -04:00
Dannon Baker c63bf911bc Merge pull request #2389 from jmchilton/checkers_restore 
[16.04] Provide backward compatible galaxy.datatypes.checkers module...
 2016-05-25 16:40:33 -04:00
John Chilton 71f9d96216 Remove HTML_CHECK_LINES from checkers export. 
As suggested by @nsoranzo and @dannon, we will restore if and only if someone finds a datatype that uses it.
 2016-05-25 16:29:02 -04:00
guerler 197f2283f9 Merge branch 'dev' into scratchbook_slider_000 2016-05-25 16:26:24 -04:00
Dannon Baker f0a1bc8cbd Merge pull request #2413 from carlfeberhard/fix.history-collection 
UI, history: correctly handle index API defaults
 2016-05-25 14:47:53 -04:00
Martin Cech 81702e7fba Merge pull request #2395 from bgruening/conda_search 
Add conda search function
 2016-05-25 14:44:45 -04:00
Martin Cech b16ad40bee Merge pull request #2412 from jmchilton/2409_followup 
Follow up on @nsoranzo comment...
 2016-05-25 14:26:03 -04:00
carlfeberhard 2e45e77fa8 UI, history: correctly handle index API defaults 
Bypasses the histories.index default `deleted=False` flag when using
HistoryCollection to fetch with `includeDeleted`.
 2016-05-25 14:24:49 -04:00
John Chilton 168ba1b130 Follow up on @nsoranzo comment... 
https://github.com/galaxyproject/galaxy/pull/2409#discussion_r64588439

\minor
 2016-05-25 14:23:41 -04:00
Dannon Baker b41e03994e Merge pull request #2409 from jmchilton/test_assertions_lib 
Enhancements to tool test output verification.
 2016-05-25 14:20:57 -04:00
Dannon Baker d72031869d Merge pull request #2411 from carlfeberhard/show-params.add-hid 
UI, datasets: show hid in 'view details' page
 2016-05-25 14:19:55 -04:00
carlfeberhard 5dcd04b0b2 UI, datasets: show hid in 'view details' page 
Adds the hid to the list of dataset/job information on the show_params/
view details/info page.
 2016-05-25 12:57:09 -04:00
guerler a12c1cb45b Cache histories individually 2016-05-25 11:37:47 -04:00
guerler 617cd2de82 Add event handlers to navigate through history 2016-05-25 11:37:47 -04:00
guerler 64cb97cfc9 Parse view instead of content dom on click 2016-05-25 11:37:47 -04:00
guerler e16c3f34f3 Remove unused class variables, reduce indention 2016-05-25 11:37:46 -04:00
guerler 44bd042624 Add support for optional header items/icons 2016-05-25 11:37:46 -04:00
guerler 53fa566a54 Use regular initialization from frame shadow view 2016-05-25 11:37:46 -04:00
guerler b9e2983e90 Remove grid lock feature 2016-05-25 11:37:46 -04:00
guerler be97d7e6db Replace frame dictionary with regular view 2016-05-25 11:37:45 -04:00
Nicola Soranzo 7479dddb85 Merge branch 'release_16.04' into dev 2016-05-25 16:28:15 +01:00
Nicola Soranzo 5db5e13958 Merge branch 'release_16.01' into release_16.04 
Conflicts:
	test/unit/managers/test_HistoryManager.py
 2016-05-25 16:23:07 +01:00
John Chilton c033544a7e Merge pull request #2410 from martenson/more-tspus-attempts 
increase range to 5, Jenkins still fails to push sometimes
 2016-05-25 10:40:48 -04:00
Martin Cech 3330a25c75 increase range to 5, Jenkins still fails to push sometimes 2016-05-25 10:39:17 -04:00
Daniel Blankenberg 7dcf850ed5 Merge pull request #2402 from natefoo/slurm-fixes 
[16.04] Catch all exceptions in slurm's _complete_terminal_job() to prevent looping job completion
 2016-05-25 09:51:06 -04:00
John Chilton caec8c838a Merge pull request #2397 from nsoranzo/edam_topics 
Add EDAM topics to tools and expose in API
 2016-05-25 09:44:32 -04:00
John Chilton 248eed81fa Merge pull request #2408 from erasche/fix-condor-universe 
Check variable's presence before calling str methods
 2016-05-25 09:42:23 -04:00
John Chilton 47a6516096 Merge pull request #2407 from carlfeberhard/fix.most_recently_used 
[16.01] API, history: fix order in most_recently_used
 2016-05-25 09:41:32 -04:00
John Chilton 4765f5876e Enhancements to tool test output verification. 
Refactor test verification into galaxy-lib-compat module.

- Refactor a bunch class methods in ``test.base.twilltestcase`` into module functions in ``galaxy.tools.verify``.
- Move ``test.base.test_data`` to ``galaxy.tools.verify.test_data``.
- Move ``test.base.asserts`` to ``galaxy.tools.verify.asserts``.

Remove duplication in execution of these methods between composite and normal test outputs. This also entailed reworking the parsing of the composite test outputs to bring them inline with normal outputs. In addition to simplify removing duplication, this means many more tests can be made over composite outputs - such as md5 checks and test assertions. I've added a new framework test tool to verify this.
 2016-05-25 09:37:49 -04:00
Eric Rasche d728d3a373 Check variable's presence before calling str methods 2016-05-24 21:48:17 +00:00
carlfeberhard 2a29e92ef9 API, history: fix order in most_recently_used 
- Fix ascending order used in HistoryManager.most_recent to descending
- Slightly update the docs to reflect actual value better
- Add tests
 2016-05-24 17:08:08 -04:00
Nate Coraor b6d65da83d Fix linting error 2016-05-24 15:13:39 -04:00
Nate Coraor 5fbb65e503 Catch all exceptions in slurm's _complete_terminal_job() to prevent 
looping job completion
 2016-05-24 14:03:19 -04:00
Björn Grüning 0b3832b952 Fix bad merge. 2016-05-24 14:12:16 +02:00
Nicola Soranzo 1652e0ceed Add EDAM topics to tools and expose in API 2016-05-24 12:17:39 +01:00
Bjoern Gruening 53604369f2 stdin and stdout needs a PIPE to retrive the stdout 2016-05-23 21:15:08 +02:00
Björn Grüning 2eee6e2abc add is_target_available() to conda utils 2016-05-23 21:15:08 +02:00
John Chilton 66947c20ef Provide backward-compatible galaxy.datatypes.checkers module. 
xref http://dev.list.galaxyproject.org/STACKS-error-td4669428.html
 2016-05-23 10:21:08 -04:00
John Chilton fa77c8f459 Merge pull request #2390 from guerler/revise_tool_framework_000 
Add a new workflow building mode variation which does access the history
 2016-05-23 09:16:14 -04:00
John Chilton a9c94bd3d7 Merge pull request #2374 from guerler/fix_error_log_000 
Revise asserts triggering false exceptions for dynamic parameters
 2016-05-23 09:14:35 -04:00
John Chilton 7c3622db40 Merge pull request #2379 from mvdbeek/edam_operations 
Add EDAM operations to tools and expose in API
 2016-05-23 09:12:54 -04:00
John Chilton ebd3250253 Merge pull request #2383 from natefoo/manylinux-support 
Drop "Galaxy pip" in favor of manylinux1 wheels (which are supported in pip >= 8.1)
 2016-05-23 09:12:08 -04:00
John Chilton 04e34f346f Merge pull request #2391 from guerler/revise_tool_framework_001 
Align and improve validation errors and value to text conversions
 2016-05-23 09:07:51 -04:00
John Chilton 4461f24588 Merge pull request #2394 from bgruening/fix_conda_install 
Fix the installed conda version to 3.19.3.
 2016-05-23 09:06:16 -04:00
Bjoern Gruening 0c4601aaec Fix the installed conda version to 3.19.3. 2016-05-21 13:33:30 +02:00
guerler 9d56eaf07a Add a new workflow building mode variation which does access the history 2016-05-20 21:56:47 -04:00