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Author SHA1 Message Date
Martin Cech 0fc0a49b4b change 'user' menu to login or register for anons 2017-04-21 14:57:47 -04:00
Martin Cech e04ac61003 Merge pull request #3953 from dannon/openid_sample_nogoogle 
Remove Google from OpenID providers in the sample.
 2017-04-21 14:41:41 -04:00
Martin Cech 0bc8d1f4ce move genomespace as the first shown provider in selection 2017-04-21 13:53:50 -04:00
John Chilton 386afbb4f6 Merge pull request #3933 from dannon/exception_logging_fixes 
Standardize usage of log.exception
 2017-04-21 08:54:24 -04:00
Dannon Baker 4adda20b0b Remove Google from OpenID providers in the sample. Google dropped OpenID support a while back. 2017-04-20 15:03:33 -04:00
Evgeny Anatskiy dc29a1a637 add support for the 'conditional' input type 2017-04-20 17:16:59 +02:00
Björn Grüning 01b3eb42d8 Merge pull request #3940 from jmchilton/collection_op_filter_from_file 
Collection Operation - Filtering from a File
 2017-04-20 15:57:21 +02:00
John Chilton 9f4fd7c449 Merge pull request #3941 from natefoo/containers-bugfixes 
Containers interface and GIE bugfixes
 2017-04-20 09:53:10 -04:00
Evgeny Anatskiy 934a26c195 improve the generator + bugfixes 2017-04-20 15:44:15 +02:00
John Chilton 49abfced09 Implement collection operation for filtering lists from a file. 2017-04-17 17:08:25 -04:00
Nate Coraor 1e536e4ec7 Add an ignore_volumes option for swarm_mode containers 2017-04-17 16:54:54 -04:00
Nate Coraor 154530994f Error handling for GIE container readiness check 2017-04-17 16:51:35 -04:00
Nate Coraor a2b8b43179 Generate proper url for readiness endpoint 2017-04-17 16:50:52 -04:00
Nate Coraor abe6434916 Update ethercalc GIE for readiness checking 2017-04-17 16:49:21 -04:00
John Chilton 2288a88ab7 Fix relabel_from_file collection operation error handling if duplicate identifiers. 2017-04-17 13:12:57 -04:00
Björn Grüning e9011488f2 Merge pull request #3938 from jj-umn/patch-6 
Update text.py  Add interaction annotations to SnpEffDb metadata
 2017-04-17 18:43:57 +02:00
Jim Johnson 77caed9861 Update text.py Add interaction annotations to SnpEffDb metadata 
Interaction annotations are now included in SnpEff v4.3
 2017-04-17 10:12:14 -05:00
Dannon Baker d43d7aa140 Fix E241, F841 from exception refactoring. 2017-04-14 08:02:33 -04:00
John Chilton 09bcdd9185 Various improvements to relabel from file collection operation. 
- Better error handling (check for bad characters when creating collections).
- Implement a strict mode parameter to do even more validation.
- Rework tabular vs txt mode to be explicit user choice.
- Mirror fix in release_17.01 for datasets not having a history,
 2017-04-13 23:15:56 -04:00
John Chilton 338130a979 Fix failing test case in relable_from_file based on comment from @mvdbeek. 2017-04-13 23:11:49 -04:00
mvdbeek d21c14f009 Add possibility to rename collection items from a tabular file 2017-04-13 23:11:49 -04:00
John Chilton 9b6a9dc0c7 Start work on a relabelling collection operation. 
I think it needs to be touched up but the basic operation seems to work so far. I think what remains to be done is:

 - Validate uniqueness of identifiers and provide nice messages if they are not unique.
 - Validate that at least the required number of lines are present in the file and provide a nice message if not.
 - Add strict mode to ensure exactly the correct number of lines is added.
 - Find where validation of identifiers happens in the API and apply same validation here - try not to let unsafe identifiers be created.
 - Consider more advanced modes - selecting a column, apply a regex replace, pick two columns for nested lists, etc.... None of this may need to be needed in the first iteration.
 - Consider another mode where a collection is labelled against an existing collection - should that be a separate tool of the same tool.
 2017-04-13 23:11:49 -04:00
John Chilton 695293f015 Merge pull request #3863 from natefoo/containers-abstraction 
Container interface abstraction
 2017-04-13 16:20:12 -04:00
Björn Grüning 040635d3dc Merge pull request #3844 from jmchilton/dev_workflow_conf 
Allow explicit configuration of handlers for workflow scheduling.
 2017-04-13 22:14:18 +02:00
Björn Grüning 55c4d52455 Merge pull request #3920 from guerler/fix_display_to_text_for_runtime_values 
Identify and handle runtime values when generating displayed text
 2017-04-13 22:09:06 +02:00
Björn Grüning 1fe9c4d066 Merge pull request #3931 from jmchilton/maf_fix_47 
[17.01] Fix another tool (GeneBed_Maf_Fasta2) requiring the legacy Galaxy environment.
 2017-04-13 21:58:13 +02:00
Dannon Baker c46e36bdee Overhaul string templating in log.exception statements -- should apply to all logs, eventually. 2017-04-13 15:03:28 -04:00
Dannon Baker d303cf5ffb Strip exception strings from being included in log.exception statements across the project. 2017-04-13 14:06:11 -04:00
Dannon Baker 8599dff7a0 Standardize usage of log.exception in datatypes registry. 2017-04-13 12:35:02 -04:00
Dannon Baker d21c8dc8f1 Merge pull request #3881 from erasche/unicode-viz-errors 
Fix inability for viz to raise loading with non-ascii messages
 2017-04-13 12:28:26 -04:00
Eric Rasche d6336b7125 Remove unnecessary print 2017-04-13 16:27:19 +00:00
Dannon Baker 23895e9ef0 Merge pull request #3926 from guerler/fix_library_parameter_style 
Fix library parameter style width to avoid second line
 2017-04-13 11:54:31 -04:00
John Chilton 33d6628dab Fix another tool (GeneBed_Maf_Fasta2) requiring the legacy Galaxy environment. 2017-04-13 10:21:14 -04:00
guerler 4f4efe6405 Fix library parameter style width to avoid second line 2017-04-12 21:53:15 -04:00
Dannon Baker 3e191c7ff4 Merge remote-tracking branch 'upstream/release_17.01' into dev 2017-04-12 11:07:23 -04:00
guerler 735e38d1a3 Adjust unit test cases 2017-04-11 13:56:13 -04:00
guerler 7f111eea52 Add missing spaces 2017-04-11 13:51:27 -04:00
guerler 9c9a7b97c5 Remove parsing of app parameter from select field wrapper 2017-04-11 13:48:52 -04:00
guerler 8ef55bca36 Remove app parameter from callers used in makos 2017-04-11 13:39:05 -04:00
guerler 18b006cb75 Remove app parameter from text conversion caller 2017-04-11 13:36:03 -04:00
guerler 278030638c Use new runtime value identifier for select field context values 2017-04-11 13:12:18 -04:00
guerler 7439d03baf Remove optional app parameter for text conversion caller 2017-04-11 13:10:12 -04:00
guerler c134dac9d5 Identify and handle runtime values when generating displayed text 2017-04-11 12:58:33 -04:00
John Chilton 93b366d75a Merge pull request #3904 from mvdbeek/fix_instance_not_bound 
[17.01] Fix Instance is not bound to a Session
 2017-04-09 22:49:19 -04:00
Martin Cech 2396befa02 Merge pull request #3846 from dannon/mq_routing_fix 
[17.01] Fix for direct message routing using a 'real' exchange like rabbitmq
 2017-04-09 13:17:40 -04:00
Evgeny Anatskiy ebf1f3903c bugfixes and small improvements 2017-04-08 23:42:20 +02:00
Evgeny Anatskiy ebcb2627df tiny changes 2017-04-08 15:58:21 +02:00
mvdbeek cda2b32ebe Fix Instance is not bound to a Session 
by refreshing the tool_version_cache, just like we do when we reload the
toolbox.
 2017-04-08 14:39:11 +02:00
Evgeny Anatskiy a3037742cf bugfixes after the previous merge 2017-04-08 01:16:51 +02:00
Evgeny Anatskiy 73e90fc7f5 Merge branch 'dev' into auto_tour_generation 
# Conflicts:
#	static/maps/mvc/tool/tool-form-base.js.map
#	static/maps/mvc/tool/tool-form.js.map
#	static/scripts/bundled/analysis.bundled.js
#	static/scripts/bundled/analysis.bundled.js.map
#	static/scripts/bundled/libs.bundled.js
#	static/scripts/bundled/libs.bundled.js.map
#	static/scripts/bundled/login.bundled.js
#	static/scripts/bundled/login.bundled.js.map
#	static/scripts/mvc/tool/tool-form-base.js
#	static/scripts/mvc/tool/tool-form.js
 2017-04-08 00:56:21 +02:00