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Author SHA1 Message Date
Nicola Soranzo 13e72e84c5 Merge pull request #5534 from natefoo/17.09-static-map-fix 
[17.09] Map static content by default for Reports and Tool Shed webapps
 2018-02-16 18:19:00 +00:00
Nate Coraor 25952e81e7 Map static content by default for Reports and Tool Shed webapps. 2018-02-14 11:12:40 -05:00
Nicola Soranzo c0c95548a3 Merge branch 'release_17.05' into release_17.09 2018-01-31 10:16:33 +00:00
Björn Grüning 34421966d4 Merge pull request #5406 from mvdbeek/conda_and_channel_order_update 
[17.05] Follow IUC and drop r channel from default conda channels
 2018-01-31 10:15:01 +01:00
Marius van den Beek 8e5d2d3214 Merge pull request #5414 from jmchilton/skip_invalid_pja 
[17.09] Fix the PJA type issue when mapping renames over nested lists.
 2018-01-31 09:20:00 +01:00
John Chilton 9fcac13145 Fix the PJA type issue when mapping renames over nested lists. 2018-01-30 11:16:20 -05:00
mvdbeek a70f2875b3 Remove r channel from more locations 2018-01-29 18:07:29 +01:00
mvdbeek 414c031247 Follow IUC and Drop r channel from default cond channels 2018-01-29 17:35:49 +01:00
Dannon Baker d6fb37071d Merge pull request #5398 from mvdbeek/subworkflow_creation_fix 
[17.09] Subworkflow creation fix
 2018-01-26 10:03:40 -05:00
mvdbeek f589a0cb5b Build client 2018-01-26 14:22:15 +01:00
mvdbeek 74d57cfc1c Fix subworkflow creation 
This fixes #5396. The problem was that we would override the content_id with an
undefined value. Broken in https://github.com/galaxyproject/galaxy/pull/5249.
 2018-01-26 14:22:15 +01:00
Martin Cech b6d0b14921 Merge pull request #5391 from dannon/release_17.09 
[17.09] Constrain workflow tool panel entries to those not deleted.
 2018-01-25 18:38:34 -05:00
Dannon Baker 9c187f0e5a Constrain workflow tool panel entries to those not deleted. 2018-01-25 13:44:40 -05:00
Martin Cech 73418ab787 Merge pull request #5343 from ValentinChCloud/fixes 
[17.09] Fix tool-shed-config-validate
 2018-01-25 10:30:55 -05:00
Dannon Baker 7996a4c0c7 Rebuild client for stable 17.09 2018-01-22 13:31:43 -05:00
Dannon Baker 177aa2e7f9 Merge branch 'release_17.05' into release_17.09 2018-01-22 13:28:42 -05:00
Dannon Baker 4288e96b77 Merge pull request #5237 from martenson/fix-image-proxy-prefix 
[17.05] fix image proxy prefix in tool form
 2018-01-22 13:20:22 -05:00
Dannon Baker 3bf9b3ab1d Merge pull request #5353 from martenson/remove-charlimit-for-fetch 
[17.09] remove charlimit for fetching urls
 2018-01-19 16:35:26 -05:00
Martin Cech 0fdb63e5e3 remove charlimit for fetching urls 
fixes #5349
this would only allow a number of urls that fit 1024 chars together
moreover it would truncate (and break) the last one
 2018-01-19 16:00:56 -05:00
Martin Cech 8fa785427c Merge pull request #5344 from mvdbeek/history_import_fixes 
[17.09] History import fixes
 2018-01-19 10:27:55 -05:00
guerler 662440e730 Add quotes 2018-01-19 14:55:57 +01:00
mvdbeek b5d0030b3e Fix history import by file on multi-handler setups 
The uploaded archive was going to be deleted before the job started running.
 2018-01-19 12:15:16 +01:00
guerler b82676b8ee Switch to transparent readmode for history tarfiles 2018-01-19 12:14:35 +01:00
mvdbeek 5554c2f9b9 Fix import by url for history archive import tool 2018-01-19 12:14:24 +01:00
ValentinChCloud 747309b278 Fix tool-shed-config-validate 2018-01-19 10:28:14 +00:00
Dannon Baker 3c85407ec8 Merge pull request #5331 from mvdbeek/data_manager_reload_fix 
[17.09] Prevent reloading when data table is being modified
 2018-01-18 10:42:33 -05:00
mvdbeek 8f91ae0db9 Reload tool data tables for 'undeclared_tables' 
Thanks @nsoranzo!
 2018-01-18 15:25:39 +01:00
mvdbeek 8c1807c287 Trigger reload for each modified data table 
In unindeted one level too much in the previous commit, which would only reload
the last table (thanks @dannon). The alternative would be to reload all tables,
but I think this is more efficient.
 2018-01-18 15:17:14 +01:00
mvdbeek d94148ff79 Prevent reloading when data table is being modified 
Fixes https://github.com/galaxyproject/galaxy/issues/4783.
 2018-01-18 15:05:47 +01:00
Dannon Baker c3d145ce99 Merge pull request #5327 from martenson/fix-structured-lib-link 
[17.09] fix link to library from history structure view
 2018-01-17 18:05:36 -05:00
Martin Cech 6bef1fcbaa remove an extra F from the folder ID 2018-01-17 15:50:06 -05:00
John Chilton a6e9504dde Merge pull request #5303 from mvdbeek/sentry_hotfix 
[17.09] Fix tool report submission with sentry
 2018-01-12 09:04:41 -05:00
mvdbeek a847dbd3d5 Fix tool report submission 2018-01-12 13:14:19 +01:00
Nicola Soranzo a81f3e4e8c Merge branch 'release_17.05' into release_17.09 
Conflicts:
	lib/galaxy/workflow/modules.py
 2018-01-11 15:42:37 +01:00
Dannon Baker 201c6ca881 Merge pull request #5298 from nsoranzo/release_17.09_backport_5233 
[17.09] Backport #5233
 2018-01-11 09:35:11 -05:00
NCEichner 27c9fff8b9 #5187 
In order to get rid of the conda error described in #5187 I raised the version number beginning from which conda is allowed to use the '--offline' parameter again to "4.4"
 2018-01-11 13:56:29 +01:00
Martin Cech 40f9c6bb85 Merge pull request #5289 from dannon/dataset_edit_fix 
[17.09] Fix dataset edit link
 2018-01-10 13:01:06 -05:00
Dannon Baker 9aabaa6859 Build client 2018-01-10 08:43:05 -05:00
Dannon Baker a19596e3ea Fix dataset-model's edit url 2018-01-10 08:39:30 -05:00
Dannon Baker 087537a7ad Merge pull request #5271 from guerler/fix_workflow_leak 
[17.09] Only collect required attributes of linked steps
 2018-01-05 17:47:56 -05:00
guerler 8602ecbfac Only collect required attributes of linked steps 2018-01-05 11:08:18 -05:00
Dannon Baker bdbc1a680e Merge pull request #5253 from mvdbeek/catch_pysam_errors_when_viewing_bam_files 
[17.09] Catch and display error when displaying broken BAM file
 2018-01-04 19:05:23 -05:00
mvdbeek 7483648b3e Catch error when displaying broken BAM file 
This should fix https://github.com/galaxyproject/galaxy/issues/5252.
 2018-01-02 11:59:47 +02:00
Martin Cech 41ce472cf2 Merge pull request #5249 from mvdbeek/fix_wrong_tool_id_after_switching_versions 
[17.09] Fix wrong tool id after switching versions
 2018-01-01 14:20:21 -05:00
Marius van den Beek d1510c7394 Merge pull request #5172 from jmchilton/1705_subworkflow_collection_outputs 
[17.05] Provide UI collection output information for subworkflows.
 2018-01-01 12:57:39 +02:00
mvdbeek cb4ef22e1b Build client 2017-12-31 20:22:58 +02:00
mvdbeek d448001fe6 Also update tool_id when switching versions in workflow editor 2017-12-31 20:18:02 +02:00
Martin Cech cb9fe3efe8 implement more restrictive selector, use jquery each isntead of _ 
thanks to jmchilton and dannon
 2017-12-20 13:23:28 -05:00
Martin Cech 40a5ddde01 fix image proxy prefix in tool form 
alternatively I think this could be fixed at the point
 when this image url is being generated on backend
 2017-12-20 11:37:22 -05:00
John Chilton 44635eae1d Merge pull request #5217 from mvdbeek/fail_if_galaxy_json_tools_write_to_stderr 
[17.09] Fail job if tools that use galaxy.json write to stderr
 2017-12-15 10:39:59 -05:00