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Author SHA1 Message Date
mvdbeek ea1f4f8666 Fix the occasional loading of the wrong workflow. Turns out that sometimes the tool_version is undefined (i.e) if the exact node had not been manipulated, but config_form.version is always up to date 2017-08-13 23:50:14 +02:00
mvdbeek db2ea853f6 Now thing are mostly working -- input and output connections are correctly altered ... but saving the workflow and reloading occasionally loads the wrong workflow 2017-08-13 23:50:14 +02:00
mvdbeek 526e98e372 Reset outputs when changing tool versions in wf-editor 2017-08-13 23:50:14 +02:00
mvdbeek 36ce9113f7 Keep spacing consistent (thx @nsoranzo) 2017-08-13 23:50:14 +02:00
mvdbeek 5afe490822 Fix qunit test 2017-08-13 23:50:14 +02:00
mvdbeek 25e05b62c7 Do postchange action only when modifiying tool versions in the workflow editor 2017-08-13 23:50:14 +02:00
mvdbeek 5f1b7d5a50 Show verison button in workflow editor and trigger on_change 2017-08-13 23:50:14 +02:00
John Chilton fc861cdf38 Merge pull request #3064 from manabuishii/install_workflow_and_tools 
Install tools and workflow
 2017-08-12 06:49:01 -04:00
Björn Grüning 331851b049 Merge pull request #3179 from jmchilton/web_config_overhaul_0 
Configuration & Server Overhaul - Tool Shed and Reports
 2017-08-12 10:36:20 +02:00
Björn Grüning c6e45e7b07 Merge pull request #4410 from jmchilton/excel97 
Add Excel97 Datatype
 2017-08-11 21:46:06 +02:00
Martin Cech cca00ea5d8 Merge pull request #4404 from jmchilton/allow_path_paste 
Generalize allow_library_path_paste to allow_path_paste.
 2017-08-11 14:42:16 -04:00
John Chilton fbde34f8c8 Add EDAM format for excel.xls datatype. 2017-08-11 14:38:49 -04:00
John Chilton 10285b8ecb Tweak Excel format phrasing based on review from @nsoranzo. 2017-08-11 14:36:58 -04:00
John Chilton 33c794d273 Merge pull request #4385 from guerler/admin_grid_roles 
Admin grid roles revision
 2017-08-11 14:26:58 -04:00
Martin Cech 600b0aad7c Merge pull request #4377 from guerler/revise_grid_forms 
Remove makos of admin user grid forms
 2017-08-11 12:48:46 -04:00
John Chilton f97efa6f90 Remove unused dataset_info in parameters.grouping. 2017-08-10 14:01:29 -04:00
John Chilton e49ba40d77 Generalize allow_library_path_paste to allow_path_paste. 
Enable pasting paths in the history upload GUI & general purpose tools API for admin users if enabled.
 2017-08-10 14:01:29 -04:00
John Chilton 6353704e4b Merge pull request #4039 from VJalili/patch-11 
Updated parameters check for OpenID
 2017-08-10 13:42:02 -04:00
John Chilton 7dd3ddccaf Require admin for new import_tools function in workflows API. 
Includes test case.
 2017-08-10 13:29:44 -04:00
John Chilton 23db89ba3d Merge remote-tracking branch 'jmchilton/dev' into install_workflow_and_tools 
Conflicts:
 lib/galaxy/webapps/galaxy/api/workflows.py
 2017-08-10 13:23:43 -04:00
John Chilton 98ca8ce7a6 Update config overhaul branch for introduction of galaxy.web.stack package. 2017-08-10 13:15:31 -04:00
John Chilton 539a62f642 Fix ORM scripts for #3179. 2017-08-10 13:15:31 -04:00
John Chilton 1ce93ccfdf Pin version of uWSGI to freshly released 2.0.15 available on wheels.galaxyproject.org. 2017-08-10 13:15:31 -04:00
John Chilton ffe295e96d Fix Python 3 linting problem with test_config_manage.py. 2017-08-10 13:15:31 -04:00
John Chilton 8191fd4928 Add pykwalify as dependency for the new config validation stuff. 
xref https://github.com/galaxyproject/starforge/pull/110
 2017-08-10 13:15:31 -04:00
John Chilton ef46a60a82 Add required dependency on uwsgi. 
Required for the new out-of-the-box configuration of tool shed and reports.
 2017-08-10 13:15:31 -04:00
John Chilton 4945f55e4f Makefile shortcuts for configuration script. 2017-08-10 13:15:31 -04:00
John Chilton 50d426ed2b Add reports documentation to `doc/`. 
- Automatically generate RST docs from config schema.
- Describe older functionality as well as new YAML-based configuration.
- Replace https://wiki.galaxyproject.org/Admin/UsageReports.
 2017-08-10 13:15:30 -04:00
John Chilton 102566dd5e Update Galaxy Reports to use newer configuration schema. 
- Implement kwalify schema to validate/define the schema.
 - Replace ini configuration with YAML (completely backward compatible).
 - Rebuild a sample configuration from the schema (config/reports.yml.sample).
 2017-08-10 13:15:30 -04:00
John Chilton 90e899d68f Update tool shed to use newer configuration schema. 
- Implement kwalify schema to validate/define the schema.
 - Replace ini configuration with YAML (completely backward compatible).
 - Rebuild a sample configuration from the schema (config/tool_shed.yml.sample).
 2017-08-10 13:15:29 -04:00
John Chilton 7973a914e0 Add uwsgi_schema.yml. 2017-08-10 13:14:55 -04:00
John Chilton 8189a1f1e2 Scripts to manage configuration infrastructure. 
This has been rebased several times and includes a variety of fixes (some thanks to martenson).
 2017-08-10 13:14:55 -04:00
John Chilton 1bdb99bbd7 Update galaxy.util.properties to allow YAML. 2017-08-10 13:14:55 -04:00
John Chilton 72e5a00ba0 Centralize launching server for reports and tool shed. 
Initial outline of allowing launch via uwsgi.
 2017-08-10 13:14:55 -04:00
John Chilton 6a7cc34e1b Bring Galaxy, reports, and shed run scripts in sync. 
- They now uniformly handle server option processing.
- Reports and Tool Shed now respect many new and important options such as --skip_venv.
- Reports and Tool Shed now do extra checking around Python version that Galaxy does.

In addition to improving the reports and tool shed startup scripts and reducing cognative load with respect to option handling, this is an important pre-condition to us being able us to switch on uwsgi by default for all three services simultaneously without a bunch of copy and pasting.
 2017-08-10 13:14:55 -04:00
guerler be19b36eca Merge branch 'revise_grid_forms' into admin_grid_roles 2017-08-10 12:30:58 -04:00
guerler 583765c7c0 Merge branch 'dev' into revise_grid_forms 2017-08-10 12:17:22 -04:00
John Chilton bcdf2c84f6 Merge pull request #4254 from ffinfo/vcf_gz_datatype 
Vcf gz datatype
 2017-08-10 12:14:05 -04:00
John Chilton e3de5e250d Merge pull request #4329 from glormph/collection_list_sort 
Created alphabetic and numerical sort tool for collection operations
 2017-08-10 12:11:10 -04:00
John Chilton fcd06a96d6 Merge pull request #4408 from erasche/grt-pardir 
Small GRT bugfixes
 2017-08-10 11:59:49 -04:00
John Chilton 6d7d4e9e8e Merge pull request #4305 from erasche/bug-report-actions 
Refactor bug reporting into plugins / Remove bug report mako
 2017-08-10 11:58:52 -04:00
E Rasche 41461235b2 rebuild client 2017-08-10 17:55:12 +02:00
John Chilton a2b02065eb Remove unneeded messages.mako. 2017-08-10 17:53:21 +02:00
E Rasche 4c36b5a7a1 not a useful test in this location 2017-08-10 17:53:21 +02:00
E Rasche 00ee109ed4 fix css class 2017-08-10 17:53:21 +02:00
E Rasche 5563ecc3ff fix import order 2017-08-10 17:53:21 +02:00
E Rasche 3e8919c416 correct name to type 2017-08-10 17:53:21 +02:00
E Rasche 538ef006f3 Also load yaml sample files. cc @jmchilton, is this ok? 2017-08-10 17:53:21 +02:00
E Rasche 1e9c31241c remove comment 2017-08-10 17:53:21 +02:00
E Rasche a6aedc6953 address flaking 2017-08-10 17:53:21 +02:00