carlfeberhard
cfb8ed3269
UI, citations: fix bad merge from 15.10
...
774487d
2016-04-19 15:35:15 -04:00
Martin Cech
b95cca862c
always fetch new permissions as we are reusing the view
2016-04-15 12:58:36 -04:00
Dannon Baker
3e79a574be
Merge #2167 manually to resolve conflicts.
2016-04-15 11:31:58 -04:00
carlfeberhard
e26bff23ed
Merge 'release_15.10' with 'release_16.01'
2016-04-14 12:59:05 -04:00
carlfeberhard
03c8573731
Multi-history: open rerun button in new tab
2016-04-14 12:12:23 -04:00
guerler
bd0439d9b7
Fix tool access rights and forwarding
2016-03-18 20:12:21 -04:00
carlfeberhard
774487ddcc
Fix citation-model to fail silently/gracefully when a non-parsable bibtex entry is tried
2016-03-07 11:07:56 -05:00
John Chilton
e14e8a074c
Allow rerun of datasets new yet queued by job manager.
2016-03-04 09:14:29 +00:00
John Chilton
dbab6f5b97
Workaround for #1739 - fixing up subworkflow inut connections.
...
Do the same relaxed thing we do for inputs of type 'input' as we do for outputs of this type. Someday we should have better tracking, but such a change is probably not wise for a release branch.
2016-02-22 21:46:03 +00:00
carlfeberhard
84de6b4ed3
Fix target or window.location when importing histories from display.mako (shared with me->view) to allow for iframes; silence popup-menu.js when menu is closed due to location change
2016-02-17 14:41:08 -05:00
Martin Cech
776180ab80
show all available information for current library and the opened folder
2016-02-09 10:24:02 -05:00
Martin Cech
7867f3e083
accept json as input for setting permissions;
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fix inconsistency by leveraging role_manager
2016-02-04 15:51:57 -05:00
guerler
61818948a1
Fix default option for repeats
2016-02-01 11:31:50 -05:00
carlfeberhard
f5fbe1c502
Client: remove older compiled backbone/backbone.js, update scatterplot and charts for same; Visualizations: fix visualization-model url; Scatterplot: fix title bug and Galaxy var
2016-01-21 13:38:12 -05:00
John Chilton
a00faba4fe
Merge pull request #1551 from guerler/fix_hidden_rerun_000
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[16.01] Keep track of hidden datasets
2016-01-21 09:39:02 -05:00
guerler
035a67d0b5
Keep track of hidden datasets
2016-01-21 03:15:23 -05:00
guerler
bbff72e0ce
Fix upgrade messages
2016-01-20 19:48:02 -05:00
John Chilton
3dda415fb9
Merge remote-tracking branch 'jmchilton/release_16.01' into release_16.01_merge_4
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Conflicts:
static/scripts/bundled/analysis.bundled.js.map
static/scripts/bundled/libs.bundled.js.map
2016-01-11 12:15:14 +00:00
carlfeberhard
54dca064fa
UI, Multi-history: fix drop event handler to use dataTransfer of original event
2016-01-11 10:21:06 -05:00
John Chilton
f8a7ac0820
Merge release_15.10 into release_16.01.
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Conflicts:
eggs.ini
lib/galaxy/tools/__init__.py
lib/galaxy/tools/actions/__init__.py
lib/galaxy/tools/toolbox/base.py
static/maps/mvc/collection/list-collection-creator.js.map
static/maps/mvc/library/library-foldertoolbar-view.js.map
static/maps/utils/uploadbox.js.map
static/scripts/mvc/collection/list-collection-creator.js
static/scripts/mvc/library/library-foldertoolbar-view.js
static/scripts/utils/uploadbox.js
test/base/twilltestcase.py
test/functional/tools/samples_tool_conf.xml
2016-01-08 18:06:28 +00:00
guerler
237ecc7789
Add form help class
2016-01-05 16:15:55 -05:00
Dannon Baker
9416e6f3f7
Merge and resolve conflicts, rebuilding.
2016-01-05 13:18:46 -05:00
Dannon Baker
5924857c2c
Fix pre/postclick that got broken somewhere along the way w/ patches&merges.
2016-01-05 13:08:33 -05:00
guerler
884b1d42db
Change scratchbook close icon
2016-01-05 11:45:31 -05:00
Dannon Baker
da8b943f53
Merge.
2016-01-04 19:23:06 -05:00
Eric Rasche
5a441044fb
Merge pull request #1308 from jmchilton/multi_collection_types
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Allow input collections to specify multiple collection types.
2016-01-04 14:43:37 -06:00
guerler
339ad57f3f
Cleanup Masthead and Scratchbook
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Cleanup Masthead and Scratchbook
2015-12-30 16:31:59 -05:00
Dannon Baker
401583d730
Move TOURS.giveTour at the top level of the namespace instead of a method of the view.
2015-12-29 09:50:47 -05:00
Dannon Baker
578e201d64
Launch tour on GET arg (?tour_id=core.galaxy_ui).
2015-12-28 14:19:34 -05:00
Dannon Baker
e325eba37c
Some tweaks care of @bgruening. This adds (slightly tweaked) functionality to support a series of clicks, still needs a delay between clicks, and since it's the most common case that pre/postclick will be a single item, a list shouldn't be required here.
2015-12-21 13:08:15 -05:00
guerler
17d733b042
Move closing events to show/hide function
2015-12-19 17:20:02 -05:00
guerler
39e7f025eb
Refine popover wrapper
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Revise popover, add tests
2015-12-19 17:08:51 -05:00
guerler
048561d282
Avoid duplicate upload entries, revise modals, add tests
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Revise styles
Add more tests
2015-12-19 17:08:49 -05:00
Dannon Baker
aecc5d864f
Make tours.js safe (but possibly not functional wrt/ listing) to use on pages without Galaxy object.
2015-12-18 16:24:19 -05:00
Dannon Baker
4efa8e73b3
Consolidate to standard options dict, minor refactorings.
2015-12-18 14:15:17 -05:00
Dannon Baker
8c1beb2af5
title override, working on fixing style.
2015-12-18 13:44:34 -05:00
Dannon Baker
5a3524245b
Actually let people end a tour.
2015-12-18 13:20:57 -05:00
Dannon Baker
9e7eaaa7aa
Finish sessionStorage and restart of tours across multiple pages.
2015-12-18 13:10:09 -05:00
Dannon Baker
1e5640163a
Tour shim in onload, check sessionStorage (or would local be more appropriate?)
2015-12-18 12:23:40 -05:00
Dannon Baker
f107b17928
Refactor a bit, adjust textinsert action to trigger 'change' on the element.
2015-12-18 12:01:07 -05:00
Dannon Baker
0203a69d88
Tours.
2015-12-18 10:26:22 -05:00
Martin Cech
b4683fbce4
raise and show specific exception and warning when no files detected
2015-12-17 12:40:09 -05:00
guerler
2ff3bf0c0c
Fix label change handling
2015-12-16 17:12:37 -05:00
guerler
12014cc225
Show correct subworkflow name
2015-12-16 17:12:23 -05:00
guerler
b4bfde4089
Fix attribute
2015-12-16 15:24:02 +00:00
guerler
f10b968075
Build section dom in js
2015-12-16 15:22:25 +00:00
guerler
f88ad8d4e3
Fix Change type label in editor form
2015-12-16 15:22:18 +00:00
John Chilton
157939aa8f
Implement nested workflows.
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Details:
- Add a new workflow module describing subworkflows.
- Add workflow list to editor side panel - with options to link in a subworkflow module or copy the target workflow into the workflow being editted node for node.
- Update workflow, workflow step, and workflow invocation models to track subworkflow connections and execution.
- Extend workflow outputs with concepts of labels (and UUIDs while I'm there) to match workflow inputs. This allow us to have something to label outputs with in the workflow editor and to reference in the format 2 workflow description language.
- Extend workflow editor UI to allow labeling workflow outputs (and enforce that these are unique across a workflow).
- Extend workflow invocation and progress tracking to allow invoking a subworkflow as part of another workflow invocation.
- Extend workflow import and export code to allow a nested representation of workflows.
- Update format 2 workflow description to allow testing nested workflows.
Most relevant new and modified test cases can be run using the following commands:
```
./run_tests.sh -api test/api/test_workflows.py:WorkflowsApiTestCase.test_run_subworkflow_simple
./run_tests.sh -api test/api/test_workflows_from_yaml.py:WorkflowsFromYamlApiTestCase.test_subworkflow_simple
./run_tests.sh -api test/api/test_workflows_from_yaml.py:WorkflowsFromYamlApiTestCase.test_outputs
nosetests test/unit/test_galaxy_mapping.py
nosetests test/unit/workflows/test_workflow_progress.py
```
2015-12-16 15:22:18 +00:00
Dannon Baker
cf5d209e0f
Manual merge of #1303 to resolve build artifact conflicts.
2015-12-16 06:51:12 -05:00
John Chilton
7f7010dbd9
Remove left over packed scripts.
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The source files have been deleted.
2015-12-14 19:38:06 +00:00
carlfeberhard