mvdbeek
1343b04380
Fix workflow step cloning
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Problem one is that passing the tool_state as the input payload doesn't
preserve the tool state, adressed with the client-part fix.
Then passing the tool state still has no effect since the state is
properly recovered in `module_factory.from_dict`, but then overwritten
by recovering the state starting with an empty dict. It looks like this
isn't necessary as we call populate_state anyway when calling
`module.get_config_form()`.
Fixes https://github.com/galaxyproject/galaxy/issues/5879 .
2018-05-08 17:05:49 +02:00
John Chilton
fdfe79f67e
Fix library to list of pairs collection builder.
2018-04-30 11:52:42 -04:00
John Chilton
68b87a0763
Merge pull request #5797 from nsoranzo/release_18.01_fix_import_directory
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[18.01] Fix missing `from Import Directory` button
2018-04-06 08:04:47 -04:00
Dannon Baker
7d394d243b
Proofreading - thanks @nsoranzo
2018-03-28 15:15:07 -04:00
Dannon Baker
4d742c3b13
Clarify make targets, update client/README
2018-03-28 10:28:54 -04:00
Nicola Soranzo
10ea150792
Fix missing from Import Directory button
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when `library_import_dir` is set in `config/galaxy.yml`, but
`allow_path_paste` is `false`.
Reported by @pvanheus.
2018-03-28 12:40:21 +01:00
guerler
30ed27f9ad
Add additional check for history items
2018-03-22 13:51:09 -04:00
guerler
36467c1e76
Add source to data entry
2018-03-22 13:51:05 -04:00
guerler
af514327cb
Validate type using collection, from @jmchilton
2018-03-22 13:51:00 -04:00
guerler
70392ddb3b
Remove debug statements, use drop data where needed
2018-03-22 13:50:55 -04:00
guerler
64648aefd7
Ignore tool xml datatype settings for dragged history items
2018-03-22 13:50:49 -04:00
John Chilton
8ef320963a
Fix for merging of HDA & DCE models into one model in the client.
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I wish they weren't merged together like this but they are so try to to handle the IDs in a less buggy way.
Should fix https://github.com/galaxyproject/galaxy/issues/3782 though I'm unsure.
2018-03-22 13:44:25 -04:00
guerler
54d91e5850
Add additional validation to numeric input element
2018-03-22 13:43:22 -04:00
John Chilton
fa3ec5f60b
Merge pull request #5261 from dannon/trackster_fixes
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[18.01] Trackster fixes.
2018-03-08 15:53:29 -05:00
Martin Cech
b655a499f8
re-add erroneously removed line
2018-03-07 13:43:50 -05:00
Martin Cech
10f8c3bc82
Merge branch 'release_17.09' into release_18.01
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dropped all static content from merge except of styles
2018-03-07 12:47:59 -05:00
Dannon Baker
f33eee105f
Fix config parameter default building in tracks.js; ideally this turns into classes when the multiple inheritance is fixed/refactored, and we can use simple static getter/setter methods.
2018-03-06 14:02:46 -05:00
Dannon Baker
4bca4a056c
Config.js fixes; it was trying to import itself and not use it.
2018-03-06 13:44:30 -05:00
Dannon Baker
f0df326e2c
Use static getters for default painter preferences, fix 'defailt' ironic typo.
2018-03-05 17:44:55 -05:00
Dannon Baker
ec8c926042
Refactoring in feature painter draw.
2018-03-05 12:46:52 -05:00
Martin Cech
10cf046ea8
replace syntax that is too new
2018-03-02 12:58:44 -05:00
guerler
7254d55e8b
Remove href from grid sorting links
2018-03-02 10:48:29 -05:00
Nuwan Goonasekera
6b782ad16d
Changed GenomeSpace token handling to use manual OpenID association only
2018-03-01 15:03:12 -05:00
Dannon Baker
7c9c977575
Misc cleanup while trying to debug nonexistent paint vars.
2018-02-28 15:07:20 -05:00
Dannon Baker
0e6e468608
Import fixes in main trackster.js
2018-02-27 12:43:46 -05:00
Martin Cech
d8585f6a6f
Merge pull request #5582 from jmchilton/indicators
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[18.01] Fix lack of feedback when slow grids are loading data from the server.
2018-02-27 10:08:28 -05:00
John Chilton
c00e772159
Fix lack of feedback when slow grids are loading data from the server.
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Fixes #5473 (after numerous other backend optimizations also).
2018-02-21 14:31:46 -05:00
Martin Cech
6a3ce34c09
Merge pull request #5443 from jmchilton/fix5117
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[18.01] Don't silently fail rest of multi-action queue when attempting to purge a collection.
2018-02-19 19:14:57 -05:00
Dannon Baker
e7f7d5e29a
Merge pull request #5558 from jmchilton/deletion_cleanup_1
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[18.01] Do not reload page when deleting collections.
2018-02-19 12:35:34 -05:00
John Chilton
d964d594a5
[18.01] Do not reload page when deleting collections.
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Fixes #5499 reported by @mvdbeek (thanks for catching that).
2018-02-19 08:57:51 -05:00
John Chilton
f6ac13568f
Don't fail rest of multi-action queue when attempting to purge a collection.
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Fixes https://github.com/galaxyproject/galaxy/issues/5117 .
2018-02-18 13:28:36 -05:00
Nuwan Goonasekera
8c941ae35a
Fix for: https://github.com/galaxyproject/galaxy/issues/5527
2018-02-15 13:28:48 -05:00
Martin Cech
755fb9fb21
style changes for history lists
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* include title for all state indicators
* shorten title
* change style of deleted indicator
* comment out unused less variables
2018-02-15 10:35:19 -05:00
John Chilton
283ab0459f
Improve performance bugs and misleading summary info in history list.
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Prefetch shared user information as counts instead of objects and do so in initial query to eliminate an extra 15 SQL queries per page and load less data related to sharing.
Replace columns that would cause HDA information to be joined into the query (history size and HDA state counts) with a spinner that will be fetched in subsequent queries on the client end. There can hundreds of thousands of datasets per history - this information shouldn't be summarized to get the initial page to render - it can be fetched one history at a time once the page is rendered.
This commit also adds a new column "Items" that corresponds to the next HID - and that I think is a good summary of the "history size" before the dataset state information is loaded and even gives additional information because that count includes collections. This also renders state information for deleted and hidden datasets that was previously missing and could cause confusion. That said I don't like the dataset summaries - I'd rather just have the item count and then job state summaries.
2018-02-14 13:21:10 -05:00
Martin Cech
b9ddec71a4
disable loading of webhooks in TS and reports apps
2018-02-13 14:16:45 -05:00
Nicola Soranzo
eba3fb4b35
Fix common_startup.sh for galaxy tarballs
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Do not assume git is installed and the `.git` directory is present.
Fix https://github.com/galaxyproject/galaxy/issues/5466
2018-02-08 11:52:24 -05:00
Dannon Baker
f0a8243f7d
Client-format post-merge
2018-02-05 13:06:29 -05:00
Dannon Baker
0704d63d0b
Merge remote-tracking branch 'jmchilton/1801_hdca_delete' into release_18.01
2018-02-05 13:06:01 -05:00
Martin Cech
b28fb7e4d7
change the history icon-btn selector to work with dropdowns
2018-02-04 20:10:36 -05:00
Martin Cech
3512096a14
remove unused classes and aria
2018-02-02 13:53:26 -05:00
Martin Cech
8019afb8b5
fix typo
2018-02-02 13:34:17 -05:00
Martin Cech
55b6d601a8
add empty href to links so the cursor is right
2018-02-02 13:32:56 -05:00
Dannon Baker
a392b5750a
Ensure jobStateSummariesCollection exists; events can fire during deletion actions causing this event to fail
2018-02-02 09:01:35 -05:00
John Chilton
ab3d53c5ce
More options for collection deletion.
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Delete button now a drop down menu (like dropdown for downloading metadata files).
- Top option just deletes the collection.
- Second option deletes the collection and attempts to delete the datasets contained within it.
- The third option deletes the collection and attempts to purge the datasets within it.
2018-02-01 23:20:59 -05:00
Evgeny Anatskiy
9b4465efd3
fix webhook's property name
2018-02-01 12:22:14 -05:00
Dannon Baker
fa0ba22f97
Fix webhook filtering, make it a bit more defensive. Minor other tweaks.
2018-02-01 12:18:02 -05:00
Dannon Baker
22b0b2f2e9
Minor tweaks/fixes while trying to sort out qunit test failures related to webhook changes.
2018-02-01 12:18:02 -05:00
Dannon Baker
3b7daece04
Delay interpolation of webhook url template; Galaxy won't exist as a configured object necessarily when this is imported.
2018-02-01 12:18:02 -05:00
Dannon Baker
57c1fc7804
Client formatting of webhooks changes.
2018-02-01 12:18:02 -05:00
Evgeny Anatskiy
ada76931d8
add weighted random webhook pick
2018-02-01 12:18:01 -05:00
mvdbeek