Dave Bouvier
5dab91f4ba
Fix functional tests for history functions.
2014-04-21 15:42:22 -04:00
John Chilton
10ffa53659
Pack scripts.
2014-04-21 14:28:47 -05:00
John Chilton
cbfa265b83
Bugfix: Workflow editor could get in invalid state when trying to preserve connections.
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Workflow editor would preserve connections when a tool would update its state (for instance switching a conditional or adding repeat) - but conditional switching can result in connections being invalid (wouldn't have passed can_accept previously). Consider the following tool for instance which changes datatypes of an input based on a conditional (https://gist.github.com/jmchilton/11152628 ).
2014-04-21 14:27:01 -05:00
John Chilton
357280ed4d
Workflow Editor: Break canAccept into smaller pieces (inputFilled and attachable).
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Want to reuse attachable right away to fix a bug - and the smaller pieces are good refactoring to support different kinds of input types in dataset collections downstream.
2014-04-21 14:27:01 -05:00
John Chilton
5caf9dd13d
Workflow Editor: Improve tests related to input terminal canAccept/datatypes.
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Elminate stub, create mock tree off inputs (demonstrates what server is feeding), add test for direct and subtype. Add tests for PJA changing output connection datatypes.
2014-04-21 14:27:01 -05:00
John Chilton
e454c738e1
Workflow Editor: Rename can_accept to canAccept.
2014-04-21 14:27:01 -05:00
John Chilton
7e56d2dc20
Fix comment in lib/galaxy/workflow/run.py
2014-04-21 14:26:56 -05:00
Carl Eberhard
e3b5612121
Client app: use in /base.mako, rework app init to use AMD definition
2014-04-21 14:44:34 -04:00
Dave Bouvier
45ff30f6e1
Fix for registering an account with custom user information when only one custom user info form is defined. Fix editing user info when custom user info forms are defined. Fix functional tests for user info.
2014-04-21 12:41:05 -04:00
Daniel Blankenberg
5ae1c9bcbb
Fix for masthead link for biostar mainpage.
2014-04-21 12:12:03 -04:00
Daniel Blankenberg
bebfa2bd42
Fix for masthead link for biostar mainpage.
2014-04-21 12:12:03 -04:00
Daniel Blankenberg
276f0b80a2
Fix for masthead link for biostar mainpage.
2014-04-21 12:12:03 -04:00
Daniel Blankenberg
9db12a5f56
Prevent redirect misuse on user log in.
2014-04-21 12:11:49 -04:00
Daniel Blankenberg
9835de1a26
Prevent redirect misuse on user log in.
2014-04-21 12:11:49 -04:00
Carl Eberhard
1a88077a9a
Metrics: make the cache use localStorage for persistence
2014-04-21 11:37:26 -04:00
John Chilton
989950c037
Workflow running - modify var names/comment to reflect 773951eb2bbf.
2014-04-21 08:36:43 -05:00
John Chilton
263efe1321
Bugfix for 439510f (reported by @saketkc).
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Previous logic for determining if state had been calculated for workflow steps in workflow run module would only work for data input steps - this new logic should work for data input or tools.
2014-04-21 08:01:22 -05:00
John Chilton
0b5b547357
Pack scripts.
2014-04-20 11:25:40 -05:00
Dave Bouvier
45733dda1e
Fix issue where install and test framework would hang if a repository was not found in the database.
2014-04-19 23:24:12 -04:00
John Chilton
84fcb55795
Bugfix for multiple input data parameters.
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Workflow editor would drop all but one multiple input data connections if and when the parameter itself was nested in repeats/conds.
2014-04-19 14:37:02 -05:00
John Chilton
8ece04ac0c
Merge pull request #363 .
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Was previously declined so that pull request #370 could be resolved first - but upon actually inspecting #370 I don't think these will conflict in anyway.
2014-04-19 11:57:53 -05:00
John Chilton
02425e7c4f
Refactor workflow API logic related to module population into run module.
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Also moves runtime parameter override logic into that module as well. This is a good refactoring because it thins out a fat controllers (slightly) - but it is of particular interest because it makes it easier to recursively invoke potentially nested workflows from the workflow running module itself. It is still an open question whether that is desirable - see discussion on Pull Request #370 - but if it proves to be this can help enable it.
2014-04-19 11:40:19 -05:00
John Chilton
073ee18f1d
Refactor galaxy.workflow.run interface to use config object.
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Number of ways to paramemterize workflow is a little bit sprawling already and it is about to get worse.
2014-04-19 11:40:19 -05:00
Aysam Guerler
a59c84319d
Charts: Fix metadata status
2014-04-19 00:53:46 -04:00
Carl Eberhard
3fcfd3ecad
Improve visualization registry warning info when datatype class not found by lookup
2014-04-18 18:04:13 -04:00
Martin Cech
8891243e69
data libraries: small API changes; bugfix; deferred queue for adding datasets from history to library; permission handling work
2014-04-18 17:16:58 -04:00
Carl Eberhard
fd5e9d2d2c
QA, metrics-logger: finish tests for existing; casperjs: restore correct return value for loggedInAs
2014-04-18 15:58:29 -04:00
Dave Bouvier
b48712928b
Merge fix from stable.
2014-04-18 14:58:04 -04:00
Aysam Guerler
36e3042278
Charts: Update nvd3
2014-04-18 14:53:48 -04:00
Carl Eberhard
b7212b0f37
QA, metrics logger: test metrics post
2014-04-18 14:42:26 -04:00
Dave Bouvier
0c1c0add3f
If a tool shed repository was updated after a tool migration without a new installable changeset revision being generated, for example by adding or removing a readme file, the migration install framework would be unable to find repository dependencies. This changeset resolves that.
2014-04-18 13:58:51 -04:00
Daniel Blankenberg
cb1f6c92f6
Update NGS read simulator to use job working directory.
2014-04-18 13:31:13 -04:00
Daniel Blankenberg
5e3e287ce3
Update MAF to BED to use job working directory and built-in primary dataset collection.
2014-04-18 13:23:38 -04:00
Carl Eberhard
302f2109ed
QA: more testing of metrics logger
2014-04-18 12:58:20 -04:00
Daniel Blankenberg
213986aa7f
Update MAF to interval to use job working directory instead of __new_file_path__.
2014-04-18 12:34:08 -04:00
Carl Eberhard
5739c37cbf
QA: add login info to api-hda-tests.js (unable to repro failure shown on buildbot)
2014-04-18 11:02:17 -04:00
Carl Eberhard
20ccb0f620
QA: add login info to api-history-permission-tests (unable to repro failure shown on buildbot), use API to check loggedInAs
2014-04-18 10:59:35 -04:00
Carl Eberhard
510d1a879f
QA: adjust HDA API test for new anon ability to create contents
2014-04-18 10:25:37 -04:00
Carl Eberhard
4f3cce5e9b
merge
2014-04-18 09:57:35 -04:00
Carl Eberhard
a3a02170cb
QA: add qunit tests for galaxy-app-base; Fix defaults in metrics-logger tests
2014-04-18 09:56:31 -04:00
John Chilton
2bda90ec6c
Add option test system environment option GALAXY_TEST_VERBOSE_ERRORS to report on dataset errors.
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Implemented a while ago to aid debugging but disabled by default because it can cause sqlite locking errors. It can now be enabled as needed using GALAXY_TEST_VERBOSE_ERRORS.
2014-04-18 08:41:59 -05:00
Carl Eberhard
a434c454f5
Client app: allow bootstrapping data as require dependency, use window-scoped 'on ready' fn (for now), mixin Backbone.Events; galaxy.panels.mako: fix app ready v. doc ready order; Fix target fo addLogging; history.mako: simplify
2014-04-18 09:34:16 -04:00
Aysam Guerler
cb6af58c66
Charts: Improve histogram module
2014-04-17 18:03:54 -04:00
John Chilton
960cf077f5
Merged in dan/galaxy-central-stable-prs/stable (pull request #369 )
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BioStar fixes
2014-04-17 15:02:44 -05:00
Dave Bouvier
5bdb75aa82
Correct usage of "it's" versus "its".
2014-04-17 15:49:32 -04:00
Daniel Blankenberg
9aa9f7d018
Add an option to biostar integration to never authenticate.
2014-04-17 15:38:42 -04:00
Daniel Blankenberg
3ed326601a
Add an option to biostar integration to never authenticate.
2014-04-17 15:38:42 -04:00
Dave Bouvier
30bc77e7ea
Fix most of the failing functional tests in test_sample_tracking.py.
2014-04-17 15:16:57 -04:00
Daniel Blankenberg
2d2c2e8344
Some better error handling for external display applications when e.g. files have been deleted but are still active in applications.
2014-04-17 15:05:18 -04:00
John Chilton
53a154df2f
Fix library permissions API controller.
2014-04-17 13:46:57 -05:00
Dave Bouvier