John Chilton
4394723ab5
Rename historyPanel.refershHdas to refreshContents.
2014-05-06 08:54:30 -05:00
John Chilton
e391dd3db5
Refactor backbone views to allow different kinds of history contents.
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This makes room for a forth coming HistoryDatasetCollectionAssociation model that will be emitted from the history contents API. Same comment as previous changeset applies - this is a potentially crude way to share duplicated functionality and a better design would be most welcome.
2014-05-06 08:54:30 -05:00
John Chilton
16b5bb875f
Refactor backbone models to allow different kinds of history contents.
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In particular, add a new backbone parent model (HistoryContent) refactored out of HistoryDatasetAssociation. This makes room for a forth coming HistoryDatasetCollectionAssociation model that will be emitted from the history contents API.
There are likely better ways to share common functionality between a dataset and a dataset collection contents - more JS savy developers should feel free to refactor into smaller mixins for instance. For now HistoryContent is just composed of the overlap in functionality between dataset and collection representations downstream and is an quick and dirty way to share said functionality.
2014-05-06 08:54:30 -05:00
Martin Cech
bba6048af9
data libraries: when importing into history set it as current and provide link to the 'Analyze page' so users can switch quickly
2014-05-05 13:51:13 -04:00
Carl Eberhard
d769895cc2
aad9eb1a8486: remove debugging statement
2014-05-05 13:36:51 -04:00
Carl Eberhard
3538c70bfc
Fixes: correct docs in histories/set_as_current to PUT; use correct empty msg when removing the last hda view in a history; remove dependency on utils.js from ui-modal.js
2014-05-05 13:34:07 -04:00
Martin Cech
fe79378599
data libraries: router improvements, detecting whether the loaded page is the first page of the app (user came from outside) or within and navigating accordingly
2014-05-05 13:03:16 -04:00
Martin Cech
033e67698b
data libraries: first take on shareable url for datasets
2014-05-02 18:00:23 -04:00
Carl Eberhard
6fbd061961
History: cruft removal from controller and associated javascript
2014-05-02 15:45:25 -04:00
Martin Cech
a1f6d2042e
data libraries: bugfix, better UI changes role handling (stilll not _good_ but better)
2014-05-01 18:21:37 -04:00
Carl Eberhard
c5ac90301e
History: remove unused server templates history_common, history_item, and history_annotation_table; Pages: remove unused dialog for annotated histories
2014-05-01 09:17:19 -04:00
Martin Cech
6ef129ed60
data libraries: streamlined deleting and undeleting datasets, filter to include deleted dataset on every folder, better errror handling, some refactoring
2014-04-30 16:38:56 -04:00
Martin Cech
89d424dae9
data libraries: new API for deleting LDAs, UI improvements, download router flow changes
2014-04-29 18:11:06 -04:00
Martin Cech
7b06f76cca
data lirbaries: support for showing deleted datasets in the folderview
2014-04-28 15:15:25 -04:00
Jeremy Goecks
09a21b6646
Do not propagate keyboard events in JS editable text plugin; this prevents unwanted side effects with other elmements on the page using keyboard events.
2014-04-25 16:58:21 -04:00
Martin Cech
514148722a
data libraries: improved folder rendering flow
2014-04-25 15:36:39 -04:00
Martin Cech
479337bd56
data libraries: default sorting; cleanup; refactor; jslint; start on getting rid of modals for library/folder creation
2014-04-23 17:31:01 -04:00
Jeremy Goecks
a36ce7abba
Trackster: add color for read track histograms so that histograms are colorful. Read blocks are still gray to allow for seeing variants easily.
2014-04-23 13:56:26 -04:00
Carl Eberhard
865805627e
History/HDA UI: pass allow_user_dataset_purge from Galaxy.config to history-panel and hda-edit and respect by not rendering purge controls if false
2014-04-22 13:16:50 -04:00
John Chilton
b5e97ea32b
Workflow Editor: Merge addDataInput and replaceDataInput into common method.
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Reduces some code duplication here and reduces even more code duplication downstream in dataset collections work.
2014-04-22 11:13:27 -05:00
John Chilton
cdeaba1f29
Workflow Editor: Replace instead of recreate terminal on update.
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This fixes at least one subtle bug related to multiple input data parameters (actually probably two bugs) because the old logic assumed there was only one connector per input terminal.
This should be more efficient, lead to some code duplication deletion in subsequent changesets, and really help dataset collections where terminals are much more complex (there are data inputs and collection inputs, and each can be mapped over by collections) - this helps manage complexity downstream.
2014-04-22 11:13:27 -05:00
John Chilton
553bbee7db
Workflow Editor: Rework InputTerminal to implement/use an update method (w/tests).
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This will enable replacing terminals instead of recreating them and reconnecting in subsequent changesets.
2014-04-22 11:13:27 -05:00
Carl Eberhard
10d5c0f920
UI: rework zh and ja locale data
2014-04-22 11:58:22 -04:00
Martin Cech
d70e804d65
rename biostar menu link
2014-04-22 10:53:35 -04:00
Martin Cech
da5ba4c711
data libraries: improved chaincall for importing datasets into history, some cleanup
2014-04-21 17:31:36 -04:00
Martin Cech
e520630b7e
data libraries: don't allow adding dataset within deleted library; better error message handling
2014-04-21 16:28:14 -04:00
Martin Cech
2c0c472f09
data libraries: don't allow creating folders within deleted library
2014-04-21 15:48:19 -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
e454c738e1
Workflow Editor: Rename can_accept to canAccept.
2014-04-21 14:27:01 -05:00
Daniel Blankenberg
276f0b80a2
Fix for masthead link for biostar mainpage.
2014-04-21 12:12:03 -04:00
Carl Eberhard
1a88077a9a
Metrics: make the cache use localStorage for persistence
2014-04-21 11:37:26 -04:00
John Chilton
0b5b547357
Pack scripts.
2014-04-20 11:25:40 -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
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
Carl Eberhard
302f2109ed
QA: more testing of metrics logger
2014-04-18 12:58:20 -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
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
Dave Bouvier
5bdb75aa82
Correct usage of "it's" versus "its".
2014-04-17 15:49:32 -04:00
Daniel Blankenberg
1899f37cd1
Remove 'galaxy' tag as default now that we are using a custom biostar site.
2014-04-17 13:03:02 -04:00
Jeremy Goecks
26051b1957
Trackster: move browser routing into TracksterView so that hash-based location routing works for both private and shared visualizations.
2014-04-17 09:47:41 -04:00
Martin Cech
db752de9d3
data libraries: API improvements; add datasets from history to folder; folder contents sorting; progressive rendering; new error code; new API endpoint; js model comparators; Galaxy.currUser defensive programming;
2014-04-16 16:27:13 -04:00
Carl Eberhard
05d113deb1
Temporary fix to galaxy.panels.mako to ensure AMD order
2014-04-15 15:06:40 -04:00
Carl Eberhard
0c5a417268
UI: add GalaxyApp to base_panels.mako; add requirejs i18n plugin and nls/zh, nls/ja locale files, wire into _l client localizer, remove previous localization cruft; remove reliance on history_panel.mako
2014-04-15 12:31:33 -04:00
Daniel Blankenberg
86f167680c
Update packed scripts
2014-04-15 12:00:02 -04:00
Daniel Blankenberg
0a40fd397a
UI, make HDAs in NEW state have delete, info and rerun buttons, as well as disabled view and edit buttons. Move new state to NOT READY STATES.
2014-04-15 11:59:14 -04:00
Martin Cech
4320c71bd8
data libraries: initial work on importing datasets from histories: fetching history list, fetching and displaying history contents
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repaired bug in unbinding nested views
2014-04-14 14:09:36 -04:00
Carl Eberhard
6672b8db2c
Metrics: remove double parsing of JSON from server-side, add GalaxyApp object with config and user, tie metrics-logger to GalaxyApp
2014-04-14 13:00:06 -04:00
John Chilton