Nate Coraor
410fcf87df
Make the job queue thread block on job recovery to avoid a race condition with jobs in the 'new' state. This should fix jobs showing up as 'ok' and then upon a later history reload showing up as 'error'.
2012-02-17 11:27:29 -05:00
Jeremy Goecks
0416175a87
Bug fixes for creating and saving visualizations.
2012-02-17 09:50:02 -05:00
Jeremy Goecks
d6c22052ec
Trackster bug fixes.
2012-02-16 23:02:14 -05:00
Jeremy Goecks
06da58a4bf
Trackster: save and restore tool state.
2012-02-14 15:34:18 -05:00
Greg Von Kuster
0a8e16c390
Encode application name and link name when sending as request params to display application.
2012-02-14 11:58:51 -05:00
Jeremy Goecks
9721927be4
Trackster: for flexibility, use dictionaries in all object constructors. Fixed bugs associated with saving/restoring visualizations.
2012-02-13 11:08:50 -05:00
Greg Von Kuster
76310510fc
Do not allow conflicting datatypes included in a tool shed repository currently being installed to override datattypes already in the datatypes registry. Also, a bit of cleanup in handling datatypes included in repositories being activated / installed / deactivated / uninstalled. A bit more cleanup is still necessary.
2012-02-10 16:33:19 -05:00
Greg Von Kuster
af72f2e36c
Fixes for handling proprietary datatypes included in installed tool shed repositories - import proprietary class modules within the registry.
2012-02-10 14:52:41 -05:00
Jeremy Goecks
f44bf96d3c
Merged in jmchilton/umn-galaxy-central/dynamic_options_memory_fix (pull request #36 )
2012-02-10 11:26:18 -05:00
Jeremy Goecks
a3d8b1240d
Trackster: filter bug fix and abstract filter display control.
2012-02-10 09:52:01 -05:00
Jeremy Goecks
b7c8477722
Trackster: save and restore single track filters.
2012-02-09 15:32:38 -05:00
Greg Von Kuster
ab648e32d2
Handle multiple relationships in the tool lineage chain at the time of repository installation.
2012-02-09 11:43:03 -05:00
Greg Von Kuster
d647177616
When handling datatype conflicts always override previously loaded datatypes with the datatype currently being loaded. Use the same behavior for sniffers.
2012-02-08 13:46:14 -05:00
Jeremy Goecks
2324294f7f
Fix bug in GFFDataProvider's data iterator.
2012-02-08 11:55:49 -05:00
Greg Von Kuster
1c94a93c81
Load proprietary datatypes from installed tool shed repositories before the datatypes in the Galaxy distribution are loaded. We do this because the distribution includes some extremely generic sniffers (eg text,xml) which will catch pretty much anything, making it impossible for proprietary sniffers to be used. Proprietary datatypes contained in installed repositories are loaded in order of oldest installation first, followed by next olderst installation, etc.
2012-02-08 11:30:58 -05:00
Nate Coraor
c43633c5cb
Pass the config file name to set_metadata.py rather than relying on a hardcoded value.
2012-02-08 11:12:10 -05:00
Greg Von Kuster
bfc3baf665
Fix for getting updates for an installed tool shed repository change set revision.
2012-02-08 09:11:19 -05:00
Greg Von Kuster
7194acdd47
Fix for loading tools from an installed tool shed repository into the tool panel outside of any sections.
2012-02-07 16:20:48 -05:00
Greg Von Kuster
2f559757dc
When an installed tool shed repository that includes tools is being reinstalled, allow the admin to select a different section in the tool panel (than was originally selected when the repository was last installed) to contain the included tools.
2012-02-07 15:10:03 -05:00
Greg Von Kuster
81edcca688
Tool version grid cleanup.
2012-02-07 13:04:52 -05:00
John Chilton
d6fb79b4a2
One more fixed typo.
2012-02-07 10:50:22 -06:00
John Chilton
2365c309ff
Fix a typo made with last commit.
2012-02-07 10:38:00 -06:00
Jeremy Goecks
f923c686c5
Fix bug in GFFDataProvider iterator.
2012-02-07 11:35:48 -05:00
John Chilton
1d18fb6cd2
Patch dynamic_options.py to just read just the first megabyte of an
...
input dataset (if it is larger than that). Otherwise Galaxy will
attempt the read the entire file into memory, this can causes crashes
and freezeups without the user even selecting a bad input (for
instance, if a large FASTQ file is the top most history item and a txt
input is sought, Galaxy will freezeup as soon as the tool is clicked
because it will try to load the options for the top item immediately
by default).
Though the implementation is not as clean, I am restricting it to a
megabyte instead of a number of lines/options in case the top most history
item has no line breaks. I imagine in that case the same problem could
occur even if the input is restricted to a reasonable number of lines
(say 100).
2012-02-07 10:35:17 -06:00
Greg Von Kuster
bc486d508e
Fix for loading proprietary datatype sniffers that are included in installed tool shed repositories.
2012-02-07 11:15:20 -05:00
Greg Von Kuster
9d4b107536
Fix for 39e03997f78f - change buffer to string so older postgres versions work.
2012-02-07 11:06:17 -05:00
Nate Coraor
d9e075a8bf
Use PG9 hex bytea fix to decode tool shed repository metadata in migration script 91.
2012-02-07 10:41:22 -05:00
Dannon Baker
40efce029a
Multiple-run workflows: When run into separate new histories, naming is now based on the varied input dataset instead of the execution number, so "<workflowname> on <varied_input>".
2012-02-07 09:45:19 -05:00
Greg Von Kuster
3668d757f1
Add a new grid to view the tool version lineage by tool id (parent/child ordered) for any tool that was ever used in the local Galaxy instance. Tool ids in this grid that are associated with tools currently loaded in the tool panel are highlighted in green and are click-able, displaying the tool. Eliminate the mappers for determining lineage, and use methods instead as the mappers were problematic.
2012-02-06 15:22:56 -05:00
Nate Coraor
32ca717251
Bugfix for the DRMAA job name commit, ensure all characters in the job name string conform to the DRMAA spec.
2012-02-06 13:16:23 -05:00
Nate Coraor
9a959c14ea
Set a descriptive job name when using the DRMAA runner
2012-02-06 13:03:24 -05:00
Nate Coraor
cf011f24d2
A couple of job running path resolution changes, fixes #713 (thanks Peter)
2012-02-06 12:39:19 -05:00
Greg Von Kuster
ca87cfd82a
Load empty tool sections into the in-memory tool_panel dictionary, just don't display them in the tool panel. Also include a fix for reactivating or unintallting a tool shed repository that includes tools - ToolVersion ovjects cannot be marked deleted.
2012-02-06 10:19:43 -05:00
Jeremy Goecks
96a370514b
Trackster: better attribute display for tracks created when rerunning tools.
2012-02-05 14:50:23 -05:00
Jeremy Goecks
90c62d93ed
Handle instance where BAMDataProvider iterator is None; this can occur when trying to fetch additional data.
2012-02-05 12:53:23 -05:00
Greg Von Kuster
bb0e8afcf6
Correctly handle ToolPanelSection objects when presenting the tool panel sectin redio buttons for selecting a section to contain tools installed with a tool shed repostory into a local Galaxy instance.
2012-02-03 16:30:30 -05:00
Greg Von Kuster
5d5c3919b3
Make sure a tool shed repository has metadata before setting versions for contained tools.
2012-02-03 15:29:02 -05:00
Greg Von Kuster
8bad5434aa
Add the ability to chain Galaxy tools into a lineage of tool versions. This enables workflows and the rerun button on history items to work when a new version of a tool is loaded into the Galaxy tool panel. Version information for tools included in tool shed repositories is maintained for each changeset revision in the tool shed, and this information can be retrieved from the Administrative "Manage installed tool shed repositories" menu item for installed tool shed repositories that contain tools. This new functionality eliminates the need for the tool_id_guid_map table and associated features, so they have all been removed.
2012-02-03 15:13:28 -05:00
Nate Coraor
74c2b69251
Use cluster_files_directory for drmaa job template.
2012-02-03 12:22:16 -05:00
Dannon Baker
0a646d1d8b
Slight cleanup of the previous workflow share removal commit.
2012-02-02 15:16:29 -05:00
Dannon Baker
68849150c4
Merge.
2012-02-02 14:55:19 -05:00
Dannon Baker
8f330863aa
Workflows: Add the ability to remove workflows that have been shared with you.
2012-02-02 14:53:34 -05:00
Dannon Baker
5a2dffdf85
History export - now works for a guest user.
2012-02-02 10:51:13 -05:00
Dannon Baker
219cf0c74f
History Size wasn't filtering out 'purged' datasets in the summary size, should now reflect accurate total on disk.
2012-02-02 10:17:25 -05:00
Dave Clements
150cb55997
Changed the default new user mailing list from galaxy-user to galaxy-announce, which is a much lower volume. Also added text to link to wiki page with all mailing lists.
2012-02-01 21:25:41 -08:00
Nate Coraor
fa25991b79
DRMAA runner no longer needs to clean up its stdout/stderr since they live in the working directory which is cleaned up by the job wrapper.
2012-02-02 13:25:59 -05:00
Jeremy Goecks
e5dceaae5b
To be compatible with distributed object store, use create() when adding data subsets for Trackster.
2012-02-01 17:34:50 -05:00
Jeremy Goecks
f7777c1d27
Change default sort for Pages list to update time.
2012-02-01 16:47:32 -05:00
Jeremy Goecks
e66ff96769
Add overwrite param when setting metadata in Trackster data subsets.
2012-02-01 15:27:53 -05:00
Jeremy Goecks
e12720f4cf
Fix bug: when setting chromInfo, do not assume a fasta file exists.
2012-02-01 14:00:21 -05:00
Nate Coraor