Nicola Soranzo
2f650b8866
Fix file extension determination
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Extension was determined uncorrectly for filenames with more than 1 dot
2013-03-06 12:37:08 +01:00
John Chilton
262413f7c0
Based on input from natefoo, replace root tool tag "upload" with inverse tag "workflow_compatible". Adjust logic in tools module accordingly.
2013-02-13 10:45:56 -06:00
John Chilton
7e6ee45bb0
Add optional "upload" attribute to tool definitions.
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When extracting workflows, such tools are treated as inputs. This eliminates the need for the hack of hardcoding 'upload1' in tools.py and allows multiple upload tools to exist and function properly when extracting workflows.
2013-02-10 11:13:51 -06:00
Daniel Blankenberg
a2a1a15b6f
Add MouseMine datasource tool provided by Howie Motenko (Howie.Motenko@jax.org).
2013-02-06 17:34:36 -05:00
Daniel Blankenberg
a273960126
Backout 3189a1bf18af
2013-02-04 06:43:35 -05:00
Daniel Blankenberg
bab984ed69
Add sentry_dsn to Tool Shed config.py' lib/galaxy/webapps/community/config.py
2013-02-04 06:33:19 -05:00
Brad Chapman
cf1407d471
Correctly set history and handle output datasets for error cases in tool API. Allow specification of dataset name during uploads, exposing through API
2012-10-04 15:31:16 -04:00
John Chilton
886a5c61b9
Merge.
2012-09-03 22:14:36 -05:00
Daniel Blankenberg
48548341fc
Handle non-ascii unicode in upload tool. Significant pre-existing refactoring still needed.
2012-08-28 19:23:39 -04:00
Daniel Blankenberg
d84ab3226e
Handle non-ascii unicode in data source tools. Add util.is_binary() method that returns true when provided string contains a null byte.
2012-08-28 19:23:39 -04:00
Richard Burhans
29d541c7be
name change: _BX main_ browser -> _BX_ table browser
2012-08-22 15:31:23 -04:00
John Chilton
d281e835ef
Remove hard-coding of unsniffable binary types array and manually
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checking each sniffable type with a seperate function in
upload.py. Information on both types is now stored dynamically as
static variables in the Binary class.
2012-08-15 23:35:28 -05:00
Daniel Blankenberg
89e347625f
Rewrite HbVar datasource tool.
2012-05-04 15:35:51 -04:00
Daniel Blankenberg
c44aee110d
Update WormBase datasource tool to use WormBase 2.
2012-05-02 17:04:33 -04:00
Daniel Blankenberg
195e08f2b1
Add GenomeSpace tools.
2012-03-29 10:24:28 -04:00
Nate Coraor
c362e6202e
A bit more actual user cleaning.
2012-01-18 14:34:00 -05:00
Nate Coraor
61062a3ae5
Merge galaxy-central.
2012-01-18 10:34:39 -05:00
Daniel Blankenberg
99c7409900
Update EBI SRA tool's input action.
2011-12-14 09:37:45 -05:00
Daniel Blankenberg
2351c4aaca
Add EBI ENA SRA tool contributed by Iain Cleland.
2011-12-13 09:45:49 -05:00
Nate Coraor
85ba013e6d
Actual User: Fix for newline conversion on upload, tighten file permissions for files in upload. Please make sure you clean your temp directory regularly.
2011-12-08 13:22:39 -05:00
Nate Coraor
03c4fa3689
The upload tool requires samtools to upload BAM files, the Pileup tool requires samtools <= 0.1.16.
2011-12-06 11:42:12 -05:00
Daniel Blankenberg
df82c9dd76
Updates for 'GenomeSpace import from file browser' tools.
2011-11-29 13:41:40 -05:00
Greg Von Kuster
17c5b27cdc
Re-engineer the datatypes registry so that it is initialized once when the Galaxy server is started, but data types can continue to be loaded throughout the Galaxy server's session (hopefully this doesn't break anything).
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Add support for a single "import_module" to be passed to the new load_datatypes() method in the datatypes registry. This provides the ability to load a single class module from an installed tool shed repository along with a datatypes_conf.xml file included in the installed repository and pass them to the new load_datatypes() method. In the future, multiple imported modules may be allowed. The datatypes_conf.xml file included in the repository must conform to a slightly different definition than the same named file that comes with the distribution. This new definition will be documented in the Galaxy tool shed wiki.
We now have the ability to load new data types into the Galaxy server from an installed tool shed repository without restarting the Galaxy server.
2011-11-23 16:16:15 -05:00
Daniel Blankenberg
7cf9b6daea
Updates for GenomeSpace file browser importer.
2011-11-21 17:12:07 -05:00
Daniel Blankenberg
e7c4d8557b
Update GenomeSpace import from file browser tool to use new versioned API.
2011-11-18 13:48:06 -05:00
ichorny
236276b132
add actual user changes to galaxy-central
2011-10-21 14:01:48 -07:00
Daniel Blankenberg
68f2b7656b
Some genomespace_file_browser tweaks.
2011-10-06 14:22:59 -04:00
Daniel Blankenberg
e8d8d8e7c3
Add test/development GenomeSpace file importer datasource tool.
2011-10-06 13:55:25 -04:00
Nate Coraor
7d8b701df6
Fix uploading sorted BAMs to libraries when using the link method rather than copying.
2011-08-26 15:59:29 -04:00
Daniel Blankenberg
aec47aa2a9
pdate EuPathDB datasource configuration file. Contributed by Mark Heiges.
2011-08-22 14:03:57 -04:00
Kanwei Li
a9370f1b72
Spacing fix
2011-08-20 02:56:33 -04:00
Daniel Blankenberg
f9759aac21
Update EuPathDB datasource configuration file. Contributed by Mark Heiges.
2011-08-02 08:55:57 -04:00
Greg Von Kuster
d8279f0e5c
Add an altered version of Jelle Scholtalbers' enhancement code to support uploding various image data types. I've moved some of the code components around from Jelle's version, and added some fixes. The cod ein the new image_util.py file enables detections of images types without the need to create a new Image() class.
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I've also added baseline support of the HDF5 data type in this change set, but it is currently required to be in the unsniffable_data_types list.
2011-07-27 16:14:15 -04:00
Nick Semenkovich
403f2c73a3
Update links to reflect Galaxy Wiki moving away from Bitbucket.
2011-07-18 18:10:55 -05:00
Ross Lazarus
d53c3e984f
Backed out changeset 48bbe32beefe which introduced a whole bunch of unintended reversions from a broken hg repository
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This is a backout of commit 5765
2011-07-06 09:44:56 +10:00
Ross Lazarus
86b55bb0c0
branch merge
2011-07-05 12:40:43 +10:00
Nate Coraor
3959897d3d
Uploading a compressed library dataset using either the server directory or path paste methods was previously overwriting the input file, which should never happen. This changeset also makes it possible to upload compressed files that remain compressed (by choosing to "link files only"), however, Galaxy does not yet open the compressed file to properly set metadata on its contents.
2011-06-08 15:35:36 -04:00
Nate Coraor
1026641425
Don't provde the output filename to the upload tool if it's outside Galaxy's files_path, since this means we're only linking data and the output paths are not used (and may contain non-shell-safe characters). Fixes issue #533 .
2011-06-08 13:25:45 -04:00
Greg Von Kuster
61c3ed305f
Move duplicate data type checker methods from sniff and upload into a new ~/datatypes/checkers.py.
2011-06-03 15:36:59 -04:00
Daniel Blankenberg
694300ce97
Some reworking of data_source tools and the standard data_source.py script. Remove hard-coded special-case handling of UCSC Table Browser and GBrowse datasource tools; functionality remains, but is now a part of the individual tools' XML configuration files. Auto-detect is now available by providing data_type=auto parameters.
2011-04-21 13:12:10 -04:00
Daniel Blankenberg
58963cc97d
Remove link target from intermine datasource tools.
2011-03-22 20:29:32 -04:00
Greg Von Kuster
7640af8e06
Don't alter the contents of a file while uploading to a data library if using the filesystem_paths option. This partially resolves the issue where a supposedly sorted BAM file was being resorted upon upload to a data library when using this option. A better imlementation of determining whether a BAM file has been sorted (so that it does not get resorted) remains to be done.
2011-03-15 09:38:29 -04:00
Greg Von Kuster
df6f94b1d0
Per request from Peter Cock, turn the "Copy data into Galaxy?" check box into a select list that clarifies the behavior. The default is to copy files into Galaxy.
2011-03-11 14:56:11 -05:00
Daniel Blankenberg
5bff82eb46
Have YeastMine datasource tool point to the production server location and add configuration to tool_conf.xml.main.
2011-03-01 13:00:27 -05:00
Daniel Blankenberg
8cd2a39cc7
Add metabolicMine datasource tool.
2011-02-09 15:42:42 -05:00
Daniel Blankenberg
6d3d3edf19
Add YeastMine datasource tool. Site is still under development.
2011-02-01 17:29:40 -05:00
Greg Von Kuster
5f9f45a068
Several data library improvements:
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1. Enhance importing library dataset into the current history by now allowing the user to select from a list of existing histories or create a new named history ( similar to copying datasets ).  This feature is available for a specific library dataset, a folder ( or root folder ), when selecting multiple datasets from in a library,  and on the results page for searched library datasets.
2. Add Brad Chapman's latest patch for fixing the lucene search implementation
3. Eliminate searches on dataset state for both whoosh and lucene searches
4. Clarify the objects being searched in the regular search and advanced search boxes in the data libraries grids.
5. Add the ability to perform certain actions on 1 or more selected library datasets on the results page for searched library datasets.
6. Add a "select all" checkbox to the browse_library.mako template.
7. Fixed library functional tests accordingly.
2011-01-31 16:41:03 -05:00
Nate Coraor
15aa3cba69
Highlight the futility of uploading files >2GB via a browser.
2011-01-14 23:52:31 -05:00
Nate Coraor
82c4a11c88
Handle a minor bug in the upload tool.
2011-01-03 12:05:13 -05:00
Nate Coraor
b140866d0b
Heh heh. Whoops.
2010-11-30 14:37:19 -05:00
Nicola Soranzo