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
Nate Coraor
a07ef2cdd3
Add Job stdout/stderr to library item info page to aid in debugging.
2010-11-30 14:34:17 -05:00
Daniel Blankenberg
365f9d6ad8
Add modENCODE modMine server tool to tool_conf.xml.sample.
2010-11-23 14:50:46 -05:00
Ross Lazarus
d1270499ea
adding hapmapmart.xml to tools/data_source
2010-11-18 10:30:27 -05:00
Nate Coraor
c9a881e114
Add a new "Files uploaded via FTP" grid to the upload form and related parameter types, form fields, etc.
2010-11-05 11:04:50 -04:00
Nate Coraor
8367cdc4a6
"Fix" zip uploads for Python < 2.6. The scare quotes are because in Python < 2.6 you can't read a zip member without loading the entire member into memory...
2010-10-25 16:10:09 -04:00
Nate Coraor
2fb759bd99
Read zipfiles in chunks when uncompressing in the upload tool. And I continue to wish zipfile was a lot more like tarfile...
2010-10-20 17:00:06 -04:00
Nate Coraor
4ca447aa70
Add support for bz2 compressed uploads.
2010-09-10 14:07:16 -04:00
Greg Von Kuster
a7e30c4441
Apply patch from Brad Chapman providing support for detecting, uploading and displaying UCSC bigWig and bigBed. Add new functional tests for uploading and detecting bigbed and bigwig formats, and correct and clean up the test_get_data.py functional test script.
2010-08-19 13:58:10 -04:00
Nate Coraor
8a66864aee
Stop ignoring the sniff order set in the datatypes config file.
2010-08-18 14:56:10 -04:00
Daniel Blankenberg
70a68cd688
Remove UCSC tablebrowser specific parameters from modmine.xml datasource tool.
2010-08-16 09:22:40 -04:00
Kanwei Li
810c2291de
Detect pdf files on upload [Brad Chapman]. Resolves #357
2010-07-02 18:10:45 -04:00
Daniel Blankenberg
3b70b41f7d
Update UCSC table browser datasource tools to treat data marked as 'gff' as 'gtf'.
2010-06-28 11:50:25 -04:00
Nate Coraor
7c71894533
Remove obsolete binseq.zip and txtseq.zip formats, and allow for uploading single files in a zip archive. Adapted from a patch from Pablo Cingolani.
2010-06-23 16:48:13 -04:00
Ross Lazarus
6c39995d19
Patch to upload.py for composite file uploads where the user supplies urls for components
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At present, the path for each component is passed as a url and there's no upload type for
composite file components, so this
temporary fix searches for :// in the path to figure out if this is an url upload.
Not ideal and in need of a more robust repair.
2010-06-11 21:21:33 -04:00
Daniel Blankenberg
183c2d3d13
Bug fix for handling 'spaces to tab' for non-binary composite datatype files.
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Add upload tests for testing 'space to tab' when uploading composite and non-composite datatypes.
2010-06-07 15:34:20 -04:00
Greg Von Kuster
15abe33231
Add the CBI Rice Mart data source tool to the distribution.
2010-06-04 15:49:58 -04:00
Daniel Blankenberg
64c68b5a66
Several Fixes for Uploading Composite datatypes. Revert changeset 3769:69e70e588a8e.
2010-05-12 15:57:05 -04:00
Greg Von Kuster
95ac03c352
Remove the hack I just committed for changing modENCODE fly and worm dbkeys, and translate the values in the tool configs.
2010-05-12 15:18:40 -04:00
Greg Von Kuster
de5de2973c
Force modENCODE worm dbkey to be ce6 and modENCODE fly dbkey to be dm2.
2010-05-12 14:50:25 -04:00
Greg Von Kuster
53363c793e
Add the modENCODEfly and modENCODEworm data source tools.
2010-05-06 19:39:27 -04:00
Nate Coraor
ca066cef04
Add a tip to the upload tool about using url paste for big files
2010-05-04 10:18:42 -04:00
Ross Lazarus
84b05c8113
Fixes to rgQC top table ordering and add offset so can use rgManQQ to make plots
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Fixes to rgManQQ to handle unsorted data - now sorts before manhattan plot
2010-04-05 14:14:09 -04:00
Nate Coraor
933944c12d
Fix bug in upload where source import files could be removed if an error occurs during detection and galaxy owns the source files.
2010-03-23 12:45:08 -04:00
Nate Coraor
482b69b749
Modify the newline conversion methods in sniff so converting in place is optional. This is necessary to fix a bug that occurs if using the 'server_dir' or 'path_paste' library upload methods: previously, they would modify the file to be imported in-place if permissions allowed (probably not what the admin wanted) or fail if permissions did not allow. New functionality is to return the converted tempfile if 'server_dir' or 'path_paste' methods are used. Also, no newline conversion will be done if the administrator uses the symlink checkbox.
2010-03-11 11:56:20 -05:00
Greg Von Kuster
19592b4e39
Update tool_conf.xml.main and the tool conf for eupathdb.
2010-01-27 08:51:23 -05:00
Kanwei Li
0f1d788690
Wiki links now point to bitbucket instead of trac
2010-01-19 18:15:27 -05:00
Greg Von Kuster
a14492c491
Added from __future__ import division to the Filter tool and increased the version, and fixed the URL in the new bx_browser tool config.
2010-01-14 11:26:08 -05:00
Greg Von Kuster
826da3acac
Add a tool config for the new bx_browser data source tool.
2010-01-14 10:24:37 -05:00
Nate Coraor