Daniel Blankenberg
c0d797e00d
Allow the uploading of composite datatypes. A new grouping parameter, UploadDataset, is used to contain and process the file_data/url_paste/space_to_tab used to upload a file - multiple sets are displayed when uploading a composite datatype (similar to a repeat). Composite files can now be declared to the datatypes registry (required for proper uploading), but they are stored in the same manner as before (the extra_files_path) and should be backwards compatible. When uploading a composite datatype, only one dataset can be uploaded at a time. The ability to upload multiple datasets (url_paste (contents or urls) + file_data) for non-composite datatypes remains unchanged.
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A more structured way of storing these files (rather than dumping in a directory) is worth considering.
2009-06-08 12:49:26 -04:00
Greg Von Kuster
49938abb76
Add EuPathDb data source tool config.
2009-06-01 10:27:04 -04:00
Greg Von Kuster
a9cd544be9
Add a defaulttimeout setting of 10 minutes to the urlopen() call for requests to remote data sources.
2009-05-28 11:10:44 -04:00
Greg Von Kuster
e608f904ee
Add tool config for GrameneMart data source.
2009-05-27 14:19:59 -04:00
Ian Schenck
feda672ffa
- Performance of indexers much improved.
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- Indexing for tracks done in background with a visual treatment done to Trackster
- DB builds can be uploaded by a user (chromInfo/len extension).
- TODO: Add ability to change the dbkey of a dataset to any arbitrary string value.
2009-04-23 13:46:52 -04:00
Greg Von Kuster
fb2441caa1
merging heads
2009-03-26 11:13:13 -04:00
Greg Von Kuster
bd41001a99
i18n fix: dataset.info should not be translated since it will generally not have an entry in the catalog. Wormbase fixes: URL to main site corrected, and all supported builds added to gbrowse_build_sites.txt.
2009-03-26 09:34:05 -04:00
Greg Von Kuster
05c2d4222b
merging from central
2009-03-20 03:06:40 -04:00
Greg Von Kuster
354d0447df
Fixes for i18n support - all charsets set to utf-8, now able to paste multi-byte chars in upload form, templates use utf-8 as output_charset, other miscellaneous fixes.
2009-03-20 02:49:30 -04:00
Greg Von Kuster
c0a4d982aa
merging from central
2009-03-19 21:44:42 -04:00
Greg Von Kuster
ad8f672677
Fixes for wormbase tools, use post as http method rather than get.
2009-03-19 21:41:06 -04:00
Nate Coraor
86eb5e62b2
Asynchronous uploads. Currently disabled in IE, since IE throws
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occasional 'permission denied' errors when jquery attempts to set the
form target. Compatible with the nginx upload module, but interrupted
uploads will remain in the 'upload' state indefinitely.
2009-03-13 13:48:59 -04:00
Greg Von Kuster
e55a4d84f8
More library work - requires database schema update:
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1) include templates in the upload form for library datasets
2) Add user_id column to library_dataset_dataset_association table
3) Add message column to library_dataset_dataset_association table
4) Several miscellaneous bug fixes related to uploading library datasets
SQL commands required:
ALTER TABLE library_dataset_dataset_association ADD COLUMN user_id INTEGER;
ALTER TABLE library_dataset_dataset_association ADD CONSTRAINT library_dataset_dataset_association_user_id_id_fkey FOREIGN KEY (user_id) REFERENCES galaxy_user(id);
ALTER TABLE library_dataset_dataset_association ADD COLUMN message VARCHAR(255);
2009-03-09 17:02:21 -04:00
Greg Von Kuster
987df32669
Fix for rendering tools / workflows in target frames, also elimnate the Workflow link in the tool panel as we're now using the menu bar.
2009-02-23 13:52:34 -05:00
Greg Von Kuster
377a5d8981
Add the Libraries tab to base panel and fix the access_libraries tool config for PrognosysBio.
2009-02-23 11:04:27 -05:00
Nate Coraor
42cbc8d893
Set a width hint for the library browser
2009-02-06 14:34:57 -05:00
Greg Von Kuster
bb2b948557
merging from central
2009-01-22 08:51:48 -05:00
Greg Von Kuster
705994a0fc
Fixes for formatting end of line chars in html when displaying dataset.info. Also change the biomart tool version.
2009-01-22 08:50:52 -05:00
Greg Von Kuster
6dd5b31c0e
merging from central
2009-01-21 17:06:02 -05:00
Greg Von Kuster
7e21fb74a3
Fixes for Biomart and UCSC to better ensure the data type is correctly set. A data type of "tabular" is now the default, and data will be sniffed if this is the data type.
2009-01-21 17:03:39 -05:00
Greg Von Kuster
19c0b7e30b
merging from central
2009-01-15 11:03:19 -05:00
Greg Von Kuster
b7aaa17bc3
Change History.copy() back to use datasets rather than active_datasets. Add checks in set_peek() to properly set peek on purged datasets. Fixes sharing a history that contains purged datasets.
2009-01-15 10:49:01 -05:00
Greg Von Kuster
df610a666c
merging from central
2009-01-13 10:56:05 -05:00
Greg Von Kuster
051a78bc39
Add new tool config for flymine production server.
2009-01-13 10:55:08 -05:00
Nate Coraor
b6d561fb42
Allow users to download a selection of datasets directly from the library in an archive format of their choosing.
2008-12-15 16:37:54 -05:00
Greg Von Kuster
dfd5e9827f
Rename gbrowse_elegans to wormbase_test, add a config for the wormbase production server.
2008-12-15 10:37:39 -05:00
Greg Von Kuster
d3b2a27cee
merging from central
2008-12-15 10:37:16 -05:00
Greg Von Kuster
7a5203fd65
Attempting to merge conflicts.
2008-12-15 08:58:33 -05:00
Greg Von Kuster
b432fd166d
merging heads
2008-12-15 08:55:16 -05:00
Greg Von Kuster
0b85700945
merging from central
2008-12-13 23:36:47 -05:00
Greg Von Kuster
2647f72e4a
Add ability for data_source tools to append parameters passed in the initial response to the value of URL prior to Galaxy's post to the URL. This is a cleaner method for Biomart and also gets GBrowse to wrok.
2008-12-13 23:35:29 -05:00
Greg Von Kuster
c3e009142a
merging from central
2008-12-02 10:55:17 -05:00
Greg Von Kuster
ffa719a9ab
Call set_size() before set_peek() on datasets, changes to set_peek() to not read entire files for some datatypes.
2008-12-02 10:50:54 -05:00
Greg Von Kuster
eeeab78b32
Fixes for accessing libraries from the analysis view.
2008-11-21 09:21:39 -05:00
Greg Von Kuster
32b4b77f74
Missed translating the primaryTable data type from UCSC in my last commit.
2008-11-13 15:17:42 -05:00
Greg Von Kuster
edf88dd149
merging from central
2008-11-13 15:17:39 -05:00
Greg Von Kuster
f6c9b706a2
merging from central
2008-11-13 15:02:30 -05:00
Greg Von Kuster
c454370ff7
Add a new <data_type_translation> tag set to data_source tools that enable the translation of an unsupported data type to a supported one in Galaxy ( currently only used in UCSC ). Also some tweaks to the jobs reports.
2008-11-13 14:56:33 -05:00
Daniel Blankenberg
374936f7aa
Merging heads
2008-10-31 14:53:20 -04:00
Daniel Blankenberg
ad21aee2a0
Small typo in one of the encode import tools.
2008-10-31 14:52:41 -04:00
Daniel Blankenberg
ec188a33cb
Resolve a bunch of merge conflicts.
2008-10-31 11:28:09 -04:00
Daniel Blankenberg
35168f40a5
Fixes for dealing with UnvalidatedValues (i.e. when running workflows) and also when passing None trans to dynamic options.
2008-10-31 11:00:50 -04:00
Greg Von Kuster
12b40f7a36
merging from central
2008-10-28 11:28:15 -04:00
Greg Von Kuster
7b49309886
Add new EpiGRAPH tools that point to EpiGRAPH production server.
2008-10-28 11:27:42 -04:00
Greg Von Kuster
f2d8ab1bc1
merging from central
2008-10-27 16:07:17 -04:00
Greg Von Kuster
b74f176613
Add a new URL_method attribute to data_source tool types whose value is either "get" or "post" ( some require a get request while others require a post request ). This fixes the Biomart problem ( along with a new, well documented hack that can be eliminated when Biomart encodes the value of URL in the initial response - they'll tell us when they've fixed this ). Also added some requested info to the "send to EpiGRAPH" tool.
2008-10-27 16:03:43 -04:00
Daniel Blankenberg
4b24e13514
Resolving Merge
2008-10-22 14:03:41 -04:00
Daniel Blankenberg
b9e242e4eb
Add a new metadata type of Metadata Files.
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These are now used to store the list of chromosomes for species as well as the index for MAF files.
MAF tools have been enhanced to make use of index files when available.
TODO: When datasets are purged from disk, these files should also be purged.
2008-10-22 13:49:22 -04:00
Daniel Blankenberg
c0ebad5659
Merging heads
2008-10-17 13:33:46 -04:00
Greg Von Kuster
288912ee87
Fixes for data_source tools, data.name, data.info, data.dbkey, and data.extension should now be properly set. Eliminated fastq data type from datatypes_conf.xml.sample since it is not a supported data type.
2008-10-17 10:46:29 -04:00
Daniel Blankenberg