Nate Coraor
d14eb4d653
Reintroduce nginx upload module support.
...
http://www.grid.net.ru/nginx/upload.en.html
The following config variables are added to universe_wsgi.ini:
nginx_upload_store = Path to nginx upload store
ex: = database/upload_store
nginx_upload_path = URL (from root of the Galaxy server) to direct upload POSTs to
ex: = /_upload
The following nginx config supports such a configuration:
location /_upload {
upload_store /path/to/galaxy/database/upload_store;
upload_pass_form_field "tool_id";
upload_pass_form_field "tool_state";
upload_pass_form_field "async_datasets";
upload_pass_form_field "^files_[0-9]+\|.*";
upload_pass_form_field "file_type";
upload_pass_form_field "dbkey";
upload_pass_form_field "runtool_btn";
upload_pass_form_field "ajax_upload";
upload_pass_form_field "upload_option";
upload_pass_form_field "library_id";
upload_pass_form_field "folder_id";
upload_pass_form_field "message";
upload_pass_form_field "roles";
upload_set_form_field "__${upload_field_name}__is_composite" "true";
upload_set_form_field "__${upload_field_name}__keys" "name path";
upload_set_form_field "${upload_field_name}_name" "$upload_file_name";
upload_set_form_field "${upload_field_name}_path" "$upload_tmp_path";
upload_pass_args on;
upload_pass /_upload_done;
}
location /_upload_done {
set $dst /tool_runner/index;
if ($args ~ nginx_redir=([^&]+)) {
set $dst $1;
}
rewrite "" $dst;
}
2009-09-29 17:14:20 -04:00
Kanwei Li
3531212ff6
typo fixes for tools in folders A-M
2009-09-27 23:11:43 -04:00
Nate Coraor
87db3952d3
Real Job(tm) support for the library upload tool. Does not include iframe upload for the library side yet.
2009-09-25 14:36:12 -04:00
Nate Coraor
6f3a169b01
Get rid of the hacky "alternate path" stuff used by the upload tool and fix setting metadata when using autodetect and set_metadata_externally
2009-09-10 14:52:38 -04:00
Nate Coraor
2e407c0b21
Fix for multi-byte file uploads
2009-08-25 14:58:37 -04:00
Nate Coraor
4158ee0833
set job state to new in upload tool action so that track_jobs_in_database works
2009-08-25 11:53:42 -04:00
Nate Coraor
3f5da01132
Real Job(tm) upload support
2009-08-20 10:49:54 -04:00
Greg Von Kuster
d0d7875192
Deprecated code corrections for supporting Python 2.6. Many of the Python 2.6 eggs are still throwing DeprecationWarning messages, so some things still won't work. Eggs for 2.6 need to be re-scrambled after corrections are made.
2009-08-14 15:37:31 -04:00
Daniel Blankenberg
b2e2b801ea
Enhance data_source.py to take advantage of the content length when known. If content length provided by external application is
...
greater than config.output_size_limit, no data will be retrieved and an error message will be provided to the user.
Tools using this script have been updated to provide the max file size on the command line.
Resolves ticket #93 .
2009-08-03 12:02:54 -04:00
Daniel Blankenberg
cc22aee3cb
Initial pass at allowing the setting of certain metadata parameters on upload (controlled via a flag). This allows the user to specify the 'base_name' to be used for Rgenetics datatypes, etc. Bunch of cleanup needed in upload.
2009-07-15 14:11:35 -04:00
James Taylor
db9c0a9870
Commenting out 'other dbkey' in upload
2009-06-11 15:41:57 -04:00
James Taylor
537f8952ef
Merging Ian's trackster update with current head
2009-06-11 12:20:03 -04:00
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.
...
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.
...
- 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
...
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:
...
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
Nate Coraor