Daniel Blankenberg
ed964dd043
Add dataset filename table. Filenames can now be assigned, setting the readonly flag on a dataset filename object
...
will prevent Galaxy from deleting the file when the dataset is purged. Copies of datasets (such as when sharing a
history), no longer copy file contents.
Database changes required:
CREATE TABLE dataset_filename (
id INTEGER NOT NULL,
create_time TIMESTAMP DEFAULT current_timestamp,
update_time TIMESTAMP DEFAULT current_timestamp,
filename TEXT,
extra_files_path TEXT,
readonly BOOLEAN,
PRIMARY KEY (id)
);
ALTER TABLE dataset ADD filename_id INTEGER;
2007-09-24 19:42:09 +00:00
Ross Lazarus
57750f52cc
Fix to local job runner so jobs run in the working directory rather than the galaxy root..
2007-09-21 20:01:39 +00:00
Greg Von Kuster
031a1f91fe
Fixed bug when sharing histories.
2007-09-21 20:00:04 +00:00
Daniel Blankenberg
47299bc371
Better guessing of dbkey when metadata version is unknown, but old_dbkey contains a key.
2007-09-21 19:36:40 +00:00
Daniel Blankenberg
5b85146754
Species are no longer selected by default in MAF tools.
2007-09-21 14:55:06 +00:00
James Taylor
9ea22cfe77
Form order for metadata editing...
2007-09-20 21:36:00 +00:00
James Taylor
85b0a3ba90
Add support for Mako templates. If a template filename ends with ".mako" then
...
Mako will be used automatically instead of Cheetah. Mako has some advantages,
particularly in terms of code reuse and template inheritance.
2007-09-20 21:11:48 +00:00
Daniel Blankenberg
1047e7728e
Improve error message on maf tools, telling users where to go to set
...
their genome build.
2007-09-20 20:39:05 +00:00
James Taylor
74d224ef71
All forms now use the tool form style. Cleaned up the edit attributes page.
...
Metadata elements can be created with "visible=False" in which case they are not display to the user on the edit attributes page.
2007-09-20 19:14:42 +00:00
James Taylor
b7ac41fbb5
Fix problem where multiple scaffolds are displayed per species when working
...
with MAFs.
2007-09-20 18:14:53 +00:00
Greg Von Kuster
20126a37a4
Bug fixes, enhancements (including a new test) for the aggregate_binned_scores_in_intervals tool and added new code file for handling tool exceptions.
2007-09-19 19:45:28 +00:00
Greg Von Kuster
23fd74c2c5
Better error handling for tools that use columnlist tool parameter.
2007-09-19 14:49:02 +00:00
Greg Von Kuster
f27c590190
Enhanced grouping tool to use columnlist tool parameter.
2007-09-18 20:31:09 +00:00
Chinmay Rao
18e2c28a45
Added support for gff3 datatype
2007-09-18 15:43:44 +00:00
Guruprasad Anada
026bc2c6c9
Changed the output type of get_flanks tool to 'interval' so as to ignore the extra BED fields while displaying the data in UCSC. Also skipped lines with negative start/end co-ordinates.
2007-09-18 15:33:01 +00:00
Greg Von Kuster
50968827e9
Enhanced sort tool to use columnlist tool parameter, altered functional test to work with new version. Some other miscellaneous cleanup.
2007-09-17 20:48:59 +00:00
Greg Von Kuster
8b951a529b
Bug fixes, enhancements for cor tool, it now uses the columnlist tool parameter.
2007-09-17 14:21:24 +00:00
Jianbin He
bed14a6837
fix the onchange bug for testing frame
2007-09-14 16:44:18 +00:00
Jianbin He
7e7b34f081
temporary solution to Count1 testing
2007-09-12 19:34:59 +00:00
Guruprasad Anada
20244dabf6
Modified "UCSC gene BED to Exon/intron BED" tool to include an option for extracting CODONS.
2007-09-12 18:54:10 +00:00
Jianbin He
f0e1e5fa0d
specify the ftype for testing data
2007-09-10 16:16:38 +00:00
Jianbin He
fefb93e6c3
test if the path/file exists before mkdir
2007-09-10 15:40:22 +00:00
Jianbin He
52c94122e7
data for testing changed
2007-09-10 15:37:56 +00:00
Greg Von Kuster
e216317ed5
I eliminated the conditional on calling Tabular.set_meta() from the ColumnList parameter.
...
This should correct metadata attributes that may have been previoulsy improperly set.
Since it is called only when tools that use the ColumnList parameter are loaded, it
should not result in concurrent update issues in the database. Keep an eye on the daily
job errors, if you see several per day that have an error state with null stderr and
traceback values, this may be the culprit. I doubt this will happen though. I also
added the customtrack and gbrowsetrack types to Tabular.set_meta() since htey are interval
types.
2007-09-08 17:41:12 +00:00
Greg Von Kuster
47f93394b0
Bug fix - can't believe our functional test didn't catch this.
2007-09-08 16:01:42 +00:00
Greg Von Kuster
dd64d676b1
Much better approach to determining datatype in order to ensure columns and column_list metadata attributes are properly set.
2007-09-08 15:53:15 +00:00
Greg Von Kuster
9235051818
Several bug fixes to sniff, determining datatypes should work better. Fixed some bugs in the Tabular and Gff classes as well.
2007-09-07 19:52:36 +00:00
Greg Von Kuster
6ebc7a706e
Fixed scatterplot tool to use ColumnList parameter and deleted some unused files.
2007-09-07 13:58:08 +00:00
Daniel Blankenberg
166893ef9d
Testing of text box controls with commas should work properly now.
2007-09-06 18:48:21 +00:00
Greg Von Kuster
543fa44fcf
Bug fix to ColumnListParameter, enhanced Count1 tool to use ColumnListParameter, cleaned up code.
2007-09-06 18:42:59 +00:00
Daniel Blankenberg
6b555a51cb
Allow tests to work with conditional statements.
2007-09-06 17:51:29 +00:00
Greg Von Kuster
21423969e5
Commented out call to Tabular().set_meta() since it is causing concurrent update problems in the database.
2007-09-06 16:56:19 +00:00
Greg Von Kuster
97fda63c73
Eliminated NoProperDataError exception so tool form will be displayed even if no dataset in history can be used by the tool.
2007-09-05 14:04:39 +00:00
Greg Von Kuster
c3538a55b7
Enhanced histogram tool to use new columnlist parameter and cleaned up the tool code.
2007-09-04 20:16:33 +00:00
Greg Von Kuster
32c24741c1
Added new ColumnList tool parameter and added a new NoProperDataError exception since tools could now require input datasets of specific type sin order to render the tool form.
2007-09-04 20:14:56 +00:00
Greg Von Kuster
c342ac4d30
I need to keep a handle on the updated state of tool input parameters.
2007-09-04 20:11:42 +00:00
Greg Von Kuster
98d509553c
A bug fix to tabular - we now always skip the 1st line of a dataset. Another bug fix to interval where we call Tabular's set_meta().
2007-09-04 18:09:20 +00:00
Anton Nekrutenko
7c6494c1c8
Unsequenced genome for sept
2007-09-04 01:13:21 +00:00
Greg Von Kuster
617dd51375
Made "refresh_on_change" work for form select fields.
2007-08-31 18:19:33 +00:00
Greg Von Kuster
db2d8dfc59
Fixed a bug I introduced in Interval.set_meta()...sheesh!
2007-08-31 17:34:14 +00:00
Daniel Blankenberg
93bf90e193
Fix Testing Framework handling of multiple select parameters.
...
If an option was selected by default, it was never cleared before setting the desired options, now it is.
2007-08-31 16:46:19 +00:00
Greg Von Kuster
9e7adb2f39
Changed Tabular numerical_columns metadata attribute to be column_types.
2007-08-31 15:49:26 +00:00
Greg Von Kuster
4c696df636
Added numerical_columns to tabular metadata.
2007-08-31 13:23:25 +00:00
Daniel Blankenberg
0f7773a8ba
Update test data for maf_to_bed and maf_thread_for_species.
2007-08-30 19:54:41 +00:00
Daniel Blankenberg
8d4e177680
Add missing_meta() to MAF datatype.
2007-08-30 19:10:04 +00:00
Daniel Blankenberg
eb580d6ec0
Bug fix for thread for species.
2007-08-30 18:44:51 +00:00
Daniel Blankenberg
477aa85f16
Update MAF tools to use species as provided by metadata. Selecting parameters for these tools should be significantly faster.
...
Still a bit of cleanup to do.
2007-08-30 18:06:39 +00:00
Daniel Blankenberg
42a90ea1f0
Script to ensure that MAF metadata is set.
2007-08-30 14:46:52 +00:00
Daniel Blankenberg
dae7fd96cb
Restore calling set_meta() on all output datasets, if metadata is missing.
2007-08-29 17:30:03 +00:00
Jianbin He
0a1588b9a9
change the output format of information file
2007-08-28 04:16:18 +00:00
Daniel Blankenberg