Nate Coraor
698e2eb0e1
Pathnames are now absolute, this broke the cluster staging.
2007-09-28 21:17:43 +00:00
Greg Von Kuster
19d06f68a0
Reverted some logging changes since James pointed out their redundancy.
2007-09-28 19:36:49 +00:00
Greg Von Kuster
882d6d6aef
Changed class sniffers to have boolean return types.
2007-09-28 19:23:31 +00:00
Greg Von Kuster
5aa8cb1e23
Changed the call from Tabular().set_meta() to dataset.set_meta() since we now have a better approach to setting meta data for tabular data types.
2007-09-28 18:42:57 +00:00
Greg Von Kuster
c6a60b6439
Added new unit test to check for obscure bug in sniff that Belinda found, also committed test data for customtrack that I previously missed.
2007-09-28 18:04:34 +00:00
Greg Von Kuster
7c68304559
Enhanced some of the logging when jobs throw exceptions, we're still seeing some job errors with null values for stderr, traceback, so hopefully this will help diagnose the issues.
2007-09-28 17:34:17 +00:00
Daniel Blankenberg
1b568f8221
Guess and set mimetype when displaying extra files associated with a dataset.
2007-09-28 15:25:25 +00:00
Greg Von Kuster
807fe98842
Introduced necessary set_meta() functions to tabular format classes. These functions will be used to determine the number of lines to skip in the dataset when calling Tabular.set_meta()
...
for them to determine the columns and column_types metadata attributes.
2007-09-28 13:50:26 +00:00
Greg Von Kuster
044d221534
Bug fix in sniff.py tabular files will no longer inadvertently be changed to txt.
2007-09-28 12:55:44 +00:00
Greg Von Kuster
3a97026d5d
Slight, but important bug fix in sniff.py.
2007-09-27 20:51:43 +00:00
Jianbin He
bda6409803
specify the input ftype for this test
2007-09-27 19:53:55 +00:00
Jianbin He
bd0a5132f3
data change for testing
2007-09-27 19:53:04 +00:00
Greg Von Kuster
4c6dab39eb
Enhanced upload utility to dynamically load the File Format select list using values from the registry's datatypes_by_extension dictionary.
2007-09-27 14:12:01 +00:00
Greg Von Kuster
1a6daca3a4
Streamlined interface for supporting new data types - requires db change and note config change.
...
db change:
update dataset set extension = 'txt' where extension = 'text';
Adding support for a new data type is now as simple as adding the new type to the config file and optionally adding the
type into the new sniff_order section in the config file, and adding the new class for the data type to the appropriate
datatypes code.
The config file now has a new section [galaxy:sniff_order] which lists the order in which datatype class sniff functions will
be called (each datatype class can now optionally include its own sniff function, although not a requirement).
Support for the 'text' file extension has been eliminated as we will standardize on the 'txt' file extension for the Text data type.
2007-09-27 14:10:16 +00:00
Greg Von Kuster
0cc15f4a51
Removed mime_types and text_types attributes from galaxy.util.__init__.py since they are no longer referenced.
2007-09-27 14:01:24 +00:00
Greg Von Kuster
db8eee7889
Changing all tools that use 'text' as file extension to now use 'txt'. We are eliminating the use of 'text' as a file extension within Galaxy and will now use only 'txt' for Text data types.
2007-09-27 12:24:27 +00:00
James Taylor
a800d13272
More aggressive error handling in job queue and local runner, Galaxy will no
...
longer die when an exception is thrown in "JobWrapper.fail"
2007-09-26 18:48:21 +00:00
James Taylor
e9ccb4f549
Use absolute paths for references to datasets and associated files.
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NOTE:
Our cluster shouldn't have a problem with this since datasets live in the same
place on the web server and computer nodes. However for the long term we need
a better way to deal with this. Different compute nodes may have files in
different locations, a more complicated resolution strategy needs to be
developed.
2007-09-26 18:47:01 +00:00
Daniel Blankenberg
a3b137d94b
Extracting Genomic DNA can now result in an interval file with the
...
sequence appended as a new column.
2007-09-25 16:12:37 +00:00
James Taylor
1c3c0d2659
Need to rollback cwd changes because they were breaking a bunch of things.
...
We need to handle the absolutization of paths differently. I believe the
correct way to do this is to handle it at the time of building command lines.
Perhaps this means the build_command_line needs to happen later in the
job running process?
2007-09-25 15:36:28 +00:00
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
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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
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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
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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
Nate Coraor