Nate Coraor
01181fa546
Include the regular (Galaxy) job_id with all the PBS debug messages,
...
should help with searching the logs and associating PBS messages with
a specific job. Also, the PBS job name is now the regular job_id,
so you'll see it in qstat and PBS error mail.
2007-10-10 17:55:21 +00:00
Guruprasad Anada
cd1b9436fe
Modified "Gene Bed to Exon/Intron/Codon BED" tool to handle codons falling in the boundary of two consecutive exons.
2007-10-10 15:08:16 +00:00
James Taylor
7db15430ad
Repacking jquery, something got borked...
2007-10-10 00:51:42 +00:00
James Taylor
0237c186b7
Update to latest released versions of jquery and jquery.ui (ui still needed
...
a one line change to work for us, but we're much closer to in sync now).
2007-10-10 00:29:00 +00:00
James Taylor
7831ea5a2a
Decorator for simplifying controller methods that return json (just return
...
and object that simplejson can understand and it will be jsonified)
2007-10-09 23:23:08 +00:00
James Taylor
2471f3222f
This doesn't seem to break anything and probably fixes Dan's problem.
2007-10-09 23:17:26 +00:00
Greg Von Kuster
5de7853b81
Fix for broken functional test.
2007-10-09 19:17:05 +00:00
Greg Von Kuster
0f9cff922c
Miscellaneous tool bug fixes.
2007-10-09 18:51:50 +00:00
Greg Von Kuster
5b4bc10b88
Functional test enhancements, history functions are now covered.
2007-10-09 18:19:44 +00:00
James Taylor
ed3185104e
Load controllers automatically rather than needing to specify each name
...
in 'buildapp.py'.
2007-10-08 20:47:04 +00:00
James Taylor
13608b5a8b
Cleaning up ColumnListParameter and related things.
...
- Dependencies between parameters and refresh_on_change are now more general.
Any parameter can assert a dependency on any other parameter by name, and
if a parameter has dependencies it will cause a refresh.
- Use "other_values" to get at the value of the associated dataset rather
than trying to look at the tool. This means that column lists now work
inside grouping constructs.
- Eliminated tool.updated_params and use of self.legal_values. These
variables are GLOBAL. Everybody using a tool has a reference to the same
instance of tool. Thus, if two people are using the same tool at once this
can cause serious problems.
2007-10-08 19:33:23 +00:00
James Taylor
fd19134676
Better __str__ method for ExpressionContext
2007-10-08 19:28:32 +00:00
James Taylor
433b118b9b
Moving MetaDataPickler out of main model module (this seems a bit cleaner)
2007-10-08 19:28:00 +00:00
Daniel Blankenberg
a9a72ee0ed
Fix for the special case of dataset tools which are not run over the cluster.
2007-10-08 13:27:53 +00:00
Greg Von Kuster
10152d8b27
Eliminating more unused test data.
2007-10-05 19:47:23 +00:00
Greg Von Kuster
dce3f2eed5
Some test data I missed.
2007-10-05 19:10:24 +00:00
Greg Von Kuster
43afaf3969
Added functional tests for sniffing and metadata settings on file upload. Fixed a test in the 'Filter Maf Blocks by size' tool. Added new test data. Commited the bug fix I really wanted in Axt.sniff().
2007-10-05 18:02:33 +00:00
James Taylor
83f7de290e
Clip long words when displaying info in history.
2007-10-05 17:13:50 +00:00
Greg Von Kuster
676db63304
Bug fix for sniffing axt files.
2007-10-05 13:08:21 +00:00
Daniel Blankenberg
6777c4ef35
When using the local job runner, run tools in the generated working directory, providing absolute paths.
2007-10-05 01:25:42 +00:00
Daniel Blankenberg
96a90a5072
Get path for twoBitToFa binary from path of executing script.
...
Should this binary be part of the distribution?
2007-10-05 00:47:35 +00:00
Daniel Blankenberg
207f3ce455
Python is used to run python scripts.
2007-10-04 23:31:38 +00:00
Greg Von Kuster
48e9652241
More functional test code cleanup and first round of additional functional tests.
2007-10-04 19:43:24 +00:00
Daniel Blankenberg
cfaeb3f4d8
url_for() is now used for displaying datasets.
2007-10-04 18:51:26 +00:00
Greg Von Kuster
aa0dcc81d5
More functional test cleanup, eliminated redundant tests, unused test data, and renamed some test data files.
2007-10-04 14:14:15 +00:00
Greg Von Kuster
7f29b2b047
More functional test cleanup, renamed many functions to make it easier to undrstand what they do.
2007-10-03 20:50:16 +00:00
Greg Von Kuster
0b80b63975
Fixed indentation problems in the submit_form() function.
2007-10-03 15:51:55 +00:00
Greg Von Kuster
b3aa4efa6f
Cleaned up functional tests, eliminating some redundant tests and unused test data files. Next step, add many missing tests.
2007-10-03 14:17:41 +00:00
Anton Nekrutenko
421cc3a3b3
Usequenced genome for October plus ashg update
2007-10-02 01:56:55 +00:00
Greg Von Kuster
ff7ecaa58d
Eliminated non-text datatypes from sniff order since galaxy hinders non-text file uploads (e.g., gmaj.zip files are sniffed as txt data types since Galaxy automaticaally changes EOL
...
characters upon upload. Fixed the guess_ext() function in sniff.py to eliminate the call to sep2tabs since this function changes the data in the file (the guess_ext() function probably
shouldn't be doing that). Added a sniff function to the Gmaj class as an example for zip data types.
2007-10-01 21:06:58 +00:00
Daniel Blankenberg
e73afecfde
Change job_parameter value type to TEXT from varchar;
...
Database change required:
ALTER TABLE job_parameter ALTER value TYPE TEXT;
2007-10-01 19:48:14 +00:00
Greg Von Kuster
7cb1bb2e47
Fix for cor2 tool functional test, also set columns and column-types meta data attributes to be invisible for all tabular data types.
2007-10-01 14:07:34 +00:00
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.
...
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
Nate Coraor