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
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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;
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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()
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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.
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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
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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
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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.
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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
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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.
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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
Daniel Blankenberg