Greg Von Kuster
5dd014a91e
Completed an old FIXME in DefaultToolAction.execute() - metadata no longer added to "incoming". Tool config params changed from things like$input_chromCol to ${input.metadata.chromCol}.
2008-07-23 15:27:39 -04:00
Greg Von Kuster
666de20b4d
Cleanup for fastqsolexa data type converters. We are currently supporting only the Solexa variant and will add support for other variants when the formats stabilize.
2008-06-09 20:15:04 +00:00
Wen-Yu Chung
2073b002d0
fix fastq sniff test.
2008-06-06 19:32:14 +00:00
Greg Von Kuster
1a23f9e55d
Requires config modification - Add Fastq sniffer, add support for fastqsolexa data type, rename convert_fatsq2fasta tool to be fastq_to_fasta_qual, add functional tests for both fastq and fastqsolexa data types, misc code cleanup.
2008-05-29 19:12:36 +00:00
James Taylor
563dbd3d0d
History test fixes.
2008-04-25 19:46:58 +00:00
Greg Von Kuster
fcebe910fe
Dynamic options will opnly prepend GALAXY_INDEX_DATA_DIR if from_file is not an absolute path. Also fixed a type in twill code.
2008-04-04 17:42:06 +00:00
Nate Coraor
c1b6226d40
When running functional tests, display the tool's stderr when a job ends in error.
2008-04-04 15:40:28 +00:00
Greg Von Kuster
1580ed8260
Functional tests will now properly handle output datasets in pdf format. Added functional tests for histogram and scatterplot. Fixed a bug where temporary files was not removed if functional test failed.
2008-04-04 14:45:29 +00:00
Greg Von Kuster
7c10de3e79
This is the file I meant to commit instead of __init__.py...
2008-03-27 17:55:48 +00:00
Greg Von Kuster
b10f59456b
Oops, forgot to change my port back to the default.
2008-03-27 17:53:49 +00:00
Greg Von Kuster
48d05cf6d8
New tools require uploaded compressed files, which the upload tool decompresses on the fly, renaming the file. The do_it function needs to take this into account when running functional tests for these tools.
2008-03-27 17:51:04 +00:00
Greg Von Kuster
717c9d8107
Fixes for functional tests for several tools.
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- Select list control options require a "value" attribute, not a "values" attribute.
- Corrected the test data for 2 tests that probably have never worked - Dan, please verify!
- Improved the information displayed ( in most cases ) if a test fails.
2008-03-26 19:07:15 +00:00
James Taylor
b5d916528c
Small fix for functional tests + grouping
2008-03-14 18:37:42 +00:00
James Taylor
962b687556
Reorganizing the galaxy.tools package. Made 'parameters' a package and moved
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all parameter related pieces underneath it.
2008-03-14 18:31:52 +00:00
James Taylor
49edae2385
Log host/port in functional tests.
2008-01-20 18:04:35 +00:00
James Taylor
32ab4396e1
Fix datatype_convertors for functional tests.
2008-01-17 03:34:15 +00:00
James Taylor
8a70a02b5a
Override datatype_convertors config in functional tests
2008-01-17 02:58:59 +00:00
James Taylor
f7decb22cb
Functional tests now use the datatypes defined in universe_wsgi.ini, this
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fixes the neighbor joining test.
2008-01-07 19:43:39 +00:00
James Taylor
2aa15eb876
More fixes. This would be much easier is the tests actually scraped the
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HTML rather than needing separate XML templates.
2008-01-05 23:41:59 +00:00
James Taylor
be49c19e2d
Change to test related to security fix in previous commit.
2008-01-05 23:20:25 +00:00
James Taylor
2da9ec3b52
Use the same HTTP server for the functional tests that is used for the
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application.
2008-01-05 19:54:49 +00:00
Greg Von Kuster
e94d18ad63
A better way to decompress UCSC gzipped files. Added functional tests for uploading binary, zipped and gzipped files. Added temp file removal to upload when exception thrown. Eliminated an unnecessary import in subtract_query.
2007-12-20 18:49:03 +00:00
Daniel Blankenberg
4db24ed949
Minor change to display of diff.
2007-11-15 17:03:00 +00:00
Daniel Blankenberg
48d718bca6
Fix comparison of file contents for test framework. It was previously using zip(), so tests would wrongly pass when one file was smaller than the other (but contained the same data up to it's end).
2007-11-14 22:00:29 +00:00
Greg Von Kuster
96e3ac8d1b
Fix for new auto-detect form. Also added a new functional test for the auto-detect form.
2007-11-13 14:02:49 +00:00
James Taylor
fe12d04355
History test fix.
2007-10-31 04:38:26 +00:00
James Taylor
575d2d2ffb
Test fixes.
2007-10-30 07:04:46 +00:00
Greg Von Kuster
8e3f797331
Initial fix for concurrent update db issue (still using psycopg). Commented out "job requeued" log statement. Changed error reporting email in config.
2007-10-11 20:09:25 +00:00
Greg Von Kuster
5de7853b81
Fix for broken functional test.
2007-10-09 19:17:05 +00:00
Greg Von Kuster
5b4bc10b88
Functional test enhancements, history functions are now covered.
2007-10-09 18:19:44 +00:00
Greg Von Kuster
10152d8b27
Eliminating more unused test data.
2007-10-05 19:47:23 +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
Greg Von Kuster
48e9652241
More functional test code cleanup and first round of additional functional tests.
2007-10-04 19:43:24 +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
Jianbin He
bda6409803
specify the input ftype for this test
2007-09-27 19:53:55 +00:00
James Taylor
9ea22cfe77
Form order for metadata editing...
2007-09-20 21:36:00 +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
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
166893ef9d
Testing of text box controls with commas should work properly now.
2007-09-06 18:48:21 +00:00
Daniel Blankenberg
6b555a51cb
Allow tests to work with conditional statements.
2007-09-06 17:51:29 +00:00
Daniel Blankenberg
93bf90e193
Fix Testing Framework handling of multiple select parameters.
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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
Jianbin He
3f0579c7a4
change the test steps, cause the tool changed
2007-08-22 17:51:50 +00:00
Jianbin He
6e56f37a19
change test value for column parameter, cause the tool changed
2007-08-22 17:31:29 +00:00
Jianbin He
6568b8a79e
fix the current test errors of several maf tools
2007-08-08 19:31:16 +00:00
James Taylor
f759427a07
Fix functional tests.
2007-07-31 20:14:58 +00:00
James Taylor
953b62c7d4
NOTE CONFIG FILE CHANGES!
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First step of the big reorganization. This moves almost everything web interface related under the web package (still a few things left to disentangle). In particular, galaxy.interfaces is now galaxy.web.controllers which is somewhat more clear. Middleware, servers, and framework are all better organized under web.
Most importantly, the configuration file has been greatly simplified, the "composite" and various static apps are now configured by the application rather than by PasteScript, so the config file really only contains user modifiable parameters now.
(Expect this to break something)
2007-07-31 20:09:51 +00:00
Greg Von Kuster