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Author SHA1 Message Date
James Taylor be49c19e2d Change to test related to security fix in previous commit. 2008-01-05 23:20:25 +00:00
James Taylor 3c0fc77b1d - Converted history to use mako template 
- No more duplicated code between ajax (dataset_code) and non-ajax history
- Fixed a security hole
 2008-01-05 23:16:31 +00:00
James Taylor 2da9ec3b52 Use the same HTTP server for the functional tests that is used for the 
application.
 2008-01-05 19:54:49 +00:00
James Taylor 7853874bd8 Paste upgrade! Too many problems with 1.0 to keep stalling (e.g. upload bugs). 
The main worry here is that substantial changes have been made to the
how the HTTP server / threadpool work so we should run this in test for a
while and hit it with the load tests.

Also, now using WebError for the interactive exception debugging, it has many
more features including much better formatting of errors in Mako templates.

Added some new eggs that Paste/WebError depend on: wsgiref, WebOb, and Tempita.
 2008-01-05 19:40:17 +00:00
Daniel Blankenberg d0cd1e506d Better handling of creation of a new history. When a user was logged in and created a new history, the center pane was being filled with the new empty history, and the actual history pane was not being refreshed. This is fixed. 2008-01-03 19:16:25 +00:00
Greg Von Kuster 05df900b3d Metadata will now be set on all output datasets when getting encode data. 2008-01-03 14:12:07 +00:00
Greg Von Kuster 637c9f02c4 Fixes for random intervals tool. 2008-01-02 21:40:59 +00:00
Greg Von Kuster be91b8eed0 Better error handling for gencode_partition tool, also added functional test for the tool. 2008-01-02 14:47:30 +00:00
Ross Lazarus 6c7570a8cb Added additional local configuration destinations for masthead urls - blog, wiki, screencasts, in addition to the brand recently added 
These are potentially useful to keep private software development sites under local control...
 2007-12-28 21:34:24 +00:00
Ross Lazarus 4ed41a9364 remove stoopid print statement in mapping.py fix 2007-12-28 17:36:58 +00:00
Ross Lazarus 1f50ab884b Has anyone actually *tested* mysql as the database backend recently? 
It won't work with the current logic in lib/galaxy/model/mapping.py fixed in this revision

(Note the wierd traceback below - looking in build/bdist.macosx-10.3-fat/egg/sqlalchemy/schema.py on a linux box!?)


[rerla@hg rgalaxy_svn]$ sh run.sh
Architecture appears to be linux-x86_64 UCS4
python path: /home/rerla/rgalaxy_svn/lib:/home/rerla/rgalaxy_svn/eggs/UCS4:/home/rerla/rgalaxy_svn/eggs
python path is: /home/rerla/rgalaxy_svn/scripts, /usr/local/lib/python2.4/site-packages/setuptools-0.6c6-py2.4.egg, /home/rerla/rgalaxy_svn/lib,
/home/rerla/rgalaxy_svn/eggs/UCS4/Cheetah-1.0-py2.4-linux-x86_64.egg, /home/rerla/rgalaxy_svn/eggs/UCS4/bx_python-0.5.0_dev-py2.4-linux-x86_64.egg,
/home/rerla/rgalaxy_svn/eggs/UCS4/pysqlite-2.3.5_3.4.2_static-py2.4-linux-x86_64.egg,
/home/rerla/rgalaxy_svn/eggs/UCS4/psycopg2-2.0.6_8.2.4_static-py2.4-linux-x86_64.egg, /home/rerla/rgalaxy_svn/eggs/UCS4,
/home/rerla/rgalaxy_svn/eggs/PasteScript-1.0-py2.4.egg, /home/rerla/rgalaxy_svn/eggs/PasteDeploy-1.0-py2.4.egg,
/home/rerla/rgalaxy_svn/eggs/Paste-1.0-py2.4.egg, /home/rerla/rgalaxy_svn/eggs/Routes-1.6.3-py2.4.egg,
/home/rerla/rgalaxy_svn/eggs/flup-0.5.dev_r2311-py2.4.egg, /home/rerla/rgalaxy_svn/eggs/docutils-0.4-py2.4.egg,
/home/rerla/rgalaxy_svn/eggs/elementtree-1.2.6_20050316-py2.4.egg, /home/rerla/rgalaxy_svn/eggs/WebHelpers-0.2-py2.4.egg,
/home/rerla/rgalaxy_svn/eggs/simplejson-1.4-py2.4.egg, /home/rerla/rgalaxy_svn/eggs/Mako-0.1.8-py2.4.egg, /home/rerla/rgalaxy_svn/eggs/Beaker-0.5-py2.4.egg,
/home/rerla/rgalaxy_svn/eggs/MyghtyUtils-0.52-py2.4.egg, /home/rerla/rgalaxy_svn/eggs/SQLAlchemy-0.3.11-py2.4.egg, /home/rerla/rgalaxy_svn/eggs,
/usr/local/lib/python24.zip, /usr/local/lib/python2.4, /usr/local/lib/python2.4/plat-linux2, /usr/local/lib/python2.4/lib-tk,
/usr/local/lib/python2.4/lib-dynload, /usr/local/lib/python2.4/site-packages, /usr/local/lib/python2.4/site-packages/Numeric,
/usr/local/lib/python2.4/site-packages/PIL
Traceback (most recent call last):
  File "./scripts/paster.py", line 7, in ?
    command.run()
  File "/home/rerla/rgalaxy_svn/eggs/PasteScript-1.0-py2.4.egg/paste/script/command.py", line 76, in run
  File "/home/rerla/rgalaxy_svn/eggs/PasteScript-1.0-py2.4.egg/paste/script/command.py", line 115, in invoke
  File "/home/rerla/rgalaxy_svn/eggs/PasteScript-1.0-py2.4.egg/paste/script/command.py", line 210, in run
  File "/home/rerla/rgalaxy_svn/eggs/PasteScript-1.0-py2.4.egg/paste/script/serve.py", line 184, in command
  File "/home/rerla/rgalaxy_svn/eggs/PasteScript-1.0-py2.4.egg/paste/script/serve.py", line 204, in loadapp
  File "/home/rerla/rgalaxy_svn/eggs/PasteDeploy-1.0-py2.4.egg/paste/deploy/loadwsgi.py", line 193, in loadapp
  File "/home/rerla/rgalaxy_svn/eggs/PasteDeploy-1.0-py2.4.egg/paste/deploy/loadwsgi.py", line 214, in loadobj
  File "/home/rerla/rgalaxy_svn/eggs/PasteDeploy-1.0-py2.4.egg/paste/deploy/loadwsgi.py", line 596, in create
  File "/home/rerla/rgalaxy_svn/eggs/PasteDeploy-1.0-py2.4.egg/paste/deploy/loadwsgi.py", line 99, in invoke
  File "/home/rerla/rgalaxy_svn/eggs/PasteDeploy-1.0-py2.4.egg/paste/deploy/util/fixtypeerror.py", line 57, in fix_call
  File "/home/rerla/rgalaxy_svn/lib/galaxy/web/buildapp.py", line 56, in app_factory
    app = UniverseApplication( global_conf = global_conf, **kwargs )
  File "/home/rerla/rgalaxy_svn/lib/galaxy/app.py", line 23, in __init__
    create_tables = True )
  File "/home/rerla/rgalaxy_svn/lib/galaxy/model/mapping.py", line 297, in init
    metadata.create_all()
  File "build/bdist.macosx-10.3-fat/egg/sqlalchemy/schema.py", line 1238, in create_all
  File "build/bdist.macosx-10.3-fat/egg/sqlalchemy/schema.py", line 1274, in _get_engine
sqlalchemy.exceptions.InvalidRequestError: This SchemaItem is not connected to any Engine or Connection.
 2007-12-28 16:18:05 +00:00
Greg Von Kuster 75b84e0e4d Eliminated Dataset.state.FAKE (requires db update), replacing it with Dataset.state.OK since fake datasets are removed, causing problems for workflow. 
Database update:
update dataset set state = 'ok' where state = 'fake'
 2007-12-21 19:31:58 +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
Greg Von Kuster 59416716eb Deleted a huge emboss test data file that is not needed. Added binary, zipped and gzipped test data files. 2007-12-20 17:43:05 +00:00
Greg Von Kuster c9b5c52cc4 Fix for get_flanks when negative value is entered for length. 2007-12-20 15:57:23 +00:00
Greg Von Kuster 73507a1aa3 Fix for reading gzipped data from UCSC larger than 1 Mb in size. 2007-12-20 14:47:11 +00:00
James Taylor 2adf669014 Improving some docs / comments in JobQueue 2007-12-19 01:59:36 +00:00
James Taylor 789fdd04d6 Workflow controller (lost when reorganizing I guess). 2007-12-18 23:25:31 +00:00
Greg Von Kuster b5a3fa02b4 Oops, forgot about workflow - reverting 2155. 2007-12-18 16:47:27 +00:00
Greg Von Kuster e54be223b2 Better way to skip invalid comment lines in filtering tool. Better numerical value checks in interval.py. 2007-12-18 14:52:04 +00:00
Greg Von Kuster 64bf669fe6 DataToolParameter should no longer list empty datasets as inputs. 2007-12-18 14:41:04 +00:00
Chinmay Rao e59df6cff4 Config files reflecting updates of EMBOSS tools to v5.0 2007-12-17 17:01:23 +00:00
Chinmay Rao 33a68b234d Adding a file required for functional tests in EMBOSS v5.0 (tool: coderet) and deleting a large test output file mistakenly added. 2007-12-17 15:25:49 +00:00
Chinmay Rao 7a366bcec4 Committing EMBOSS v5.0 tools tcode textsearch tmap twofeat vectorstrip wordmatch with associated functional test files 2007-12-17 14:38:16 +00:00
Chinmay Rao f955d77ec3 Adding EMBOSS v5.0 tools seqret showfeat shuffleseq sigcleave sixpack skipseq supermatcher syco 2007-12-17 14:35:58 +00:00
Chinmay Rao 1843e0034c Adding EMBOSS v5.0 newcpgreport noreturn patmatdb pepinfo pepnet pepwheel pepwindow pepwindowall plotcon pepcoil pepstats plotorf polydot noreturn octanol oddcomp 2007-12-17 14:26:48 +00:00
Chinmay Rao 9cbcae2402 Committing EMBOSS v5.0 tools marscan maskfeat maskseq matcher megamerger merger and associated test files. 2007-12-17 14:16:37 +00:00
Chinmay Rao 3b4bfb49c0 Adding EMBOSS tools version 5.0 for helixturnhelix, hmoment, iep infoseq lindna and associated test files 2007-12-17 14:10:03 +00:00
Chinmay Rao 87ce8bd4b4 Committing EMBOSS v5 tools: epestfind, est2genome extractseq freak fuzzpro garnier geecee 2007-12-17 14:02:48 +00:00
Chinmay Rao d009d08342 Adding EMBOSS v5 tools coderet cpgplot diffseq digest dotmatcher dotpath dottup dreg and associated wrapper files 2007-12-17 13:58:30 +00:00
Greg Von Kuster 737bdf23f9 Enhanced upload to handle certain binary and zip files. Cleaned up the upload config. Added 4 new data types: ab1, scf, binseq.zip and txtseq.zip. Added Regional Variation section to tool_conf.xml.main. 2007-12-14 21:07:11 +00:00
Anton Nekrutenko f763e89947 some more corrections 2007-12-14 17:19:41 +00:00
Anton Nekrutenko 5eb23e091c Fixed welcome page styles. Unseq genome for Dec 2007-12-14 17:17:16 +00:00
Greg Von Kuster d83c0f13f9 Bug fix in history.tmpl that eliminates an infinite loop under certain "corner-case" conditions. 2007-12-14 15:05:15 +00:00
Greg Von Kuster 58afe0f9ce Cleaned up error handling, added exception handling in ucsc_tablebrowser.py 2007-12-13 15:01:45 +00:00
Chinmay Rao c2c4cf84b4 EMBOSS Version 5 for primersearch revseq seqmatchall sirna splitter tranalign transeq 2007-12-12 22:56:38 +00:00
Chinmay Rao 4421fce049 Upgrading EMBOSS tools to version 5.0 - trimest trimseq wobble union water wordcount prettyseq pasteseq 2007-12-12 22:27:21 +00:00
Greg Von Kuster a6cb37aa79 A fix for the UCSCOutWrapper class resulting in a better exception handler for wiggle_to_simple. 2007-12-12 20:01:26 +00:00
Greg Von Kuster 7718b28839 Better error condition handling for some tools. I've made these changes because anything printed to stderr now results in the tool state being "error" and tools with this state are no longer allowed as input datasets for tools. 2007-12-12 19:30:26 +00:00
Greg Von Kuster 02ef201032 Added exception handling to wiggle_to_simple. 2007-12-12 18:15:22 +00:00
Chinmay Rao 19c4601e90 Adding version 5.0 of EMBOSS tools dan degapseq descseq codcmp and palindrome 2007-12-12 16:38:36 +00:00
Chinmay Rao 4d6a115f74 Upgrading EMBOSS tools newseq notseq nthseq to version 5.0 2007-12-11 23:25:49 +00:00
Greg Von Kuster 4fda68c476 Bug fix in histogram tool. 2007-12-11 21:41:31 +00:00
Chinmay Rao 5f4ea17fd8 EMBOSS tools upgrade to version 5.0 - msbar, needle and newcpgseek 2007-12-11 21:17:10 +00:00
Chinmay Rao 73e52be7a0 Version 5.0 for EMBOSS tools fuzztran, getorf and isochore 2007-12-11 21:01:52 +00:00
Greg Von Kuster 523323ccd5 Bug fix in Job.finish(), metadata from input datasets should now be properly propogated to output datasets. 2007-12-11 19:31:06 +00:00
James Taylor 4b88be5e25 1) Modified index page so progressive loading works better for slower 
connections

2) Added a script for packing the javascripts, everything is now repacked
   with yui-compressor (the packed versions are slightly large, but they
   gzip better resulting in an overall reduction).
 2007-12-11 19:30:03 +00:00
Greg Von Kuster d61ae1181e Bug fix in biomart - metadata will now be correctly set for biomart data. 2007-12-11 18:40:30 +00:00
Greg Von Kuster 4eeecaea63 Corrected unsupported 'text' datatype extensions to be the supported 'txt' extension. 2007-12-11 18:38:28 +00:00
Chinmay Rao 54aa1bf33e Upgrading EMBOSS tools equicktandem, etandem and fuzznuc to version 5.0 2007-12-11 17:17:49 +00:00