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376 Commits
Author SHA1 Message Date
Greg Von Kuster e06602f808 Make minimum file size smaller. 2008-01-12 01:09:28 +00:00
Greg Von Kuster df085f9c20 Kind of rummy with my last 2 commits - one more try... 2008-01-12 00:58:51 +00:00
Greg Von Kuster 498e616209 Another (really the same) bug in system controller. 2008-01-11 22:01:59 +00:00
Greg Von Kuster 262f254b7f System controller bug fix. 2008-01-11 21:35:34 +00:00
Greg Von Kuster 01378424b4 New reports app server and 1st report showing disk usage for dataset file system - still need to mess with styles a bit. 
Also fixed update_dataset_size script and delete deprecatd random_intervals code file.
 2008-01-11 21:24:21 +00:00
James Taylor fe1d1d895c Many workflow fixes, and a preliminary interface for running workflow (not 
functional! still working on security).
 2008-01-09 02:13:32 +00:00
James Taylor e6f8954d52 Implement value_to_display_text for select params, tries to translate values 
back to labels (still not great).
 2008-01-09 02:12:24 +00:00
James Taylor 518e544169 Metadata validator will now not fail if the dataset is "None" 2008-01-09 02:10:50 +00:00
James Taylor da8aee8983 Make engine_options argument optional (for unit tests) 2008-01-09 01:06:51 +00:00
James Taylor 067abf55dc Allow specifying SQLAlchemy engine options in universe_wsgi.ini 
For example you can do:

database_connection = postgres:///galaxy_test
database_engine_option_echo = true
database_engine_option_echo_pool = true
database_engine_option_pool_size = 30

To increase the pool size to 30 and turn on SQL and Pool debug echoing
 2008-01-09 00:42:27 +00:00
Greg Von Kuster 9bd4ab86a3 Set file_size to 0 when purging dataset. 2008-01-08 23:26:08 +00:00
Greg Von Kuster 6d80665988 Added file_size column to dataset table, requires db schema alteration: 
alter table dataset add column file_size numeric(15,0)
Also added new script update_dataset_size.py
 2008-01-08 16:19:25 +00:00
Greg Von Kuster 69505c9cb5 Fixed indentation error in pbs.py 2008-01-08 15:14:35 +00:00
Greg Von Kuster 31d1a87141 Better error handling in interval_to_bd_converter, a couple of other small tool fixes. 2008-01-07 18:49:12 +00:00
James Taylor 10a413936c Action needed for async history updates. 2008-01-07 06:58:18 +00:00
James Taylor 2aa15eb876 More fixes. This would be much easier is the tests actually scraped the 
HTML rather than needing separate XML templates.
 2008-01-05 23:41:59 +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 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
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
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
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
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 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
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
Greg Von Kuster f7f7aeab26 Fixed a security flaw in upload.py. Added a unit test for get_file_peek() to data.py, along with outher cleanup. Corrected gbrowse display links in interval.py. Bug fixes in root.py where google bots were throwing exceptions. 2007-12-10 21:00:21 +00:00
Greg Von Kuster bbba08b89d Gzipped files from UCSC will now be decompressed on the fly. Also fixed a bug in biomart_filter. 2007-12-10 16:13:05 +00:00
Greg Von Kuster 0160211343 Fix for 1 line interval files that do not include a commented header. Added default values for chrom, start, end for interval format and enhanced set_meta() so that auto-detect button on edit form will work for interval files. 2007-12-04 16:32:14 +00:00
Greg Von Kuster ab1d867915 More dynamic options cleanup. Eliminated the "tool_type" attribute, among other cleanup chores. 2007-11-30 20:08:21 +00:00
Greg Von Kuster 6c4df387b7 Fixed bug when setting peek on a binary dataset. Also fixed up code in 2 functions in root.py. 2007-11-29 21:20:29 +00:00
Greg Von Kuster 79745f4012 Modified all tools to use the new <options> tag for dynamic select lists. Completely eliminated the <select_options> tag approach. With the exception of find_clusters_mysql, the old dynamic_options approach is not being used by any tool, although dynamic_options is still supported in parameters.py. 2007-11-29 17:04:42 +00:00
James Taylor 2a6cb86131 Consolidating workflow templates / controllers 2007-11-28 20:28:46 +00:00
Daniel Blankenberg b5de2e878e Enhance validation of dynamic options when no data/info is available. 2007-11-28 17:46:04 +00:00
Greg Von Kuster 300d66fb11 Modified tools using the <select_options> tag approach for dynamic options to use the new <select> tag approach. I modified the microbial import tool to use the older <select_options> approach last week and will modify it to use the new <select> approach next week. A few tools still use the oldest dynamic_options attribute approach, but modifying them to use the new <select> tag will be trivial. I'll do this when I return. 2007-11-21 18:48:37 +00:00
Greg Von Kuster 71d16671bc First pass at final phase of cleaning up approach to dynamic select lists. Added a functional test to phastOdds tool. The following tools now use this latest approach to dynamic optioons: 
axt_to_fasta, phastOdds, axt_to_lav, random_intervals, extractAxt_wrapper, axt_to_concat_fasta, aggregate_binned_scores.
 2007-11-16 20:08:31 +00:00
Greg Von Kuster e97522b3a5 Enhanced select list displayed as radio buttons to handle refresh_on_change if we need it in the future. 2007-11-16 20:04:06 +00:00
Daniel Blankenberg 41a885a875 Add validation of metadata before tool run. 2007-11-14 20:50:33 +00:00
Greg Von Kuster 6e8ff8c545 Anything printed to stderr will once again result in a job error. 2007-11-14 14:12:42 +00:00
Greg Von Kuster f638adb5d3 Added an "Auto-dectect" button to the Edit (metadata) Attributes form. 
Cleaned up some bugs in Bed and Interval set_meta associated functions.
set_meta() will no longer be called prior to the edit form being displayed since doing this displayed attribute values that were not from the database (misleading the user).
 2007-11-12 22:20:06 +00:00
Nate Coraor 2d1a7f08f4 a tab accidentally snuck in. 2007-11-09 18:13:08 +00:00
Nate Coraor 3ab97ed098 Added the ability to "brand" Galaxy in the masthead from the ini file. 2007-11-09 16:52:02 +00:00