Greg Von Kuster 17c5b27cdc Re-engineer the datatypes registry so that it is initialized once when the Galaxy server is started, but data types can continue to be loaded throughout the Galaxy server's session (hopefully this doesn't break anything). ...

Add support for a single "import_module" to be passed to the new load_datatypes() method in the datatypes registry.  This provides the ability to load a single class module from an installed tool shed repository along with a datatypes_conf.xml file included in the installed repository and pass them to the new load_datatypes() method.  In the future, multiple imported modules may be allowed.  The datatypes_conf.xml file included in the repository must conform to a slightly different definition than the same named file that comes with the distribution.  This new definition will be documented in the Galaxy tool shed wiki.

We now have the ability to load new data types into the Galaxy server from an installed tool shed repository without restarting the Galaxy server.

2011-11-23 16:16:15 -05:00

..

access_libraries.xml

Several data library improvements:

2011-01-31 16:41:03 -05:00

bed_convert.xml

Moving james-wsgi branch to new trunk.

2006-11-15 16:28:21 +00:00

biomart_test.xml

Enhance tool parameter sanitization. Sanitization rules can now be defined on a per input parameter basis. Resolves ticket #38 and #142.

2009-12-07 10:19:41 -05:00

biomart.xml

Enhance tool parameter sanitization. Sanitization rules can now be defined on a per input parameter basis. Resolves ticket #38 and #142.

2009-12-07 10:19:41 -05:00

bx_browser.xml

Added from __future__ import division to the Filter tool and increased the version, and fixed the URL in the new bx_browser tool config.

2010-01-14 11:26:08 -05:00

cbi_rice_mart.xml

Add the CBI Rice Mart data source tool to the distribution.

2010-06-04 15:49:58 -04:00

data_source.py

Re-engineer the datatypes registry so that it is initialized once when the Galaxy server is started, but data types can continue to be loaded throughout the Galaxy server's session (hopefully this doesn't break anything).

2011-11-23 16:16:15 -05:00

echo.py

Eliminated all Python2.4 references, added necessary assert statements to ensure minimum version of Python 2.4.

2008-03-28 15:24:50 +00:00

echo.xml

Change History.copy() back to use datasets rather than active_datasets. Add checks in set_peek() to properly set peek on purged datasets. Fixes sharing a history that contains purged datasets.

2009-01-15 10:49:01 -05:00

encode_db.xml

Change database schema to separate Dataset and HistoryDatasetAssociation. This is a significant change, be sure to follow the migration notes exactly.

2008-07-09 17:41:08 +00:00

epigraph_import_test.xml

Enhance tool parameter sanitization. Sanitization rules can now be defined on a per input parameter basis. Resolves ticket #38 and #142.

2009-12-07 10:19:41 -05:00

epigraph_import.xml

Enhance tool parameter sanitization. Sanitization rules can now be defined on a per input parameter basis. Resolves ticket #38 and #142.

2009-12-07 10:19:41 -05:00

eupathdb.xml

pdate EuPathDB datasource configuration file. Contributed by Mark Heiges.

2011-08-22 14:03:57 -04:00

fetch.py

Eliminated all Python2.4 references, added necessary assert statements to ensure minimum version of Python 2.4.

2008-03-28 15:24:50 +00:00

fly_modencode.xml

Some reworking of data_source tools and the standard data_source.py script. Remove hard-coded special-case handling of UCSC Table Browser and GBrowse datasource tools; functionality remains, but is now a part of the individual tools' XML configuration files. Auto-detect is now available by providing data_type=auto parameters.

2011-04-21 13:12:10 -04:00

flymine_test.xml

Remove link target from intermine datasource tools.

2011-03-22 20:29:32 -04:00

flymine.xml

Some reworking of data_source tools and the standard data_source.py script. Remove hard-coded special-case handling of UCSC Table Browser and GBrowse datasource tools; functionality remains, but is now a part of the individual tools' XML configuration files. Auto-detect is now available by providing data_type=auto parameters.

2011-04-21 13:12:10 -04:00

genbank.py

Deprecated code corrections for supporting Python 2.6. Many of the Python 2.6 eggs are still throwing DeprecationWarning messages, so some things still won't work. Eggs for 2.6 need to be re-scrambled after corrections are made.

2009-08-14 15:37:31 -04:00

genbank.xml

Moving james-wsgi branch to new trunk.

2006-11-15 16:28:21 +00:00

genomespace_file_browser_dev.xml

Update GenomeSpace import from file browser tool to use new versioned API.

2011-11-18 13:48:06 -05:00

genomespace_file_browser_prod.xml

Updates for GenomeSpace file browser importer.

2011-11-21 17:12:07 -05:00

genomespace_file_browser_test.xml

Updates for GenomeSpace file browser importer.

2011-11-21 17:12:07 -05:00

genomespace_file_browser.py

Update GenomeSpace import from file browser tool to use new versioned API.

2011-11-18 13:48:06 -05:00

gramene_mart.xml

Enhance tool parameter sanitization. Sanitization rules can now be defined on a per input parameter basis. Resolves ticket #38 and #142.

2009-12-07 10:19:41 -05:00

hapmapmart.xml

adding hapmapmart.xml to tools/data_source

2010-11-18 10:30:27 -05:00

hbvar_filter.py

Better approach to altering initial content of output dataset if necessary. The upload tool will now call the data type's groom_output_dataset() method ( a better name than before_setting_metadata since it is not related to metadata ). This will now also run on the cluster.

2009-12-08 11:46:13 -05:00

hbvar.xml

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

import.py

Eliminated all Python2.4 references, added necessary assert statements to ensure minimum version of Python 2.4.

2008-03-28 15:24:50 +00:00

import.xml

Moving james-wsgi branch to new trunk.

2006-11-15 16:28:21 +00:00

metabolicmine.xml

Remove link target from intermine datasource tools.

2011-03-22 20:29:32 -04:00

microbial_import_code.py

Eliminate the _monkeypatch_session_method from assignmapper by cleaning up remaining object flushes. The _monkeypatch_query_method remains due to a single object query in ~/datatypes/metadata.py in the FileParameter.wrap() method. The sqlalchemy session is now also passed into the __init__ methods for both HistoryDatasetAssociation and LibraryDatasetDatasetAssociation when the create_dataset param is True to enable methods in the DatasetInstance class to correctly add the created dataset to the sqlalchemy session and flush it.

2009-11-12 15:25:48 -05:00

microbial_import.py

Eliminated all Python2.4 references, added necessary assert statements to ensure minimum version of Python 2.4.

2008-03-28 15:24:50 +00:00

microbial_import.xml

Update links to reflect Galaxy Wiki moving away from Bitbucket.

2011-07-18 18:10:55 -05:00

modmine.xml

Remove link target from intermine datasource tools.

2011-03-22 20:29:32 -04:00

ratmine.xml

Some reworking of data_source tools and the standard data_source.py script. Remove hard-coded special-case handling of UCSC Table Browser and GBrowse datasource tools; functionality remains, but is now a part of the individual tools' XML configuration files. Auto-detect is now available by providing data_type=auto parameters.

2011-04-21 13:12:10 -04:00

ucsc_archaea.xml

There has to be at least one tool named 'ucsc_proxy' for the proxies to work. They all use the same code with different urls, but they have to submit back to the tool_runner at the end. This closes ticket 121.

2007-05-30 15:47:59 +00:00

ucsc_filter.py

Call set_size() before set_peek() on datasets, changes to set_peek() to not read entire files for some datatypes.

2008-12-02 10:50:54 -05:00

ucsc_proxy.py

Deprecated code corrections for supporting Python 2.6. Many of the Python 2.6 eggs are still throwing DeprecationWarning messages, so some things still won't work. Eggs for 2.6 need to be re-scrambled after corrections are made.

2009-08-14 15:37:31 -04:00

ucsc_proxy.xml

Update UCSC direct connection to use main ucsc site. Add direct test

2007-03-21 19:52:01 +00:00

ucsc_tablebrowser_archaea.xml

Some reworking of data_source tools and the standard data_source.py script. Remove hard-coded special-case handling of UCSC Table Browser and GBrowse datasource tools; functionality remains, but is now a part of the individual tools' XML configuration files. Auto-detect is now available by providing data_type=auto parameters.

2011-04-21 13:12:10 -04:00

ucsc_tablebrowser_test.xml

Some reworking of data_source tools and the standard data_source.py script. Remove hard-coded special-case handling of UCSC Table Browser and GBrowse datasource tools; functionality remains, but is now a part of the individual tools' XML configuration files. Auto-detect is now available by providing data_type=auto parameters.

2011-04-21 13:12:10 -04:00

ucsc_tablebrowser.xml

Backed out changeset 48bbe32beefe which introduced a whole bunch of unintended reversions from a broken hg repository

2011-07-06 09:44:56 +10:00

ucsc_testproxy.xml

Update UCSC direct connection to use main ucsc site. Add direct test

2007-03-21 19:52:01 +00:00

upload.py

Re-engineer the datatypes registry so that it is initialized once when the Galaxy server is started, but data types can continue to be loaded throughout the Galaxy server's session (hopefully this doesn't break anything).

2011-11-23 16:16:15 -05:00

upload.xml

Spacing fix

2011-08-20 02:56:33 -04:00

worm_modencode.xml

Some reworking of data_source tools and the standard data_source.py script. Remove hard-coded special-case handling of UCSC Table Browser and GBrowse datasource tools; functionality remains, but is now a part of the individual tools' XML configuration files. Auto-detect is now available by providing data_type=auto parameters.

2011-04-21 13:12:10 -04:00

wormbase_test.xml

Some reworking of data_source tools and the standard data_source.py script. Remove hard-coded special-case handling of UCSC Table Browser and GBrowse datasource tools; functionality remains, but is now a part of the individual tools' XML configuration files. Auto-detect is now available by providing data_type=auto parameters.

2011-04-21 13:12:10 -04:00

wormbase.xml

Some reworking of data_source tools and the standard data_source.py script. Remove hard-coded special-case handling of UCSC Table Browser and GBrowse datasource tools; functionality remains, but is now a part of the individual tools' XML configuration files. Auto-detect is now available by providing data_type=auto parameters.

2011-04-21 13:12:10 -04:00

yeastmine.xml

Some reworking of data_source tools and the standard data_source.py script. Remove hard-coded special-case handling of UCSC Table Browser and GBrowse datasource tools; functionality remains, but is now a part of the individual tools' XML configuration files. Auto-detect is now available by providing data_type=auto parameters.

2011-04-21 13:12:10 -04:00