Greg Von Kuster dc8e7c1039 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

..

access_libraries.xml

Fix for rendering tools / workflows in target frames, also elimnate the Workflow link in the tool panel as we're now using the menu bar.

2009-02-23 13:52:34 -05:00

bed_convert.xml

Moving james-wsgi branch to new trunk.

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

biomart_test.xml

Enhance data_source.py to take advantage of the content length when known. If content length provided by external application is

2009-08-03 12:02:54 -04:00

biomart.xml

Enhance data_source.py to take advantage of the content length when known. If content length provided by external application is

2009-08-03 12:02:54 -04:00

data_source.py

Enhance data_source.py to take advantage of the content length when known. If content length provided by external application is

2009-08-03 12:02:54 -04:00

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 data_source.py to take advantage of the content length when known. If content length provided by external application is

2009-08-03 12:02:54 -04:00

epigraph_import.xml

Enhance data_source.py to take advantage of the content length when known. If content length provided by external application is

2009-08-03 12:02:54 -04:00

eupathdb.xml

Enhance data_source.py to take advantage of the content length when known. If content length provided by external application is

2009-08-03 12:02:54 -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

flymine_test.xml

Enhance data_source.py to take advantage of the content length when known. If content length provided by external application is

2009-08-03 12:02:54 -04:00

flymine.xml

Enhance data_source.py to take advantage of the content length when known. If content length provided by external application is

2009-08-03 12:02:54 -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

gramene_mart.xml

Enhance data_source.py to take advantage of the content length when known. If content length provided by external application is

2009-08-03 12:02:54 -04:00

hbvar_filter.py

Fix most of the db flushes to be compatibel with sqlalchemy 05. Add the _monkeypatch_query_method() back into assignmapper due to a single object.get() method in the MetadataCollection class since Metadata has no current hook into mapping.context ( the sqlalchemy session ). There a 4 flushes in metadata,py and 20 flushes in model.__init__.py that still use the _monkeypatch_session_method in assignmapper due to the same issue, but all other flushes are fixed.

2009-11-11 15:59:41 -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

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

Rewrite of dynamic options for select lists. There are no more 'special cases' and new filters are much easier to incorporate, as neeeded.

2008-05-29 17:38:46 +00:00

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

Enhance data_source.py to take advantage of the content length when known. If content length provided by external application is

2009-08-03 12:02:54 -04:00

ucsc_tablebrowser_test.xml

Enhance data_source.py to take advantage of the content length when known. If content length provided by external application is

2009-08-03 12:02:54 -04:00

ucsc_tablebrowser.xml

Enhance data_source.py to take advantage of the content length when known. If content length provided by external application is

2009-08-03 12:02:54 -04:00

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

Added sff datatype

2009-11-11 17:55:08 -05:00

upload.xml

Make Galaxy attempt to honor the user's umask and primary group (output datasets can have the wrong primary group if the primary group differs on the cluster). Also fixed a composite datatype files_path bug in the upload tool.

2009-10-23 14:33:23 -04:00

wormbase_test.xml

Enhance data_source.py to take advantage of the content length when known. If content length provided by external application is

2009-08-03 12:02:54 -04:00

wormbase.xml

Enhance data_source.py to take advantage of the content length when known. If content length provided by external application is

2009-08-03 12:02:54 -04:00