Nate Coraor dfdbef9d36 Reintroduce roles. Unfinished stuff: setting default user and history ...

permissions, user-side permissions settings on datasets, viewing
associated datasets under the role page in the admin controler (is this
even necessary?), filtering out roles by type.  I haven't addressed
tests, so the security-related functional tests will fail.  I haven't
looked at history sharing yet either.  Cleanup to remove unused methods
is needed in the admin controller.  And the admin templates are a
bit messy.

2008-10-09 17:05:57 -04:00

..

access_libraries.xml

Spiffy new library browser interface. Also, dim datasets in your

2008-09-10 10:10:13 -04:00

bed_convert.xml

Moving james-wsgi branch to new trunk.

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

biomart_test.xml

Use only 1 underlying executable ( data_source.py ) for data source tools. A new tag set is added to the data source tool configs to handle tranlsation of request param names sent by remote apps ( something like <param_trans galaxy_name="dbkey" remote_name="GENOME" missing="?" /> ).

2008-10-07 15:21:46 -04:00

biomart.xml

Use only 1 underlying executable ( data_source.py ) for data source tools. A new tag set is added to the data source tool configs to handle tranlsation of request param names sent by remote apps ( something like <param_trans galaxy_name="dbkey" remote_name="GENOME" missing="?" /> ).

2008-10-07 15:21:46 -04:00

data_source.py

Use only 1 underlying executable ( data_source.py ) for data source tools. A new tag set is added to the data source tool configs to handle tranlsation of request param names sent by remote apps ( something like <param_trans galaxy_name="dbkey" remote_name="GENOME" missing="?" /> ).

2008-10-07 15:21:46 -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

Moving james-wsgi branch to new trunk.

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

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

encode_import_all_latest_datasets.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

encode_import_chromatin_and_chromosomes.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

encode_import_code.py

Reintroduce roles. Unfinished stuff: setting default user and history

2008-10-09 17:05:57 -04:00

encode_import_gencode.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

encode_import_genes_and_transcripts.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

encode_import_multi-species_sequence_analysis.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

encode_import_transcription_regulation.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

encode_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

epigraph_import.xml

Use only 1 underlying executable ( data_source.py ) for data source tools. A new tag set is added to the data source tool configs to handle tranlsation of request param names sent by remote apps ( something like <param_trans galaxy_name="dbkey" remote_name="GENOME" missing="?" /> ).

2008-10-07 15:21:46 -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.xml

Use only 1 underlying executable ( data_source.py ) for data source tools. A new tag set is added to the data source tool configs to handle tranlsation of request param names sent by remote apps ( something like <param_trans galaxy_name="dbkey" remote_name="GENOME" missing="?" /> ).

2008-10-07 15:21:46 -04:00

gbrowse_datasource.py

Revert 2715.

2008-06-04 13:02:15 +00:00

gbrowse_elegans.xml

Change C Elegans server URL to wormbase using GBrowse version 1.69.

2008-07-24 13:59:23 -04:00

gbrowse_filter_code.py

Fix for sniffing datatypes, sniff order is now retrieved from app.datatypes_registry rather than the default sniff_order list in the Registry class.

2008-05-28 21:20:15 +00:00

genbank.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

genbank.xml

Moving james-wsgi branch to new trunk.

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

hbvar_filter.py

Revert 2715.

2008-06-04 13:02:15 +00:00

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

Reintroduce roles. Unfinished stuff: setting default user and history

2008-10-09 17:05:57 -04:00

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

Added file_size column to dataset table, requires db schema alteration:

2008-01-08 16:19:25 +00:00

ucsc_proxy.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

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

Use only 1 underlying executable ( data_source.py ) for data source tools. A new tag set is added to the data source tool configs to handle tranlsation of request param names sent by remote apps ( something like <param_trans galaxy_name="dbkey" remote_name="GENOME" missing="?" /> ).

2008-10-07 15:21:46 -04:00

ucsc_tablebrowser_test.xml

Use only 1 underlying executable ( data_source.py ) for data source tools. A new tag set is added to the data source tool configs to handle tranlsation of request param names sent by remote apps ( something like <param_trans galaxy_name="dbkey" remote_name="GENOME" missing="?" /> ).

2008-10-07 15:21:46 -04:00

ucsc_tablebrowser.xml

Use only 1 underlying executable ( data_source.py ) for data source tools. A new tag set is added to the data source tool configs to handle tranlsation of request param names sent by remote apps ( something like <param_trans galaxy_name="dbkey" remote_name="GENOME" missing="?" /> ).

2008-10-07 15:21:46 -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.xml

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