Daniel Blankenberg c0d797e00d Allow the uploading of composite datatypes. A new grouping parameter, UploadDataset, is used to contain and process the file_data/url_paste/space_to_tab used to upload a file - multiple sets are displayed when uploading a composite datatype (similar to a repeat). Composite files can now be declared to the datatypes registry (required for proper uploading), but they are stored in the same manner as before (the extra_files_path) and should be backwards compatible. When uploading a composite datatype, only one dataset can be uploaded at a time. The ability to upload multiple datasets (url_paste (contents or urls) + file_data) for non-composite datatypes remains unchanged. ...

A more structured way of storing these files (rather than dumping in a directory) is worth considering.

2009-06-08 12:49:26 -04:00

..

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

Fixes for formatting end of line chars in html when displaying dataset.info. Also change the biomart tool version.

2009-01-22 08:50:52 -05:00

biomart.xml

Fixes for formatting end of line chars in html when displaying dataset.info. Also change the biomart tool version.

2009-01-22 08:50:52 -05:00

data_source.py

Add a defaulttimeout setting of 10 minutes to the urlopen() call for requests to remote data sources.

2009-05-28 11:10:44 -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

encode_import_all_latest_datasets.xml

Small typo in one of the encode import tools.

2008-10-31 14:52:41 -04:00

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

merging from central

2008-12-02 10:55:17 -05:00

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_test.xml

Add new EpiGRAPH tools that point to EpiGRAPH production server.

2008-10-28 11:27:42 -04:00

epigraph_import.xml

Add new EpiGRAPH tools that point to EpiGRAPH production server.

2008-10-28 11:27:42 -04:00

eupathdb.xml

Add EuPathDb data source tool config.

2009-06-01 10:27:04 -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

Add new tool config for flymine production server.

2009-01-13 10:55:08 -05:00

flymine.xml

Add new tool config for flymine production server.

2009-01-13 10:55:08 -05:00

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

gramene_mart.xml

Add tool config for GrameneMart data source.

2009-05-27 14:19:59 -04:00

hbvar_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

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

merging from central

2008-12-02 10:55:17 -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

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

Fixes for Biomart and UCSC to better ensure the data type is correctly set. A data type of "tabular" is now the default, and data will be sniffed if this is the data type.

2009-01-21 17:03:39 -05:00

ucsc_tablebrowser_test.xml

Fixes for Biomart and UCSC to better ensure the data type is correctly set. A data type of "tabular" is now the default, and data will be sniffed if this is the data type.

2009-01-21 17:03:39 -05:00

ucsc_tablebrowser.xml

More library work - requires database schema update:

2009-03-09 17:02:21 -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

Allow the uploading of composite datatypes. A new grouping parameter, UploadDataset, is used to contain and process the file_data/url_paste/space_to_tab used to upload a file - multiple sets are displayed when uploading a composite datatype (similar to a repeat). Composite files can now be declared to the datatypes registry (required for proper uploading), but they are stored in the same manner as before (the extra_files_path) and should be backwards compatible. When uploading a composite datatype, only one dataset can be uploaded at a time. The ability to upload multiple datasets (url_paste (contents or urls) + file_data) for non-composite datatypes remains unchanged.

2009-06-08 12:49:26 -04:00

wormbase_test.xml

Fixes for i18n support - all charsets set to utf-8, now able to paste multi-byte chars in upload form, templates use utf-8 as output_charset, other miscellaneous fixes.

2009-03-20 02:49:30 -04:00

wormbase.xml

i18n fix: dataset.info should not be translated since it will generally not have an entry in the catalog. Wormbase fixes: URL to main site corrected, and all supported builds added to gbrowse_build_sites.txt.

2009-03-26 09:34:05 -04:00