1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/b883d2f75382/
Changeset: b883d2f75382
User: jmchilton
Date: 2014-01-24 05:21:27
Summary: Get rid of unused is_convertable nested function.
Affected #: 1 file
diff -r f443913ea49987da0bb651621743fefd03328cea -r b883d2f753824cf615fd4b3acb04d815f919bba9 lib/galaxy/tools/parameters/basic.py
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -1693,11 +1693,6 @@
pass # no valid options
def dataset_collector( datasets ):
- def is_convertable( dataset ):
- target_ext, converted_dataset = dataset.find_conversion_destination( self.formats )
- if target_ext is not None:
- return True
- return False
for i, data in enumerate( datasets ):
if data.visible and not data.deleted and data.state not in [data.states.ERROR, data.states.DISCARDED]:
is_valid = False
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/117fef56513f/
Changeset: 117fef56513f
User: jeremy goecks
Date: 2014-01-23 21:29:14
Summary: Update tool template's chrom_info to correctly point to len file for custom builds defined by len files. This was broken was len files were moved from the len_file directory to HDAs.
Affected #: 1 file
diff -r 7fd2f3f098840a5a1b9d7041330100c4f2af70df -r 117fef56513fc563dd231516196cfd601c1635e2 lib/galaxy/tools/actions/__init__.py
--- a/lib/galaxy/tools/actions/__init__.py
+++ b/lib/galaxy/tools/actions/__init__.py
@@ -213,7 +213,7 @@
db_datasets[ "chromInfo" ] = db_dataset
incoming[ "chromInfo" ] = db_dataset.file_name
else:
- # -- Get chrom_info from either a custom or built-in build. --
+ # -- Get chrom_info (len file) from either a custom or built-in build. --
chrom_info = None
if trans.user and ( 'dbkeys' in trans.user.preferences ) and ( input_dbkey in from_json_string( trans.user.preferences[ 'dbkeys' ] ) ):
@@ -226,9 +226,13 @@
# condition below to avoid getting chrom_info when running the
# fasta-to-len converter.
if 'fasta' in custom_build_dict and tool.id != 'CONVERTER_fasta_to_len':
+ # Build is defined by fasta; get len file, which is obtained from converting fasta.
build_fasta_dataset = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( custom_build_dict[ 'fasta' ] )
chrom_info = build_fasta_dataset.get_converted_dataset( trans, 'len' ).file_name
-
+ elif 'len' in custom_build_dict:
+ # Build is defined by len file, so use it.
+ chrom_info = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( custom_build_dict[ 'len' ] ).file_name
+
if not chrom_info:
# Default to built-in build.
chrom_info = os.path.join( trans.app.config.len_file_path, "%s.len" % input_dbkey )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/658d07c0f844/
Changeset: 658d07c0f844
User: martenson
Date: 2014-01-23 16:05:09
Summary: removed bug in libraries API (prepending ‘F’ to library id, should be only for folders)
Affected #: 1 file
diff -r 7e9ef97e04496434313430ee71aff7033c50c390 -r 658d07c0f8442657229062cfdc5f3fe6b6bd00e8 lib/galaxy/webapps/galaxy/api/libraries.py
--- a/lib/galaxy/webapps/galaxy/api/libraries.py
+++ b/lib/galaxy/webapps/galaxy/api/libraries.py
@@ -50,7 +50,7 @@
for library in query:
item = library.to_dict( view='element' )
item['url'] = url_for( route, id=trans.security.encode_id( library.id ) )
- item['id'] = 'F' + trans.security.encode_id( item['id'] )
+ item['id'] = trans.security.encode_id( item['id'] )
item['root_folder_id'] = 'F' + trans.security.encode_id( item['root_folder_id'] )
libraries.append( item )
return libraries
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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