1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/459cb941107e/
changeset: r5456:459cb941107e
user: dan
date: 2011-04-25 23:21:21
summary: Bug fix for 5454:2379785017d7
affected #: 1 file (0 bytes)
--- a/lib/galaxy/tools/parameters/dynamic_options.py Mon Apr 25 15:30:21 2011 -0400
+++ b/lib/galaxy/tools/parameters/dynamic_options.py Mon Apr 25 17:21:21 2011 -0400
@@ -332,7 +332,7 @@
value = other_values.get( self.ref_name )
else:
data_ref = other_values.get( self.meta_ref )
- if not isinstance( data.ref, self.dynamic_option.tool_param.tool.app.model.HistoryDatasetAssociation ) and not ( isinstance( data.ref, galaxy.tools.DatasetFilenameWrapper ) ):
+ if not isinstance( data_ref, self.dynamic_option.tool_param.tool.app.model.HistoryDatasetAssociation ) and not ( isinstance( data_ref, galaxy.tools.DatasetFilenameWrapper ) ):
return options #cannot modify options
value = data_ref.metadata.get( self.metadata_key, None )
return [ ( disp_name, optval, selected ) for disp_name, optval, selected in options if not compare_value( optval, value ) ]
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/2379785017d7/
changeset: r5454:2379785017d7
user: dan
date: 2011-04-25 20:41:54
summary: Fix for dynamic options when referencing a DataToolParameter that has already been wrapped.
affected #: 1 file (159 bytes)
--- a/lib/galaxy/tools/parameters/dynamic_options.py Mon Apr 25 11:10:45 2011 -0400
+++ b/lib/galaxy/tools/parameters/dynamic_options.py Mon Apr 25 14:41:54 2011 -0400
@@ -6,6 +6,7 @@
import operator, sys, os, logging
import basic, validation
from galaxy.util import string_as_bool
+import galaxy.tools
log = logging.getLogger(__name__)
@@ -105,7 +106,7 @@
return file_value == dataset_value
assert self.ref_name in other_values or ( trans is not None and trans.workflow_building_mode), "Required dependency '%s' not found in incoming values" % self.ref_name
ref = other_values.get( self.ref_name, None )
- if not isinstance( ref, self.dynamic_option.tool_param.tool.app.model.HistoryDatasetAssociation ):
+ if not isinstance( ref, self.dynamic_option.tool_param.tool.app.model.HistoryDatasetAssociation ) and not ( isinstance( ref, galaxy.tools.DatasetFilenameWrapper ) ):
return [] #not a valid dataset
meta_value = ref.metadata.get( self.key, None )
if meta_value is None: #assert meta_value is not None, "Required metadata value '%s' not found in referenced dataset" % self.key
@@ -331,7 +332,7 @@
value = other_values.get( self.ref_name )
else:
data_ref = other_values.get( self.meta_ref )
- if not isinstance( data_ref, self.dynamic_option.tool_param.tool.app.model.HistoryDatasetAssociation ):
+ if not isinstance( data.ref, self.dynamic_option.tool_param.tool.app.model.HistoryDatasetAssociation ) and not ( isinstance( data.ref, galaxy.tools.DatasetFilenameWrapper ) ):
return options #cannot modify options
value = data_ref.metadata.get( self.metadata_key, None )
return [ ( disp_name, optval, selected ) for disp_name, optval, selected in options if not compare_value( optval, value ) ]
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/74c973f5a473/
changeset: r5453:74c973f5a473
user: kellyv
date: 2011-04-25 17:10:45
summary: Fix circular references between Picard and SRMA entries in data tables sample file
affected #: 1 file (2 bytes)
--- a/tool_data_table_conf.xml.sample Fri Apr 22 19:01:12 2011 -0400
+++ b/tool_data_table_conf.xml.sample Mon Apr 25 11:10:45 2011 -0400
@@ -68,7 +68,7 @@
<!-- Location of Picard dict file and other files --><table name="picard_indexes" comment_char="#"><columns>value, dbkey, name, path</columns>
- <file path="tool-data/srma_index.loc" />
+ <file path="tool-data/picard_index.loc" /></table><!-- Location of SRMA dict file and other files --><table name="srma_indexes" comment_char="#">
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/31570d16b96c/
changeset: r5451:31570d16b96c
user: kanwei
date: 2011-04-22 22:43:43
summary: Update Mako to 0.4.1
affected #: 1 file (0 bytes)
--- a/eggs.ini Fri Apr 22 15:10:04 2011 -0400
+++ b/eggs.ini Fri Apr 22 16:43:43 2011 -0400
@@ -37,7 +37,7 @@
elementtree = 1.2.6_20050316
GeneTrack = 2.0.0_beta_1
lrucache = 0.2
-Mako = 0.2.5
+Mako = 0.4.1
nose = 0.11.1
NoseHTML = 0.4.1
NoseTestDiff = 0.1
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/e736f8d97c3e/
changeset: r5442:e736f8d97c3e
user: richard_burhans
date: 2011-04-21 23:22:27
summary: initial version of Webb's genome diversity tools
affected #: 22 files (97 bytes)
--- a/datatypes_conf.xml.sample Thu Apr 21 13:12:10 2011 -0400
+++ b/datatypes_conf.xml.sample Thu Apr 21 17:22:27 2011 -0400
@@ -122,6 +122,7 @@
<converter file="vcf_to_interval_index_converter.xml" target_datatype="interval_index"/><converter file="vcf_to_summary_tree_converter.xml" target_datatype="summary_tree"/></datatype>
+ <datatype extension="wsf" type="galaxy.datatypes.wsf:SnpFile" display_in_upload="true"/><datatype extension="velvet" type="galaxy.datatypes.assembly:Velvet" display_in_upload="false"/><datatype extension="wig" type="galaxy.datatypes.interval:Wiggle" display_in_upload="true"><converter file="wig_to_bigwig_converter.xml" target_datatype="bigwig"/>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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