1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/b90d953f77fa/
Changeset: b90d953f77fa
User: guerler
Date: 2014-02-20 19:27:57
Summary: Fix default parameter in universe config
Affected #: 1 file
diff -r c36dc4155beb0ae5e117ca33e0ad231535186d6d -r b90d953f77fa633f0c4a46e177118562191bc1b7 universe_wsgi.ini.sample
--- a/universe_wsgi.ini.sample
+++ b/universe_wsgi.ini.sample
@@ -183,7 +183,7 @@
#datatypes_config_file = datatypes_conf.xml
# Disable the 'Auto-detect' option for file uploads
-#datatypes_disable_auto = True
+#datatypes_disable_auto = False
# Visualizations config directory: where to look for individual visualization plugins.
# The path is relative to the Galaxy root dir. To use an absolute path begin the path
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/1480f00e6bdc/
Changeset: 1480f00e6bdc
Branch: stable
User: dan
Date: 2014-02-18 21:09:46
Summary: Fix for server error caused by unicode substitution in url_for.
Affected #: 1 file
diff -r 15e8a74a95215bf2cc775e9848ca4a5ecc7e945f -r 1480f00e6bdcebe043b695fa1daaa0220fc0c086 templates/webapps/galaxy/mobile/history/detail.mako
--- a/templates/webapps/galaxy/mobile/history/detail.mako
+++ b/templates/webapps/galaxy/mobile/history/detail.mako
@@ -12,7 +12,7 @@
if data.state in ['no state','',None]:
data_state = "queued"
else:
- data_state = data.state
+ data_state = str( data.state )
%><li id="historyItemContainer-${data.id}">
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/c36dc4155beb/
Changeset: c36dc4155beb
User: dannon
Date: 2014-02-20 19:10:00
Summary: Add PyYAML 3.10 egg.
Affected #: 1 file
diff -r c7fa535a805f0cc654984fe9344ba70c90238a15 -r c36dc4155beb0ae5e117ca33e0ad231535186d6d eggs.ini
--- a/eggs.ini
+++ b/eggs.ini
@@ -25,6 +25,7 @@
pysam = 0.4.2
pysqlite = 2.5.6
python_lzo = 1.08_2.03_static
+PyYAML = 3.10
threadframe = 0.2
guppy = 0.1.10
SQLAlchemy = 0.7.9
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/baf2a8cc97ed/
Changeset: baf2a8cc97ed
User: dan
Date: 2014-02-20 17:52:52
Summary: Fix for ToolEvaluator with optional Dataset Input selected with multiple inputs.
Affected #: 1 file
diff -r d01fc0370afece3ef77b63a116fd9a1c2105c2e4 -r baf2a8cc97ed720e10b6148254d7dd7478d8e839 lib/galaxy/tools/evaluation.py
--- a/lib/galaxy/tools/evaluation.py
+++ b/lib/galaxy/tools/evaluation.py
@@ -232,10 +232,11 @@
tool=self,
name=name,
)
- real_path = data.file_name
- if real_path in input_dataset_paths:
- dataset_path = input_dataset_paths[ real_path ]
- wrapper_kwds[ 'dataset_path' ] = dataset_path
+ if data:
+ real_path = data.file_name
+ if real_path in input_dataset_paths:
+ dataset_path = input_dataset_paths[ real_path ]
+ wrapper_kwds[ 'dataset_path' ] = dataset_path
param_dict[name] = DatasetFilenameWrapper( data, **wrapper_kwds )
if data:
for child in data.children:
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/32eadec01e3e/
Changeset: 32eadec01e3e
User: dan
Date: 2014-02-20 17:31:07
Summary: Rework logic for setting selection of DataToolParameter. Fixes issue seen with rerun where incorrect options were selected.
Affected #: 1 file
diff -r 01a572fb8b4c463efa1b2091298fad3ec7ea2958 -r 32eadec01e3ebeb076b68938269e22f45fb202bb lib/galaxy/tools/parameters/basic.py
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -1621,7 +1621,7 @@
if type( value ) != list:
value = [ value ]
field = form_builder.SelectField( self.name, self.multiple, None, self.refresh_on_change, refresh_on_change_values=self.refresh_on_change_values )
-
+
# CRUCIAL: the dataset_collector function needs to be local to DataToolParameter.get_html_field()
def dataset_collector( hdas, parent_hid ):
current_user_roles = trans.get_current_user_roles()
@@ -1659,20 +1659,18 @@
# Also collect children via association object
dataset_collector( hda.children, hid )
dataset_collector( history.active_datasets_children_and_roles, None )
- some_data = bool( field.options )
- if some_data:
- if value is None or len( field.options ) == 1:
- # Ensure that the last item is always selected
- a, b, c = field.options[-1]
- if self.optional:
- field.options[-1] = a, b, False
- else:
- field.options[-1] = a, b, True
+
+ set_selected = field.get_selected( return_label=True, return_value=True, multi=False ) is not None
+ # Ensure than an item is always selected
if self.optional:
- if not value:
+ if set_selected:
+ field.add_option( "Selection is Optional", 'None', False )
+ else:
field.add_option( "Selection is Optional", 'None', True )
- else:
- field.add_option( "Selection is Optional", 'None', False )
+ elif not set_selected and bool( field.options ):
+ # Select the last item
+ a, b, c = field.options[-1]
+ field.options[-1] = a, b, True
return field
def get_initial_value( self, trans, context, history=None ):
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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