1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/450594312d80/
Changeset: 450594312d80
User: dan
Date: 2014-01-22 17:13:13
Summary: Fix for installing migrated tools with dependencies.
Affected #: 1 file
diff -r 6c3c24b83d97adc4b946f01321c540fc48e6bb21 -r 450594312d802a518964c7955528ea759001b2ad lib/tool_shed/galaxy_install/migrate/common.py
--- a/lib/tool_shed/galaxy_install/migrate/common.py
+++ b/lib/tool_shed/galaxy_install/migrate/common.py
@@ -2,7 +2,7 @@
import os
import sys
import galaxy.config
-from tool_shed.galaxy_install import install_manager
+from tool_shed.galaxy_install import install_manager, installed_repository_manager
class MigrateToolsApplication( object, galaxy.config.ConfiguresGalaxyMixin ):
@@ -41,6 +41,8 @@
self._configure_toolbox()
self._configure_tool_shed_registry()
+
+ self.installed_repository_manager = installed_repository_manager.InstalledRepositoryManager( self )
# Get the latest tool migration script number to send to the Install manager.
latest_migration_script_number = int( tools_migration_config.split( '_' )[ 0 ] )
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/2aeae8e4603c/
Changeset: 2aeae8e4603c
User: dan
Date: 2014-01-21 23:21:04
Summary: Fix for upload tool importing from ftp uploaded file.
Affected #: 1 file
diff -r 13114825942ff71c6dac143bba6ed31a7cb8d584 -r 2aeae8e4603c8cec297e165c6aa40bfc06fdb1db lib/galaxy/tools/parameters/grouping.py
--- a/lib/galaxy/tools/parameters/grouping.py
+++ b/lib/galaxy/tools/parameters/grouping.py
@@ -361,6 +361,7 @@
'filename' : os.path.basename( ftp_file ) }
file_bunch = get_data_file_filename( ftp_data_file, override_name = name, override_info = info )
if file_bunch.path:
+ file_bunch.to_posix_lines = to_posix_lines
file_bunch.space_to_tab = space_to_tab
rval.append( file_bunch )
return rval
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/54defa390a91/
Changeset: 54defa390a91
User: greg
Date: 2014-01-21 22:04:34
Summary: Fix typos in error messages displayed when importing repository capsules into a tool shed.
Affected #: 3 files
diff -r a4825028799be0f5ba846ac52ee357c53dfc4a08 -r 54defa390a91ec1db34141f97711e673218cde13 lib/galaxy/webapps/tool_shed/api/repositories.py
--- a/lib/galaxy/webapps/tool_shed/api/repositories.py
+++ b/lib/galaxy/webapps/tool_shed/api/repositories.py
@@ -213,7 +213,7 @@
capsule_dict = import_util.validate_capsule( trans, **capsule_dict )
status = capsule_dict.get( 'status', 'error' )
if status == 'error':
- log.debug( 'The capsule contents are invalid and cannpt be imported:<br/>%s' % \
+ log.debug( 'The capsule contents are invalid and cannot be imported:<br/>%s' % \
str( capsule_dict.get( 'error_message', '' ) ) )
return {}
encoded_file_path = capsule_dict.get( 'encoded_file_path', None )
diff -r a4825028799be0f5ba846ac52ee357c53dfc4a08 -r 54defa390a91ec1db34141f97711e673218cde13 lib/galaxy/webapps/tool_shed/controllers/repository.py
--- a/lib/galaxy/webapps/tool_shed/controllers/repository.py
+++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py
@@ -2908,7 +2908,8 @@
action='import_capsule',
**capsule_dict ) )
else:
- message = 'The capsule contents are invalid and cannpt be imported:<br/>%s' % str( capsule_dict.get( 'error_message', '' ) )
+ message = 'The capsule contents are invalid and cannot be imported:<br/>%s' % \
+ str( capsule_dict.get( 'error_message', '' ) )
return trans.fill_template( '/webapps/tool_shed/repository/upload_capsule.mako',
url=url,
message=message,
diff -r a4825028799be0f5ba846ac52ee357c53dfc4a08 -r 54defa390a91ec1db34141f97711e673218cde13 lib/tool_shed/util/xml_util.py
--- a/lib/tool_shed/util/xml_util.py
+++ b/lib/tool_shed/util/xml_util.py
@@ -46,8 +46,8 @@
def create_element( tag, attributes=None, sub_elements=None ):
"""
- Create a new element whose tag is the value of the received tag, and whose attributes are all key / value pairs in the received the attributes
- and sub_elements.
+ Create a new element whose tag is the value of the received tag, and whose attributes are all
+ key / value pairs in the received the attributes and sub_elements.
"""
if tag:
elem = XmlET.Element( tag )
@@ -56,14 +56,15 @@
for k, v in attributes.items():
elem.set( k, v )
if sub_elements:
- # The received attributes is an odict as well. These handle information that tends to be long text including paragraphs (e.g.,
- # description and long_description.
+ # The received attributes is an odict as well. These handle information that tends to be
+ # long text including paragraphs (e.g., description and long_description.
for k, v in sub_elements.items():
# Don't include fields that are blank.
if v:
sub_elem = XmlET.SubElement( elem, k )
if isinstance( v, list ):
- # If the sub_elem is a list, then it must be a list of tuples where the first item is the tag and the second item is the text value.
+ # If the sub_elem is a list, then it must be a list of tuples where the first
+ # item is the tag and the second item is the text value.
for v_tuple in v:
if len( v_tuple ) == 2:
v_tag = v_tuple[ 0 ]
@@ -79,9 +80,11 @@
def indent( elem, level=0 ):
"""
- Prints an XML tree with each node indented according to its depth. This method is used to print the shed tool config (e.g., shed_tool_conf.xml
- from the in-memory list of config_elems because each config_elem in the list may be a hierarchical structure that was not created using the
- parse_xml() method below, and so will not be properly written with xml.etree.ElementTree.tostring() without manually indenting the tree first.
+ Prints an XML tree with each node indented according to its depth. This method is used to print the
+ shed tool config (e.g., shed_tool_conf.xml from the in-memory list of config_elems because each config_elem
+ in the list may be a hierarchical structure that was not created using the parse_xml() method below,
+ and so will not be properly written with xml.etree.ElementTree.tostring() without manually indenting
+ the tree first.
"""
i = "\n" + level * " "
if len( elem ):
@@ -125,7 +128,8 @@
def xml_to_string( elem, encoding='utf-8', use_indent=False, level=0 ):
if elem is not None:
if use_indent:
- # We were called from suc.config_elems_to_xml_file(), so set the level to 1 since level 0 is the <toolbox> tag set.
+ # We were called from suc.config_elems_to_xml_file(), so set the level to 1 since level 0
+ # is the <toolbox> tag set.
indent( elem, level=level )
if using_python_27:
xml_str = '%s\n' % xml.etree.ElementTree.tostring( elem, encoding=encoding, method="xml" )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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