2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/fa8bdf1f6fc7/
Changeset: fa8bdf1f6fc7
Branch: stable
User: inithello
Date: 2014-02-14 21:59:35
Summary: Also check for tool config path when installing migrated tools and rewriting the tool_conf.xml. This resolves the issue described in pull request 324.
Affected #: 1 file
diff -r 75672e1cba2bd569b729156f3d8f8f1f994240f0 -r fa8bdf1f6fc7318d120a3420c50e4045dbdb1e8b lib/tool_shed/galaxy_install/install_manager.py
--- a/lib/tool_shed/galaxy_install/install_manager.py
+++ b/lib/tool_shed/galaxy_install/install_manager.py
@@ -197,8 +197,7 @@
file_path = section_elem.get( 'file', None )
if file_path:
file_name = suc.strip_path( file_path )
-
- if file_name in tool_configs_to_filter:
+ if file_name in tool_configs_to_filter or file_path in tool_configs_to_filter:
elem.remove( section_elem )
persist_required = True
if persist_required:
@@ -223,7 +222,7 @@
# The proprietary_tool_panel_elem looks something like <tool file="emboss_5/emboss_antigenic.xml" />.
proprietary_tool_config = proprietary_tool_panel_elem.get( 'file' )
proprietary_name = suc.strip_path( proprietary_tool_config )
- if tool_config == proprietary_name:
+ if tool_config == proprietary_name or tool_config == proprietary_tool_config:
# The tool is loaded outside of any sections.
tool_sections.append( None )
if not is_displayed:
@@ -235,7 +234,7 @@
# The section_elem looks something like <tool file="emboss_5/emboss_antigenic.xml" />.
proprietary_tool_config = section_elem.get( 'file' )
proprietary_name = suc.strip_path( proprietary_tool_config )
- if tool_config == proprietary_name:
+ if tool_config == proprietary_name or tool_config == proprietary_tool_config:
# The tool is loaded inside of the section_elem.
tool_sections.append( ToolSection( proprietary_tool_panel_elem ) )
if not is_displayed:
@@ -314,7 +313,7 @@
file_path = elem.get( 'file', None )
if file_path:
name = suc.strip_path( file_path )
- if name in migrated_tool_configs:
+ if name in migrated_tool_configs or file_path in migrated_tool_configs:
if elem not in tool_panel_elems:
tool_panel_elems.append( elem )
elif elem.tag == 'section':
@@ -324,7 +323,7 @@
file_path = section_elem.get( 'file', None )
if file_path:
name = suc.strip_path( file_path )
- if name in migrated_tool_configs:
+ if name in migrated_tool_configs or file_path in migrated_tool_configs:
# Append the section, not the tool.
if elem not in tool_panel_elems:
tool_panel_elems.append( elem )
https://bitbucket.org/galaxy/galaxy-central/commits/5079dae08441/
Changeset: 5079dae08441
User: inithello
Date: 2014-02-14 22:00:00
Summary: Merge bugfix from stable.
Affected #: 1 file
diff -r 479b72075bc8a68ec602081987375ca1dfa20a2f -r 5079dae08441dcf125cc9fee87b28aaba7a38f9d lib/tool_shed/galaxy_install/install_manager.py
--- a/lib/tool_shed/galaxy_install/install_manager.py
+++ b/lib/tool_shed/galaxy_install/install_manager.py
@@ -197,8 +197,7 @@
file_path = section_elem.get( 'file', None )
if file_path:
file_name = suc.strip_path( file_path )
-
- if file_name in tool_configs_to_filter:
+ if file_name in tool_configs_to_filter or file_path in tool_configs_to_filter:
elem.remove( section_elem )
persist_required = True
if persist_required:
@@ -223,7 +222,7 @@
# The proprietary_tool_panel_elem looks something like <tool file="emboss_5/emboss_antigenic.xml" />.
proprietary_tool_config = proprietary_tool_panel_elem.get( 'file' )
proprietary_name = suc.strip_path( proprietary_tool_config )
- if tool_config == proprietary_name:
+ if tool_config == proprietary_name or tool_config == proprietary_tool_config:
# The tool is loaded outside of any sections.
tool_sections.append( None )
if not is_displayed:
@@ -235,7 +234,7 @@
# The section_elem looks something like <tool file="emboss_5/emboss_antigenic.xml" />.
proprietary_tool_config = section_elem.get( 'file' )
proprietary_name = suc.strip_path( proprietary_tool_config )
- if tool_config == proprietary_name:
+ if tool_config == proprietary_name or tool_config == proprietary_tool_config:
# The tool is loaded inside of the section_elem.
tool_sections.append( ToolSection( proprietary_tool_panel_elem ) )
if not is_displayed:
@@ -314,7 +313,7 @@
file_path = elem.get( 'file', None )
if file_path:
name = suc.strip_path( file_path )
- if name in migrated_tool_configs:
+ if name in migrated_tool_configs or file_path in migrated_tool_configs:
if elem not in tool_panel_elems:
tool_panel_elems.append( elem )
elif elem.tag == 'section':
@@ -324,7 +323,7 @@
file_path = section_elem.get( 'file', None )
if file_path:
name = suc.strip_path( file_path )
- if name in migrated_tool_configs:
+ if name in migrated_tool_configs or file_path in migrated_tool_configs:
# Append the section, not the tool.
if elem not in tool_panel_elems:
tool_panel_elems.append( elem )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/6f9059801faf/
Changeset: 6f9059801faf
Branch: stable
User: greg
Date: 2014-02-14 16:40:31
Summary: Change log.warning to log.debug for messages regarding conflicting datatypes since recent changes in the Galaxy framework now result in job errors when using log.warning.
Affected #: 1 file
diff -r e088f2dc8b070d13e9fb7319463786d7ff4f5024 -r 6f9059801fafb3b7ae2cf844b07848beab0846fa lib/galaxy/datatypes/registry.py
--- a/lib/galaxy/datatypes/registry.py
+++ b/lib/galaxy/datatypes/registry.py
@@ -223,7 +223,7 @@
if extension in self.datatypes_by_extension:
# Because of the way that the value of can_process_datatype was set above, we know that the value of
# override is True.
- self.log.warning( "Overriding conflicting datatype with extension '%s', using datatype from %s." % \
+ self.log.debug( "Overriding conflicting datatype with extension '%s', using datatype from %s." % \
( str( extension ), str( config ) ) )
if make_subclass:
datatype_class = type( datatype_class_name, ( datatype_class, ), {} )
@@ -277,7 +277,7 @@
if not override:
# Do not load the datatype since it conflicts with an existing datatype which we are not supposed
# to override.
- self.log.warning( "Ignoring conflicting datatype with extension '%s' from %s." % ( extension, config ) )
+ self.log.debug( "Ignoring conflicting datatype with extension '%s' from %s." % ( extension, config ) )
# Load datatype sniffers from the config - we'll do this even if one or more datatypes were not properly processed in the config
# since sniffers are not tightly coupled with datatypes.
self.load_datatype_sniffers( root,
https://bitbucket.org/galaxy/galaxy-central/commits/b71c9af7c17c/
Changeset: b71c9af7c17c
User: inithello
Date: 2014-02-14 16:43:10
Summary: Merge grafted bugfix from stable.
Affected #: 0 files
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/0b0018fa5d20/
Changeset: 0b0018fa5d20
User: greg
Date: 2014-02-14 16:40:31
Summary: Change log.warning to log.debug for messages regarding conflicting datatypes since recent changes in the Galaxy framework now result in job errors when using log.warning.
Affected #: 1 file
diff -r 955e973c5b33eba4e0e68979a7c20c0bd0558e37 -r 0b0018fa5d20228bb7a8c0dc6566b8239873610d lib/galaxy/datatypes/registry.py
--- a/lib/galaxy/datatypes/registry.py
+++ b/lib/galaxy/datatypes/registry.py
@@ -223,7 +223,7 @@
if extension in self.datatypes_by_extension:
# Because of the way that the value of can_process_datatype was set above, we know that the value of
# override is True.
- self.log.warning( "Overriding conflicting datatype with extension '%s', using datatype from %s." % \
+ self.log.debug( "Overriding conflicting datatype with extension '%s', using datatype from %s." % \
( str( extension ), str( config ) ) )
if make_subclass:
datatype_class = type( datatype_class_name, ( datatype_class, ), {} )
@@ -277,7 +277,7 @@
if not override:
# Do not load the datatype since it conflicts with an existing datatype which we are not supposed
# to override.
- self.log.warning( "Ignoring conflicting datatype with extension '%s' from %s." % ( extension, config ) )
+ self.log.debug( "Ignoring conflicting datatype with extension '%s' from %s." % ( extension, config ) )
# Load datatype sniffers from the config - we'll do this even if one or more datatypes were not properly processed in the config
# since sniffers are not tightly coupled with datatypes.
self.load_datatype_sniffers( root,
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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