2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/d270d3cf7627/
Changeset: d270d3cf7627
Branch: stable
User: greg
Date: 2014-02-19 19:05:25
Summary: Make managing an in-memory registry of bi-directional installed repository dependency relationships a configurable option for Galaxy instances.
Affected #: 6 files
diff -r 1298d3f6aca59825d0eb3d32afd5686c4b1b9294 -r d270d3cf7627a42b6fac2aa69701deadb89c8ffc lib/galaxy/config.py
--- a/lib/galaxy/config.py
+++ b/lib/galaxy/config.py
@@ -95,6 +95,7 @@
self.tool_data_table_config_path = resolve_path( kwargs.get( 'tool_data_table_config_path', 'tool_data_table_conf.xml' ), self.root )
self.shed_tool_data_table_config = resolve_path( kwargs.get( 'shed_tool_data_table_config', 'shed_tool_data_table_conf.xml' ), self.root )
self.enable_tool_shed_check = string_as_bool( kwargs.get( 'enable_tool_shed_check', False ) )
+ self.manage_dependency_relationships = string_as_bool( kwargs.get( 'manage_dependency_relationships', True ) )
self.running_functional_tests = string_as_bool( kwargs.get( 'running_functional_tests', False ) )
self.hours_between_check = kwargs.get( 'hours_between_check', 12 )
try:
diff -r 1298d3f6aca59825d0eb3d32afd5686c4b1b9294 -r d270d3cf7627a42b6fac2aa69701deadb89c8ffc lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
--- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
@@ -271,9 +271,10 @@
if remove_from_disk_checked:
tool_shed_repository.status = trans.install_model.ToolShedRepository.installation_status.UNINSTALLED
tool_shed_repository.error_message = None
- # Remove the uninstalled repository and any tool dependencies from the in-memory dictionaries in the
- # installed_repository_manager.
- trans.app.installed_repository_manager.handle_repository_uninstall( tool_shed_repository )
+ if trans.app.config.manage_dependency_relationships:
+ # Remove the uninstalled repository and any tool dependencies from the in-memory dictionaries in the
+ # installed_repository_manager.
+ trans.app.installed_repository_manager.handle_repository_uninstall( tool_shed_repository )
else:
tool_shed_repository.status = trans.install_model.ToolShedRepository.installation_status.DEACTIVATED
trans.install_model.context.add( tool_shed_repository )
diff -r 1298d3f6aca59825d0eb3d32afd5686c4b1b9294 -r d270d3cf7627a42b6fac2aa69701deadb89c8ffc lib/tool_shed/galaxy_install/installed_repository_manager.py
--- a/lib/tool_shed/galaxy_install/installed_repository_manager.py
+++ b/lib/tool_shed/galaxy_install/installed_repository_manager.py
@@ -62,8 +62,9 @@
# whose values are a list of tuples defining tool_dependency objects (whose status is 'Installed') that require the key
# at runtime. The value defines the entire tool dependency tree.
self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies = {}
- # Load defined dependency relationships for installed tool shed repositories and their contents.
- self.load_dependency_relationships()
+ if app.config.manage_dependency_relationships:
+ # Load defined dependency relationships for installed tool shed repositories and their contents.
+ self.load_dependency_relationships()
def add_entry_to_installed_repository_dependencies_of_installed_repositories( self, repository ):
"""
diff -r 1298d3f6aca59825d0eb3d32afd5686c4b1b9294 -r d270d3cf7627a42b6fac2aa69701deadb89c8ffc lib/tool_shed/galaxy_install/repository_util.py
--- a/lib/tool_shed/galaxy_install/repository_util.py
+++ b/lib/tool_shed/galaxy_install/repository_util.py
@@ -602,8 +602,9 @@
suc.update_tool_shed_repository_status( trans.app,
tool_shed_repository,
trans.install_model.ToolShedRepository.installation_status.INSTALLED )
- # Add the installed repository and any tool dependencies to the in-memory dictionaries in the installed_repository_manager.
- trans.app.installed_repository_manager.handle_repository_install( tool_shed_repository )
+ if trans.app.config.manage_dependency_relationships:
+ # Add the installed repository and any tool dependencies to the in-memory dictionaries in the installed_repository_manager.
+ trans.app.installed_repository_manager.handle_repository_install( tool_shed_repository )
else:
# An error occurred while cloning the repository, so reset everything necessary to enable another attempt.
set_repository_attributes( trans,
diff -r 1298d3f6aca59825d0eb3d32afd5686c4b1b9294 -r d270d3cf7627a42b6fac2aa69701deadb89c8ffc lib/tool_shed/util/common_install_util.py
--- a/lib/tool_shed/util/common_install_util.py
+++ b/lib/tool_shed/util/common_install_util.py
@@ -507,8 +507,9 @@
if tool_dependency and tool_dependency.status in [ app.install_model.ToolDependency.installation_status.INSTALLED,
app.install_model.ToolDependency.installation_status.ERROR ]:
installed_tool_dependencies.append( tool_dependency )
- # Add the tool_dependency to the in-memory dictionaries in the installed_repository_manager.
- app.installed_repository_manager.handle_tool_dependency_install( tool_shed_repository, tool_dependency )
+ if app.config.manage_dependency_relationships:
+ # Add the tool_dependency to the in-memory dictionaries in the installed_repository_manager.
+ app.installed_repository_manager.handle_tool_dependency_install( tool_shed_repository, tool_dependency )
elif elem.tag == 'set_environment':
# <set_environment version="1.0">
# <environment_variable name="R_SCRIPT_PATH"action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
diff -r 1298d3f6aca59825d0eb3d32afd5686c4b1b9294 -r d270d3cf7627a42b6fac2aa69701deadb89c8ffc universe_wsgi.ini.sample
--- a/universe_wsgi.ini.sample
+++ b/universe_wsgi.ini.sample
@@ -152,6 +152,11 @@
#enable_tool_shed_check = False
#hours_between_check = 12
+# Enable use of an in-memory registry with bi-directional relationships
+# between repositories (i.e., in addition to lists of dependencies for a
+# repository, keep an in-memory registry of dependent items for each repository.
+#manage_dependency_relationships = True
+
# XML config file that contains data table entries for the ToolDataTableManager. This file is manually
# maintained by the Galaxy administrator.
#tool_data_table_config_path = tool_data_table_conf.xml
https://bitbucket.org/galaxy/galaxy-central/commits/ef0654f99261/
Changeset: ef0654f99261
User: inithello
Date: 2014-02-19 19:09:03
Summary: Merge bugfix from stable.
Affected #: 1 file
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/4df1be355e4f/
Changeset: 4df1be355e4f
User: greg
Date: 2014-02-19 19:05:25
Summary: Make managing an in-memory registry of bi-directional installed repository dependency relationships a configurable option for Galaxy instances.
Affected #: 6 files
diff -r e51429649b44d5b434a6b6f4e10daa1dbf390c20 -r 4df1be355e4f7cdbbc927027ce60b81cf222956f lib/galaxy/config.py
--- a/lib/galaxy/config.py
+++ b/lib/galaxy/config.py
@@ -95,6 +95,7 @@
self.tool_data_table_config_path = resolve_path( kwargs.get( 'tool_data_table_config_path', 'tool_data_table_conf.xml' ), self.root )
self.shed_tool_data_table_config = resolve_path( kwargs.get( 'shed_tool_data_table_config', 'shed_tool_data_table_conf.xml' ), self.root )
self.enable_tool_shed_check = string_as_bool( kwargs.get( 'enable_tool_shed_check', False ) )
+ self.manage_dependency_relationships = string_as_bool( kwargs.get( 'manage_dependency_relationships', True ) )
self.running_functional_tests = string_as_bool( kwargs.get( 'running_functional_tests', False ) )
self.hours_between_check = kwargs.get( 'hours_between_check', 12 )
try:
diff -r e51429649b44d5b434a6b6f4e10daa1dbf390c20 -r 4df1be355e4f7cdbbc927027ce60b81cf222956f lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
--- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
@@ -271,9 +271,10 @@
if remove_from_disk_checked:
tool_shed_repository.status = trans.install_model.ToolShedRepository.installation_status.UNINSTALLED
tool_shed_repository.error_message = None
- # Remove the uninstalled repository and any tool dependencies from the in-memory dictionaries in the
- # installed_repository_manager.
- trans.app.installed_repository_manager.handle_repository_uninstall( tool_shed_repository )
+ if trans.app.config.manage_dependency_relationships:
+ # Remove the uninstalled repository and any tool dependencies from the in-memory dictionaries in the
+ # installed_repository_manager.
+ trans.app.installed_repository_manager.handle_repository_uninstall( tool_shed_repository )
else:
tool_shed_repository.status = trans.install_model.ToolShedRepository.installation_status.DEACTIVATED
trans.install_model.context.add( tool_shed_repository )
diff -r e51429649b44d5b434a6b6f4e10daa1dbf390c20 -r 4df1be355e4f7cdbbc927027ce60b81cf222956f lib/tool_shed/galaxy_install/installed_repository_manager.py
--- a/lib/tool_shed/galaxy_install/installed_repository_manager.py
+++ b/lib/tool_shed/galaxy_install/installed_repository_manager.py
@@ -62,8 +62,9 @@
# whose values are a list of tuples defining tool_dependency objects (whose status is 'Installed') that require the key
# at runtime. The value defines the entire tool dependency tree.
self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies = {}
- # Load defined dependency relationships for installed tool shed repositories and their contents.
- self.load_dependency_relationships()
+ if app.config.manage_dependency_relationships:
+ # Load defined dependency relationships for installed tool shed repositories and their contents.
+ self.load_dependency_relationships()
def add_entry_to_installed_repository_dependencies_of_installed_repositories( self, repository ):
"""
diff -r e51429649b44d5b434a6b6f4e10daa1dbf390c20 -r 4df1be355e4f7cdbbc927027ce60b81cf222956f lib/tool_shed/galaxy_install/repository_util.py
--- a/lib/tool_shed/galaxy_install/repository_util.py
+++ b/lib/tool_shed/galaxy_install/repository_util.py
@@ -602,8 +602,9 @@
suc.update_tool_shed_repository_status( trans.app,
tool_shed_repository,
trans.install_model.ToolShedRepository.installation_status.INSTALLED )
- # Add the installed repository and any tool dependencies to the in-memory dictionaries in the installed_repository_manager.
- trans.app.installed_repository_manager.handle_repository_install( tool_shed_repository )
+ if trans.app.config.manage_dependency_relationships:
+ # Add the installed repository and any tool dependencies to the in-memory dictionaries in the installed_repository_manager.
+ trans.app.installed_repository_manager.handle_repository_install( tool_shed_repository )
else:
# An error occurred while cloning the repository, so reset everything necessary to enable another attempt.
set_repository_attributes( trans,
diff -r e51429649b44d5b434a6b6f4e10daa1dbf390c20 -r 4df1be355e4f7cdbbc927027ce60b81cf222956f lib/tool_shed/util/common_install_util.py
--- a/lib/tool_shed/util/common_install_util.py
+++ b/lib/tool_shed/util/common_install_util.py
@@ -507,8 +507,9 @@
if tool_dependency and tool_dependency.status in [ app.install_model.ToolDependency.installation_status.INSTALLED,
app.install_model.ToolDependency.installation_status.ERROR ]:
installed_tool_dependencies.append( tool_dependency )
- # Add the tool_dependency to the in-memory dictionaries in the installed_repository_manager.
- app.installed_repository_manager.handle_tool_dependency_install( tool_shed_repository, tool_dependency )
+ if app.config.manage_dependency_relationships:
+ # Add the tool_dependency to the in-memory dictionaries in the installed_repository_manager.
+ app.installed_repository_manager.handle_tool_dependency_install( tool_shed_repository, tool_dependency )
elif elem.tag == 'set_environment':
# <set_environment version="1.0">
# <environment_variable name="R_SCRIPT_PATH"action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
diff -r e51429649b44d5b434a6b6f4e10daa1dbf390c20 -r 4df1be355e4f7cdbbc927027ce60b81cf222956f universe_wsgi.ini.sample
--- a/universe_wsgi.ini.sample
+++ b/universe_wsgi.ini.sample
@@ -152,6 +152,11 @@
#enable_tool_shed_check = False
#hours_between_check = 12
+# Enable use of an in-memory registry with bi-directional relationships
+# between repositories (i.e., in addition to lists of dependencies for a
+# repository, keep an in-memory registry of dependent items for each repository.
+#manage_dependency_relationships = True
+
# XML config file that contains data table entries for the ToolDataTableManager. This file is manually
# maintained by the Galaxy administrator.
#tool_data_table_config_path = tool_data_table_conf.xml
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/742b4ffd3b99/
Changeset: 742b4ffd3b99
User: guerler
Date: 2014-02-19 18:51:52
Summary: Add get data back to to tool panel (will be replaced by a placeholder soon)
Affected #: 1 file
diff -r 7ebec9da47844efbf37942faab3809cb0169e5c2 -r 742b4ffd3b99160cae864049f09defe710dd7ee4 tools/data_source/upload.xml
--- a/tools/data_source/upload.xml
+++ b/tools/data_source/upload.xml
@@ -1,7 +1,6 @@
<?xml version="1.0"?><tool name="Upload File" id="upload1" version="1.1.4" workflow_compatible="false">
- <hidden>True</hidden><description>
from your computer
</description>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/e9d3248c6fc3/
Changeset: e9d3248c6fc3
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 26e37f6af3a8a090d9d6e923fa3e90acb0e64572 -r e9d3248c6fc312f8c7671a8e1233265c4ff0a0b1 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/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.