1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/05528b8aa8a1/
Changeset: 05528b8aa8a1
User: greg
Date: 2013-06-25 12:57:32
Summary: Fix for browsing a tool dependency installed with a tol shed repository.
Affected #: 2 files
diff -r 80dcf7e41b4aec1d5608c05c870a634651af2924 -r
05528b8aa8a1decc291f582b34265918c68f798e
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
@@ -155,7 +155,8 @@
def browse_tool_dependency( self, trans, **kwd ):
message = kwd.get( 'message', '' )
status = kwd.get( 'status', 'done' )
- tool_dependency = tool_dependency_util.get_tool_dependency( trans, kwd[
'id' ] )
+ tool_dependency_ids = tool_dependency_util.get_tool_dependency_ids(
as_string=False, **kwd )
+ tool_dependency = tool_dependency_util.get_tool_dependency( trans,
tool_dependency_ids[ 0 ] )
if tool_dependency.in_error_state:
message = "This tool dependency is not installed correctly (see the
<b>Tool dependency installation error</b> below). "
message += "Choose <b>Uninstall this tool dependency</b>
from the <b>Repository Actions</b> menu, correct problems "
@@ -1166,6 +1167,18 @@
initiate_repository_installation_ids=encoded_repository_ids,
reinstalling=True )
+ @web.expose
+ @web.require_admin
+ def repair_repository( self, trans, **kwd ):
+ """
+ Inspect the repository dependency hierarchy for a specified repository and
attempt to make sure they are all properly installed as well as
+ each repository's tool dependencies.
+ """
+ message = kwd.get( 'message', '' )
+ status = kwd.get( 'status', 'done' )
+ repository_id = kwd[ 'id' ]
+ tool_shed_repository = suc.get_installed_tool_shed_repository( trans,
repository_id )
+
@web.json
def repository_installation_status_updates( self, trans, ids=None, status_list=None
):
# Avoid caching
diff -r 80dcf7e41b4aec1d5608c05c870a634651af2924 -r
05528b8aa8a1decc291f582b34265918c68f798e
templates/webapps/tool_shed/repository/common.mako
--- a/templates/webapps/tool_shed/repository/common.mako
+++ b/templates/webapps/tool_shed/repository/common.mako
@@ -863,7 +863,7 @@
${tool_dependency.name | h}
%elif trans.webapp.name == 'galaxy' and
tool_dependency.tool_dependency_id:
%if tool_dependency.repository_id and tool_dependency.installation_status
in [ trans.model.ToolDependency.installation_status.INSTALLED ]:
- <a class="action-button" href="${h.url_for(
controller='admin_toolshed', action='browse_tool_dependency',
id=trans.security.encode_id( tool_dependency.tool_dependency_id ),
repository_id=trans.security.encode_id( tool_dependency.repository_id ) )}">
+ <a class="action-button" href="${h.url_for(
controller='admin_toolshed', action='browse_tool_dependency',
id=trans.security.encode_id( tool_dependency.tool_dependency_id ) )}">
${tool_dependency.name | h}
</a>
%elif tool_dependency.installation_status not in [
trans.model.ToolDependency.installation_status.UNINSTALLED ]:
Repository URL:
https://bitbucket.org/galaxy/galaxy-central/
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