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When loading a tool from Tool Shed, check that the <installed_changeset_revision> element matches the tool path.

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Workaround for issue #1283, which causes the loaded tool to have a
StockLineage instead of a ToolShedLineage, thus creating multiple entries
for the tool in the panel.

Conflicts:
	lib/galaxy/tools/toolbox/base.py
This commit is contained in:
Nicola Soranzo
2016-01-08 14:17:12 +00:00
committed by John Chilton
parent 47361f12ec
commit e8e01bdfb1
1 changed files with 14 additions and 0 deletions
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lib/galaxy/tools/toolbox/base.py
+14
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@@ -556,6 +556,20 @@ class AbstractToolBox( Dictifiable, ManagesIntegratedToolPanelMixin, object ):
# Backward compatibility issue - the tag used to be named 'changeset_revision'.
installed_changeset_revision_elem = item.elem.find( "changeset_revision" )
installed_changeset_revision = installed_changeset_revision_elem.text
try:
splitted_path = path.split('/')
assert splitted_path[0] == tool_shed
assert splitted_path[2] == repository_owner
assert splitted_path[3] == repository_name
if splitted_path[4] != installed_changeset_revision:
# This can happen if the Tool Shed repository has been
# updated to a new revision and the installed_changeset_revision
# element in shed_tool_conf.xml file has been updated too
log.debug("The installed_changeset_revision for tool %s is %s, using %s instead", path, installed_changeset_revision, splitted_path[4])
installed_changeset_revision = splitted_path[4]
except Exception as e:
log.debug("Error while loading tool %s : %s", path, e)
pass
tool_shed_repository = self._get_tool_shed_repository( tool_shed,
repository_name,
repository_owner,