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[18.01] fix for cases where panel elements have to_dict with different signature #5615

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merged 3 commits into from Mar 1, 2018
Merged

[18.01] fix for cases where panel elements have to_dict with different signature #5615

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d648e22
fix for cases where panel elements have to_dict with different signature
martenson Feb 27, 2018
5406a71
pass the toolbox obj to make sure cache is available
martenson Feb 28, 2018
b96fd2c
enable cache for tools that inherit from Tool
martenson Feb 28, 2018
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11 changes: 8 additions & 3 deletions lib/galaxy/tools/toolbox/base.py
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Expand Up @@ -927,7 +927,7 @@ def tool_panel_contents(self, trans, **kwds):
if elt:
yield elt

def _get_tool_to_dict(self, trans, tool):
def get_tool_to_dict(self, trans, tool):
"""Return tool's to_dict.
Use cache if present, store to cache otherwise.
Note: The cached tool's to_dict is specific to the calls from toolbox.
Expand All @@ -953,14 +953,19 @@ def to_dict(self, trans, in_panel=True, **kwds):
if in_panel:
panel_elts = list(self.tool_panel_contents(trans, **kwds))
for elt in panel_elts:
rval.append(self._get_tool_to_dict(trans, elt))
# Only use cache for objects that are Tools.
if hasattr(elt, "tool_type"):
rval.append(self.get_tool_to_dict(trans, elt))
else:
kwargs = dict(trans=trans, link_details=True, toolbox=self)
rval.append(elt.to_dict(**kwargs))
else:
filter_method = self._build_filter_method(trans)
for id, tool in self._tools_by_id.items():
tool = filter_method(tool, panel_item_types.TOOL)
if not tool:
continue
rval.append(self._get_tool_to_dict(trans, tool))
rval.append(self.get_tool_to_dict(trans, tool))
return rval

def _lineage_in_panel(self, panel_dict, tool=None, tool_lineage=None):
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7 changes: 5 additions & 2 deletions lib/galaxy/tools/toolbox/panel.py
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Expand Up @@ -69,7 +69,7 @@ def copy(self):
copy.elems = self.elems.copy()
return copy

def to_dict(self, trans, link_details=False):
def to_dict(self, trans, link_details=False, toolbox=None):
""" Return a dict that includes section's attributes. """

section_dict = super(ToolSection, self).to_dict()
Expand All @@ -79,7 +79,10 @@ def to_dict(self, trans, link_details=False):
link_details=link_details
)
for elt in self.elems.values():
section_elts.append(elt.to_dict(**kwargs))
if hasattr(elt, "tool_type") and toolbox:
section_elts.append(toolbox.get_tool_to_dict(trans, elt))
else:
section_elts.append(elt.to_dict(**kwargs))
section_dict['elems'] = section_elts

return section_dict
Expand Down