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Scottx611x/expose extra directories #2447

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merged 8 commits into from
Dec 19, 2017
Merged

Scottx611x/expose extra directories #2447

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e03ec44
Fix bug when casting parameters to their expected types
scottx611x Dec 19, 2017
af54348
Add test coverage
scottx611x Dec 19, 2017
a44a59b
Expose `extra_directories` information in input.json
scottx611x Dec 19, 2017
847b8aa
Update tests
scottx611x Dec 19, 2017
6803569
Merge branch 'develop' into scottx611x/expose_extra_directories
scottx611x Dec 19, 2017
6629c28
Update Parameter tests to use stronger assertions; Unfortunealy can't…
scottx611x Dec 19, 2017
1b088f1
Remove redundant parens
scottx611x Dec 19, 2017
eb8551d
Merge branch 'scottx611x/expose_extra_directories' of https://github.…
scottx611x Dec 19, 2017
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16 changes: 11 additions & 5 deletions refinery/tool_manager/models.py
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Original file line number Diff line number Diff line change
Expand Up @@ -159,7 +159,7 @@ class ToolDefinition(models.Model):
Visualizations, Other) will need to know about their expected inputs,
outputs, and input file structuring.
"""

EXTRA_DIRECTORIES = "extra_directories"
PARAMETERS = "parameters"
WORKFLOW = 'WORKFLOW'
VISUALIZATION = 'VISUALIZATION'
Expand Down Expand Up @@ -204,14 +204,16 @@ def get_extra_directories(self):
"""
if self.tool_type == ToolDefinition.VISUALIZATION:
try:
return self.get_annotation()["extra_directories"]
return self.get_annotation()[self.EXTRA_DIRECTORIES]
except KeyError:
logger.error("ToolDefinition: %s's annotation is missing its "
"`extra_directories` key.", self.name)
"`%s` key.", self.name, self.EXTRA_DIRECTORIES)
raise
else:
raise NotImplementedError(
"Workflow-based tools don't utilize `extra_directories`"
"Workflow-based tools don't utilize `{}`".format(
self.EXTRA_DIRECTORIES
)
)

def get_parameters(self):
Expand Down Expand Up @@ -428,7 +430,11 @@ def _create_container_input_dict(self):
return {
self.FILE_RELATIONSHIPS: self.get_file_relationships_urls(),
ToolDefinition.PARAMETERS: self._get_visualization_parameters(),
self.NODE_INFORMATION: self._get_detailed_input_nodes_dict()
self.NODE_INFORMATION: self._get_detailed_input_nodes_dict(),
ToolDefinition.EXTRA_DIRECTORIES: (
self.tool_definition.get_extra_directories()
)
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I don't think you need the surrounding paren here: There's no syntactic ambiguity without it.

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I don't think this should block, but the mix of self and ToolDefinition, or public and underscored confuses me, a little. Are those distinctions useful, and meaningful?


}

def _get_detailed_input_nodes_dict(self):
Expand Down
6 changes: 4 additions & 2 deletions refinery/tool_manager/tests.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1522,7 +1522,7 @@ def test_get_detailed_input_nodes_dict(self):
)
self.assertTrue(self.search_solr_mock.called)

def test__create_input_dict(self):
def test__create_container_input_dict(self):
tool_input_dict = self.tool._create_container_input_dict()
file_relationships = self.tool.get_file_relationships_urls()

Expand All @@ -1533,7 +1533,9 @@ def test__create_input_dict(self):
VisualizationTool.NODE_INFORMATION:
self.tool._get_detailed_input_nodes_dict(),
ToolDefinition.PARAMETERS:
self.tool._get_visualization_parameters()
self.tool._get_visualization_parameters(),
ToolDefinition.EXTRA_DIRECTORIES:
self.tool.tool_definition.get_extra_directories()
}
)

Expand Down