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Scottx611x/td api fixes #1653

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merged 13 commits into from
Apr 3, 2017
Merged

Scottx611x/td api fixes #1653

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32acdeb
Rename and add more test-data
scottx611x Mar 28, 2017
4ec7a35
Fix typo
scottx611x Mar 28, 2017
5c62462
Provide logic for checking if a user-defined output_file aligns with …
scottx611x Mar 28, 2017
164a48e
Update Tests
scottx611x Mar 28, 2017
407bb43
Add even more test data
scottx611x Mar 28, 2017
1df94e3
Add constraint for at least one `output_file` to be present in annota…
scottx611x Mar 28, 2017
5732fd1
Remove `mock_get_workflow_listt()` and provide mock `side_effects` di…
scottx611x Mar 29, 2017
c275876
These `else`s are necessary to avoid `UnboundLocalError`
scottx611x Mar 30, 2017
ee621fa
update test data
scottx611x Mar 30, 2017
64ff494
Fix typo
scottx611x Mar 30, 2017
a94ea27
Update schema to include different reqs. for a LIST vs a PAIR
scottx611x Mar 30, 2017
76bf5c7
Add test cases to reflect a PAIR's two input file requirement
scottx611x Mar 30, 2017
d9bb73b
Place "tool_manager/test_data" into reuseable TEST_DATA_PATH
scottx611x Apr 1, 2017
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69 changes: 44 additions & 25 deletions refinery/tool_manager/management/commands/generate_tool_definitions.py
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Original file line number Diff line number Diff line change
Expand Up @@ -83,36 +83,55 @@ def handle(self, **options):
except KeyError:
# `parameters` aren't required for each workflow step
pass

for parameter in parameters:
# Check User-defined parameters in
# annotation data against the available
# parameters of the Workflow step's
# `tool_inputs`
if parameter["name"] not in step["tool_inputs"]:
raise CommandError(
"{} is not a valid parameter for {}".
format(
parameter["name"],
step["tool_id"]
else:
for parameter in parameters:
# Check User-defined parameters in
# annotation data against the available
# parameters of the Workflow step's
# `tool_inputs`
if parameter["name"] not in step["tool_inputs"]:
raise CommandError(
"{} is not a valid parameter for {}".
format(
parameter["name"],
step["tool_id"]
)
)
)
else:
parameter["galaxy_workflow_step"] = int(
step_index
)
workflow["annotation"]["parameters"]\
.append(parameter)
else:
parameter["galaxy_workflow_step"] = int(
step_index
)
workflow["annotation"]["parameters"]\
.append(parameter)
try:
output_files = step_annotation["output_files"]
except KeyError:
# `ouput_files` aren't required for each workflow step
# `output_files` aren't required for each workflow step
pass

for output_file in output_files:
workflow["annotation"]["output_files"].append(
output_file
)
else:
for output_file in output_files:
# Check User-defined output_files in
# annotation data against the available
# output_file of the Workflow step's
# `tool_inputs`
valid_output_names = []
for key in step["input_steps"].iterkeys():
valid_output_names.append(
step["input_steps"][key]["step_output"]
)
if output_file["name"] not in valid_output_names:
raise CommandError(
"`{}` is not a valid output file for {}. "
"Valid ouput_file names are: {}".format(
output_file["name"],
step["tool_id"],
valid_output_names
)
)
else:
workflow["annotation"]["output_files"].append(
output_file
)
try:
validate_tool_annotation(workflow)
except RuntimeError as e:
Expand Down
105 changes: 77 additions & 28 deletions refinery/tool_manager/schemas/FileRelationship.json
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Original file line number Diff line number Diff line change
@@ -1,34 +1,83 @@
{
"$schema": "http://json-schema.org/draft-04/schema",
"type": "object",
"required": [
"name",
"value_type",
"file_relationship"
],
"properties": {
"name": {
"type": "string"
},
"value_type": {
"type": "string",
"enum": [
"PAIR",
"LIST"
]
},
"input_files": {
"type": "array",
"minItems": 1,
"items": {
"$ref": "InputFile.json#"
"oneOf": [
{
"required": [
"name",
"value_type",
"file_relationship"
],
"properties": {
"name": {
"type": "string"
},
"value_type": {
"type": "string",
"enum": [
"PAIR"
]
},
"input_files": {
"type": "array",
"minItems": 2,
"maxItems": 2,
"items": {
"$ref": "InputFile.json#"
}
},
"file_relationship": {
"oneOf": [
{
"type": "object",
"$ref": "FileRelationship.json#"
},
{
"type": "object",
"additionalProperties": false,
"properties": {}
}
]
}
}
},
"file_relationship": {
"oneOf": [
{"type": "object", "$ref": "FileRelationship.json#"},
{"type": "object", "additionalProperties": false, "properties": {}}
]
{
"required": [
"name",
"value_type",
"file_relationship"
],
"properties": {
"name": {
"type": "string"
},
"value_type": {
"type": "string",
"enum": [
"LIST"
]
},
"input_files": {
"type": "array",
"minItems": 1,
"items": {
"$ref": "InputFile.json#"
}
},
"file_relationship": {
"oneOf": [
{
"type": "object",
"$ref": "FileRelationship.json#"
},
{
"type": "object",
"additionalProperties": false,
"properties": {}
}
]
}
}
}
}

]
}
3 changes: 2 additions & 1 deletion refinery/tool_manager/schemas/ToolDefinition.json
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Original file line number Diff line number Diff line change
Expand Up @@ -29,7 +29,8 @@
"type": "array",
"items": {
"$ref": "OutputFile.json#"
}
},
"minItems": 1
},
"parameters": {
"type": "array",
Expand Down
0 ...l_manager/test_data/galaxy_workflows.json → ...r/test_data/invalid_galaxy_workflows.json
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File renamed without changes.