Merge branch 'main' of https://github.com/InformaticsMatters/data-manager-job-decoder into main

Author: Alan Christie

decoder/decoder.py

@@ -328,6 +328,16 @@ def get_jobs_replaced(job_definition: Dict[str, Any]) -> Optional[List[str]]:
     return list(replaced)
 
 
+def get_outputs(job_definition: Dict[str, Any]) -> Optional[Dict[str, Any]]:
+    """Given a Job Definition this function returns the outputs declared."""
+    return job_definition.get("variables", {}).get("outputs", {}).get("properties", {})
+
+
+def get_inputs(job_definition: Dict[str, Any]) -> Optional[Dict[str, Any]]:
+    """Given a Job Definition this function returns the inputs declared."""
+    return job_definition.get("variables", {}).get("inputs", {}).get("properties", {})
+
+
 def decode(
     template_text: str,
     variable_map: Optional[Dict[str, str]],

tests/test_get_inputs.py

@@ -0,0 +1,46 @@
+# Tests for the decoder's get_inputs() function.
+from typing import Dict
+
+import pytest
+
+pytestmark = pytest.mark.unit
+
+from decoder import decoder
+
+
+def test_get_inputs_when_none():
+    # Arrange
+    job_definition: Dict = {}
+
+    # Act
+    inputs = decoder.get_inputs(job_definition)
+
+    # Assert
+    assert inputs == {}
+
+
+def test_get_inputs():
+    # Arrange
+    job_definition: Dict = {
+        "variables": {
+            "inputs": {
+                "properties": {
+                    "inputFile": {
+                        "title": "PDB File",
+                        "mime-types": ["chemical/x-pdb"],
+                        "type": "file",
+                    }
+                }
+            }
+        }
+    }
+
+    # Act
+    inputs = decoder.get_inputs(job_definition)
+
+    # Assert
+    assert inputs
+    assert "inputFile" in inputs
+    assert inputs["inputFile"]["title"] == "PDB File"
+    assert inputs["inputFile"]["mime-types"] == ["chemical/x-pdb"]
+    assert inputs["inputFile"]["type"] == "file"

tests/test_get_outputs.py

@@ -0,0 +1,46 @@
+# Tests for the decoder's get_outputs() function.
+from typing import Dict
+
+import pytest
+
+pytestmark = pytest.mark.unit
+
+from decoder import decoder
+
+
+def test_get_outputs_when_none():
+    # Arrange
+    job_definition: Dict = {}
+
+    # Act
+    outputs = decoder.get_outputs(job_definition)
+
+    # Assert
+    assert outputs == {}
+
+
+def test_get_outputs():
+    # Arrange
+    job_definition: Dict = {
+        "variables": {
+            "outputs": {
+                "properties": {
+                    "pdbFile": {
+                        "title": "PDB File",
+                        "mime-types": ["chemical/x-pdb"],
+                        "type": "file",
+                    }
+                }
+            }
+        }
+    }
+
+    # Act
+    outputs = decoder.get_outputs(job_definition)
+
+    # Assert
+    assert outputs
+    assert "pdbFile" in outputs
+    assert outputs["pdbFile"]["title"] == "PDB File"
+    assert outputs["pdbFile"]["mime-types"] == ["chemical/x-pdb"]
+    assert outputs["pdbFile"]["type"] == "file"