feat: Add a smiles-to-file job and definition

Author: Alan Christie

tests/job-definitions/job-definitions.yaml

@@ -23,8 +23,36 @@ jobs:
 
   nop:
     command: >-
-      python --version
+      nop.py
 
   nop-fail:
     command: >-
-      python --version
+      nop-fail.py
+
+  smiles-to-file:
+    command: >-
+      string-to-file.py --smiles {{ smiles }} --output {{ outputFile }}
+    variables:
+      outputs:
+        type: object
+        properties:
+          title: Output file
+          mime-types:
+          - chemical/x-mdl-sdfile
+          - squonk/x-smiles
+          creates: '{{ outputFile }}'
+          type: file
+      options:
+        type: object
+        required:
+        - outputFile
+        - smiles
+        properties:
+          outputFile:
+            title: Output file
+            type: string
+            default: clustered.sdf
+            pattern: "^[A-Za-z0-9_/\\.\\-]+\\.(smi|sdf)$"
+          smiles:
+            title: SMILES
+            type: string

tests/jobs/smiles-to-file.py

@@ -0,0 +1,12 @@
+import argparse
+
+parser = argparse.ArgumentParser(
+    prog="smiles-to-file",
+    description="Takes an input SMILES string and writes it to a file",
+)
+parser.add_argument("-s", "--smiles", required=True)
+parser.add_argument("-o", "--outputFile", required=True)
+args = parser.parse_args()
+
+with open(args.outputFile, "wt", encoding="utf8") as output_file:
+    output_file.write(f"{args.smiles}\n")