review fixes

prymer/primer3/primer3.py

@@ -385,9 +385,8 @@ def design(self, design_input: Primer3Input) -> Primer3Result:  # noqa: C901
         seq_args = {}
         global_args = {}
         for tag, value in assembled_primer3_tags.items():
-            tag_str = f"{tag}"
-            if tag_str.startswith("SEQUENCE"):
-                seq_args[tag_str] = value
+            if tag.is_sequence_arg:
+                seq_args[tag] = value
             else:
                 global_args[tag] = value
         design_primers_retval = primer3.design_primers(seq_args=seq_args, global_args=global_args)
@@ -397,22 +396,16 @@ def design(self, design_input: Primer3Input) -> Primer3Result:  # noqa: C901
             # Because Primer3 will emit both the input given and the output generated, we
             # discard the input that is echo'ed back by looking for tags (keys)
             # that do not match any Primer3InputTag
-            if not any(key == item.value for item in Primer3InputTag):
+            if key not in Primer3InputTag:
                 primer3_results[key] = value
 
-        def primer3_error(message: str) -> None:
-            """Formats the Primer3 error and raises a ValueError."""
-            error_message = f"{message}: "
-            # add in any reported PRIMER_ERROR
-            if "PRIMER_ERROR" in primer3_results:
-                error_message += primer3_results["PRIMER_ERROR"]
-            # raise the exception now
-            raise ValueError(error_message)
-
         # Check for any errors.  Typically, these are in error_lines, but also the results can
         # contain the PRIMER_ERROR key.
-        if "PRIMER_ERROR" in primer3_results :
-            primer3_error("Primer3 failed")
+        if "PRIMER_ERROR" in primer3_results:
+            if "PRIMER_ERROR" in primer3_results:
+                raise ValueError("Primer3 failed: " + primer3_results["PRIMER_ERROR"])
+            else:
+                raise ValueError("Primer3 failed")
 
         match design_input.task:
             case DesignPrimerPairsTask():  # Primer pair design

prymer/primer3/primer3_input_tag.py

@@ -29,6 +29,18 @@ class Primer3InputTag(UppercaseStrEnum):
        Errors in these "global" input tags are fatal.
     """
 
+    # Developer note: sequence-specific tags must be specified prior to global tags
+
+    @property
+    def is_sequence_arg(self) -> bool:
+        """True if this is a sequence input tag (query-specific)"""
+        return self.name.startswith("SEQUENCE")
+
+    @property
+    def is_global_arg(self) -> bool:
+        """True if this is a global input tags (will persist across primer3 queries)"""
+        return not self.is_sequence_arg
+
     # Sequence input tags; query-specific
     SEQUENCE_EXCLUDED_REGION = auto()
     SEQUENCE_INCLUDED_REGION = auto()

tests/primer3/test_primer3.py

@@ -361,9 +361,7 @@ def test_fasta_close_valid(
         task=DesignLeftPrimersTask(),
     )
 
-    with pytest.raises(
-        ValueError, match="I/O operation on closed file"
-    ):
+    with pytest.raises(ValueError, match="I/O operation on closed file"):
         designer.design(design_input=design_input)
 
 

tests/primer3/test_primer3_input_tag.py

@@ -0,0 +1,9 @@
+from prymer.primer3 import Primer3InputTag
+
+
+def test_primer3_input_tag() -> None:
+    # 17
+    for tag in Primer3InputTag:
+        assert tag.is_sequence_arg == tag.startswith("S")
+        assert tag.is_global_arg == tag.startswith("P")
+        assert tag.is_global_arg != tag.is_sequence_arg