Unify networkparser, structs, and rulemod error handling

bionetgen/modelapi/rulemod.py

@@ -1,3 +1,6 @@
+from bionetgen.core.exc import BNGParseError
+
+
 class RuleMod:
     """
     Rule modifiers class for storage and printing.
@@ -42,4 +45,6 @@ def type(self, val):
         if val in self.valid_mod_names or val is None:
             self._type = val
         else:
-            print(f"Rule modifier type {val} is not a valid type")
+            raise BNGParseError(
+                message=f": Rule modifier type {val} is not a valid type"
+            )

bionetgen/modelapi/structs.py

@@ -69,7 +69,7 @@ def line_label(self, val) -> None:
         try:
             ll = int(val)
             self._line_label = "{} ".format(ll)
-        except:
+        except (TypeError, ValueError):
             self._line_label = "{}: ".format(val)
 
     def print_line(self) -> str:
@@ -423,7 +423,12 @@ def set_rate_constants(self, rate_cts):
             self.rate_constants = [rate_cts[0], rate_cts[1]]
             self.bidirectional = True
         else:
-            print("1 or 2 rate constants allowed")
+            raise BNGParseError(
+                message=(
+                    f": Rule {self.name} requires 1 or 2 rate constants, "
+                    f"got {len(rate_cts)}"
+                )
+            )
 
     def gen_string(self):
         if self.bidirectional:

bionetgen/network/networkparser.py

@@ -1,4 +1,6 @@
 import re, os
+from bionetgen.core.exc import BNGParseError
+from bionetgen.core.utils.logging import BNGLogger
 from bionetgen.main import BioNetGen
 from bionetgen.network.blocks import (
     NetworkGroupBlock,
@@ -16,6 +18,7 @@
 app.setup()
 conf = app.config["bionetgen"]
 def_bng_path = conf["bngpath"]
+logger = BNGLogger()
 
 
 class BNGNetworkParser:
@@ -92,16 +95,25 @@ def parse_network(self, network_obj) -> None:
             spec_block = NetworkSpeciesBlock()
             for iline in range(sblock[0] + 1, sblock[1]):
                 m = re.match("([^#]*)(#.*)?", self.network_lines[iline])
-                if m.group(1).strip() != "":
-                    splt = m.group(1).split()
+                if m is None:
+                    continue
+                line_text = m.group(1) or ""
+                if line_text.strip() != "":
+                    splt = line_text.split()
+                    if len(splt) < 3:
+                        msg = (
+                            f"Malformed species line at {self.path}:{iline + 1}; "
+                            "expected '<id> <species> <count>', "
+                            f"got {line_text.strip()!r}"
+                        )
+                        logger.error(
+                            msg,
+                            loc=f"{__file__} : BNGNetworkParser.parse_network()",
+                        )
+                        raise BNGParseError(self.path, message=f": {msg}")
                     sid = splt[0]
                     name = splt[1]
-                    try:
-                        count = splt[2]
-                    except:
-                        import IPython
-
-                        IPython.embed()
+                    count = splt[2]
                     spec_block.add_species(sid, name, count)
             network_obj.add_block(spec_block)
         # add reactions
@@ -137,4 +149,3 @@ def parse_network(self, network_obj) -> None:
                     comment = m.group(2)
                     grps_block.add_group(rid, name, members, comment=comment)
             network_obj.add_block(grps_block)
-        # import IPython,sys;IPython.embed();sys.exit()

bionetgen/network/structs.py

@@ -69,7 +69,7 @@ def line_label(self, val) -> None:
         try:
             ll = int(val)
             self._line_label = "{} ".format(ll)
-        except:
+        except (TypeError, ValueError):
             self._line_label = "{}: ".format(val)
 
     def print_line(self) -> str:

tests/test_networkparser_structs_errors.py

@@ -0,0 +1,88 @@
+from unittest.mock import patch
+
+import pytest
+
+from bionetgen.core.exc import BNGParseError
+from bionetgen.modelapi.rulemod import RuleMod
+from bionetgen.modelapi.structs import Parameter, Rule
+from bionetgen.network.structs import NetworkObj
+
+
+class FakePattern:
+    def __init__(self, text):
+        self._text = text
+
+    def __str__(self):
+        return self._text
+
+
+NET_MALFORMED_SPECIES = """\
+# NET file
+begin species
+  1 A(b)
+end species
+"""
+
+
+def test_networkparser_malformed_species_line_raises_parse_error(tmp_path):
+    net_file = tmp_path / "bad_species.net"
+    net_file.write_text(NET_MALFORMED_SPECIES)
+    from bionetgen.network import networkparser as networkparser_module
+    from bionetgen.network.network import Network
+
+    with patch.object(networkparser_module, "logger") as mock_logger:
+        with pytest.raises(BNGParseError, match="Malformed species line"):
+            Network(str(net_file))
+
+    mock_logger.error.assert_called_once()
+    error_args, error_kwargs = mock_logger.error.call_args
+    assert "Malformed species line" in error_args[0]
+    assert "expected '<id> <species> <count>'" in error_args[0]
+    assert "bad_species.net:3" in error_args[0]
+    assert "BNGNetworkParser.parse_network()" in error_kwargs["loc"]
+
+
+def test_model_struct_line_label_none_uses_string_fallback():
+    parameter = Parameter("k1", "1")
+    parameter.line_label = None
+    assert parameter.line_label == "None: "
+
+
+def test_network_struct_line_label_none_uses_string_fallback():
+    obj = NetworkObj()
+    obj.line_label = None
+    assert obj.line_label == "None: "
+
+
+def test_rule_set_rate_constants_invalid_length_raises_parse_error():
+    rule = Rule(
+        name="r",
+        reactants=[FakePattern("A()")],
+        products=[FakePattern("B()")],
+        rate_constants=("k1",),
+    )
+    with pytest.raises(BNGParseError, match="1 or 2 rate constants"):
+        rule.set_rate_constants(("k1", "k2", "k3"))
+    assert rule.bidirectional is False
+    assert rule.rate_constants == ["k1"]
+
+
+def test_rule_init_without_rate_constants_raises_parse_error():
+    with pytest.raises(BNGParseError, match="1 or 2 rate constants"):
+        Rule(
+            name="r",
+            reactants=[FakePattern("A()")],
+            products=[FakePattern("B()")],
+        )
+
+
+def test_rulemod_invalid_init_raises_parse_error():
+    with pytest.raises(BNGParseError, match="Rule modifier type InvalidMod"):
+        RuleMod(mod_type="InvalidMod")
+
+
+def test_rulemod_invalid_setter_raises_parse_error():
+    rule_mod = RuleMod()
+    with pytest.raises(BNGParseError, match="Rule modifier type BadType"):
+        rule_mod.type = "BadType"
+    assert rule_mod.type is None