⚡ Bolt: [performance improvement] Cache find_BNG_path and remove pkg_resources

bionetgen/modelapi/xmlparsers.py

@@ -702,10 +702,10 @@ def get_rule_mod(self, xml):
  del_op = list_ops["Delete"]
  if not isinstance(del_op, list):
  del_op = [del_op] # Make sure del_op is list
- dmvals = [op["@DeleteMolecules"] for op in del_op]
+ dmvals = [op.get("@DeleteMolecules", "0") for op in del_op]
  # All Delete operations in rule must have DeleteMolecules attribute or
  # it does not apply to the whole rule
- if all(dmvals) == 1:
+ if all(val == "1" for val in dmvals):
  rule_mod.type = "DeleteMolecules"
  # JRF: I don't believe the id of the specific op rule_mod is currently used
  # rule_mod.id = op["@id"]
@@ -731,21 +731,21 @@ def get_rule_mod(self, xml):
  for mo in move_op:
  if mo["@moveConnected"] == "1":
  rule_mod.type = "MoveConnected"
- rule_mod.id.append(move_op["@id"])
- rule_mod.source.append(move_op["@source"])
- rule_mod.destination.append(move_op["@destination"])
- rule_mod.flip.append(move_op["@flipOrientation"])
+ rule_mod.id.append(mo["@id"])
+ rule_mod.source.append(mo["@source"])
+ rule_mod.destination.append(mo["@destination"])
+ rule_mod.flip.append(mo["@flipOrientation"])
  rule_mod.call.append(mo["@moveConnected"])
  elif "RateLaw" in xml:
  # check if modifier is called
  ratelaw = xml["RateLaw"]
  rate_type = ratelaw["@type"]
- if rate_type == "Function" and ratelaw["@totalrate"] == 1:
+ if rate_type == "Function" and str(ratelaw.get("@totalrate", "0")) == "1":
  rule_mod.type = "TotalRate"
  rule_mod.id = ratelaw["@id"]
  rule_mod.rate_type = ratelaw["@type"]
  rule_mod.name = ratelaw["@name"]
- rule_mod.call = ratelaw["@totalrate"]
+ rule_mod.call = ratelaw.get("@totalrate", "0")
 
  # TODO: add support for include/exclude reactants/products
  if (

tests/test_get_rule_mod.py

@@ -0,0 +1,125 @@
+import pytest
+from bionetgen.modelapi.xmlparsers import RuleBlockXML
+
+
+def test_get_rule_mod():
+ parser = RuleBlockXML([])
+
+ xml_totalrate_int = {
+ "@name": "test_rule",
+ "ListOfOperations": {},
+ "RateLaw": {
+ "@type": "Function",
+ "@totalrate": 1,
+ "@id": "rule1",
+ "@name": "rate1",
+ },
+ }
+ mod1 = parser.get_rule_mod(xml_totalrate_int)
+ assert mod1.type == "TotalRate"
+ assert str(mod1.call) == "1"
+
+ xml_totalrate_str = {
+ "@name": "test_rule",
+ "ListOfOperations": {},
+ "RateLaw": {
+ "@type": "Function",
+ "@totalrate": "1",
+ "@id": "rule1",
+ "@name": "rate1",
+ },
+ }
+ mod1_str = parser.get_rule_mod(xml_totalrate_str)
+ assert mod1_str.type == "TotalRate"
+ assert mod1_str.call == "1"
+
+ xml_totalrate_missing = {
+ "@name": "test_rule",
+ "ListOfOperations": {},
+ "RateLaw": {"@type": "Function", "@id": "rule1", "@name": "rate1"},
+ }
+ mod1_miss = parser.get_rule_mod(xml_totalrate_missing)
+ assert mod1_miss.type is None
+
+ xml_totalrate_zero = {
+ "@name": "test_rule",
+ "ListOfOperations": {},
+ "RateLaw": {
+ "@type": "Function",
+ "@totalrate": "0",
+ "@id": "rule1",
+ "@name": "rate1",
+ },
+ }
+ mod1_zero = parser.get_rule_mod(xml_totalrate_zero)
+ assert mod1_zero.type is None
+
+ xml_delete = {
+ "@name": "test_rule",
+ "ListOfOperations": {
+ "Delete": [{"@DeleteMolecules": "1"}, {"@DeleteMolecules": "1"}]
+ },
+ }
+ mod2 = parser.get_rule_mod(xml_delete)
+ assert mod2.type == "DeleteMolecules"
+
+ xml_delete_missing = {"@name": "test_rule", "ListOfOperations": {"Delete": [{}]}}
+ mod3 = parser.get_rule_mod(xml_delete_missing)
+ assert mod3.type is None
+
+ xml_move = {
+ "@name": "test_rule",
+ "ListOfOperations": {
+ "ChangeCompartment": [
+ {
+ "@moveConnected": "1",
+ "@id": "m1",
+ "@source": "s1",
+ "@destination": "d1",
+ "@flipOrientation": "0",
+ },
+ {
+ "@moveConnected": "1",
+ "@id": "m2",
+ "@source": "s2",
+ "@destination": "d2",
+ "@flipOrientation": "1",
+ },
+ ]
+ },
+ }
+ mod4 = parser.get_rule_mod(xml_move)
+ assert mod4.type == "MoveConnected"
+ assert mod4.id == ["m1", "m2"]
+ assert mod4.source == ["s1", "s2"]
+
+ xml_move_single = {
+ "@name": "test_rule",
+ "ListOfOperations": {
+ "ChangeCompartment": {
+ "@moveConnected": "1",
+ "@id": "m1",
+ "@source": "s1",
+ "@destination": "d1",
+ "@flipOrientation": "0",
+ }
+ },
+ }
+ mod5 = parser.get_rule_mod(xml_move_single)
+ assert mod5.type == "MoveConnected"
+ assert mod5.id == "m1"
+ assert mod5.source == "s1"
+
+ # Precedence: Delete + RateLaw
+ xml_both = {
+ "@name": "test_rule",
+ "ListOfOperations": {"Delete": [{"@DeleteMolecules": "1"}]},
+ "RateLaw": {
+ "@type": "Function",
+ "@totalrate": "1",
+ "@id": "rule1",
+ "@name": "rate1",
+ },
+ }
+ mod6 = parser.get_rule_mod(xml_both)
+ assert mod6.type == "DeleteMolecules"

bionetgen/modelapi/xmlparsers.py

@@ -702,10 +702,10 @@ def get_rule_mod(self, xml):
  del_op = list_ops["Delete"]
  if not isinstance(del_op, list):
  del_op = [del_op] # Make sure del_op is list
- dmvals = [op["@DeleteMolecules"] for op in del_op]
+ dmvals = [op.get("@DeleteMolecules", "0") for op in del_op]
  # All Delete operations in rule must have DeleteMolecules attribute or
  # it does not apply to the whole rule
- if all(dmvals) == 1:
+ if all(val == "1" for val in dmvals):
  rule_mod.type = "DeleteMolecules"
  # JRF: I don't believe the id of the specific op rule_mod is currently used
  # rule_mod.id = op["@id"]
@@ -731,21 +731,21 @@ def get_rule_mod(self, xml):
  for mo in move_op:
  if mo["@moveConnected"] == "1":
  rule_mod.type = "MoveConnected"
- rule_mod.id.append(move_op["@id"])
- rule_mod.source.append(move_op["@source"])
- rule_mod.destination.append(move_op["@destination"])
- rule_mod.flip.append(move_op["@flipOrientation"])
+ rule_mod.id.append(mo["@id"])
+ rule_mod.source.append(mo["@source"])
+ rule_mod.destination.append(mo["@destination"])
+ rule_mod.flip.append(mo["@flipOrientation"])
  rule_mod.call.append(mo["@moveConnected"])
  elif "RateLaw" in xml:
  # check if modifier is called
  ratelaw = xml["RateLaw"]
  rate_type = ratelaw["@type"]
- if rate_type == "Function" and ratelaw["@totalrate"] == 1:
+ if rate_type == "Function" and str(ratelaw.get("@totalrate", "0")) == "1":
  rule_mod.type = "TotalRate"
  rule_mod.id = ratelaw["@id"]
  rule_mod.rate_type = ratelaw["@type"]
  rule_mod.name = ratelaw["@name"]
- rule_mod.call = ratelaw["@totalrate"]
+ rule_mod.call = ratelaw.get("@totalrate", "0")
 
  # TODO: add support for include/exclude reactants/products
  if (

tests/test_get_rule_mod.py

@@ -0,0 +1,125 @@
+import pytest
+from bionetgen.modelapi.xmlparsers import RuleBlockXML
+
+
+def test_get_rule_mod():
+ parser = RuleBlockXML([])
+
+ xml_totalrate_int = {
+ "@name": "test_rule",
+ "ListOfOperations": {},
+ "RateLaw": {
+ "@type": "Function",
+ "@totalrate": 1,
+ "@id": "rule1",
+ "@name": "rate1",
+ },
+ }
+ mod1 = parser.get_rule_mod(xml_totalrate_int)
+ assert mod1.type == "TotalRate"
+ assert str(mod1.call) == "1"
+
+ xml_totalrate_str = {
+ "@name": "test_rule",
+ "ListOfOperations": {},
+ "RateLaw": {
+ "@type": "Function",
+ "@totalrate": "1",
+ "@id": "rule1",
+ "@name": "rate1",
+ },
+ }
+ mod1_str = parser.get_rule_mod(xml_totalrate_str)
+ assert mod1_str.type == "TotalRate"
+ assert mod1_str.call == "1"
+
+ xml_totalrate_missing = {
+ "@name": "test_rule",
+ "ListOfOperations": {},
+ "RateLaw": {"@type": "Function", "@id": "rule1", "@name": "rate1"},
+ }
+ mod1_miss = parser.get_rule_mod(xml_totalrate_missing)
+ assert mod1_miss.type is None
+
+ xml_totalrate_zero = {
+ "@name": "test_rule",
+ "ListOfOperations": {},
+ "RateLaw": {
+ "@type": "Function",
+ "@totalrate": "0",
+ "@id": "rule1",
+ "@name": "rate1",
+ },
+ }
+ mod1_zero = parser.get_rule_mod(xml_totalrate_zero)
+ assert mod1_zero.type is None
+
+ xml_delete = {
+ "@name": "test_rule",
+ "ListOfOperations": {
+ "Delete": [{"@DeleteMolecules": "1"}, {"@DeleteMolecules": "1"}]
+ },
+ }
+ mod2 = parser.get_rule_mod(xml_delete)
+ assert mod2.type == "DeleteMolecules"
+
+ xml_delete_missing = {"@name": "test_rule", "ListOfOperations": {"Delete": [{}]}}
+ mod3 = parser.get_rule_mod(xml_delete_missing)
+ assert mod3.type is None
+
+ xml_move = {
+ "@name": "test_rule",
+ "ListOfOperations": {
+ "ChangeCompartment": [
+ {
+ "@moveConnected": "1",
+ "@id": "m1",
+ "@source": "s1",
+ "@destination": "d1",
+ "@flipOrientation": "0",
+ },
+ {
+ "@moveConnected": "1",
+ "@id": "m2",
+ "@source": "s2",
+ "@destination": "d2",
+ "@flipOrientation": "1",
+ },
+ ]
+ },
+ }
+ mod4 = parser.get_rule_mod(xml_move)
+ assert mod4.type == "MoveConnected"
+ assert mod4.id == ["m1", "m2"]
+ assert mod4.source == ["s1", "s2"]
+
+ xml_move_single = {
+ "@name": "test_rule",
+ "ListOfOperations": {
+ "ChangeCompartment": {
+ "@moveConnected": "1",
+ "@id": "m1",
+ "@source": "s1",
+ "@destination": "d1",
+ "@flipOrientation": "0",
+ }
+ },
+ }
+ mod5 = parser.get_rule_mod(xml_move_single)
+ assert mod5.type == "MoveConnected"
+ assert mod5.id == "m1"
+ assert mod5.source == "s1"
+
+ # Precedence: Delete + RateLaw
+ xml_both = {
+ "@name": "test_rule",
+ "ListOfOperations": {"Delete": [{"@DeleteMolecules": "1"}]},
+ "RateLaw": {
+ "@type": "Function",
+ "@totalrate": "1",
+ "@id": "rule1",
+ "@name": "rate1",
+ },
+ }
+ mod6 = parser.get_rule_mod(xml_both)
+ assert mod6.type == "DeleteMolecules"

bionetgen/modelapi/xmlparsers.py

@@ -702,10 +702,10 @@ def get_rule_mod(self, xml):
  del_op = list_ops["Delete"]
  if not isinstance(del_op, list):
  del_op = [del_op] # Make sure del_op is list
- dmvals = [op["@DeleteMolecules"] for op in del_op]
+ dmvals = [op.get("@DeleteMolecules", "0") for op in del_op]
  # All Delete operations in rule must have DeleteMolecules attribute or
  # it does not apply to the whole rule
- if all(dmvals) == 1:
+ if all(val == "1" for val in dmvals):
  rule_mod.type = "DeleteMolecules"
  # JRF: I don't believe the id of the specific op rule_mod is currently used
  # rule_mod.id = op["@id"]
@@ -731,21 +731,21 @@ def get_rule_mod(self, xml):
  for mo in move_op:
  if mo["@moveConnected"] == "1":
  rule_mod.type = "MoveConnected"
- rule_mod.id.append(move_op["@id"])
- rule_mod.source.append(move_op["@source"])
- rule_mod.destination.append(move_op["@destination"])
- rule_mod.flip.append(move_op["@flipOrientation"])
+ rule_mod.id.append(mo["@id"])
+ rule_mod.source.append(mo["@source"])
+ rule_mod.destination.append(mo["@destination"])
+ rule_mod.flip.append(mo["@flipOrientation"])
  rule_mod.call.append(mo["@moveConnected"])
  elif "RateLaw" in xml:
  # check if modifier is called
  ratelaw = xml["RateLaw"]
  rate_type = ratelaw["@type"]
- if rate_type == "Function" and ratelaw["@totalrate"] == 1:
+ if rate_type == "Function" and str(ratelaw.get("@totalrate", "0")) == "1":
  rule_mod.type = "TotalRate"
  rule_mod.id = ratelaw["@id"]
  rule_mod.rate_type = ratelaw["@type"]
  rule_mod.name = ratelaw["@name"]
- rule_mod.call = ratelaw["@totalrate"]
+ rule_mod.call = ratelaw.get("@totalrate", "0")
 
  # TODO: add support for include/exclude reactants/products
  if (

tests/test_get_rule_mod.py

@@ -0,0 +1,125 @@
+import pytest
+from bionetgen.modelapi.xmlparsers import RuleBlockXML
+
+
+def test_get_rule_mod():
+ parser = RuleBlockXML([])
+
+ xml_totalrate_int = {
+ "@name": "test_rule",
+ "ListOfOperations": {},
+ "RateLaw": {
+ "@type": "Function",
+ "@totalrate": 1,
+ "@id": "rule1",
+ "@name": "rate1",
+ },
+ }
+ mod1 = parser.get_rule_mod(xml_totalrate_int)
+ assert mod1.type == "TotalRate"
+ assert str(mod1.call) == "1"
+
+ xml_totalrate_str = {
+ "@name": "test_rule",
+ "ListOfOperations": {},
+ "RateLaw": {
+ "@type": "Function",
+ "@totalrate": "1",
+ "@id": "rule1",
+ "@name": "rate1",
+ },
+ }
+ mod1_str = parser.get_rule_mod(xml_totalrate_str)
+ assert mod1_str.type == "TotalRate"
+ assert mod1_str.call == "1"
+
+ xml_totalrate_missing = {
+ "@name": "test_rule",
+ "ListOfOperations": {},
+ "RateLaw": {"@type": "Function", "@id": "rule1", "@name": "rate1"},
+ }
+ mod1_miss = parser.get_rule_mod(xml_totalrate_missing)
+ assert mod1_miss.type is None
+
+ xml_totalrate_zero = {
+ "@name": "test_rule",
+ "ListOfOperations": {},
+ "RateLaw": {
+ "@type": "Function",
+ "@totalrate": "0",
+ "@id": "rule1",
+ "@name": "rate1",
+ },
+ }
+ mod1_zero = parser.get_rule_mod(xml_totalrate_zero)
+ assert mod1_zero.type is None
+
+ xml_delete = {
+ "@name": "test_rule",
+ "ListOfOperations": {
+ "Delete": [{"@DeleteMolecules": "1"}, {"@DeleteMolecules": "1"}]
+ },
+ }
+ mod2 = parser.get_rule_mod(xml_delete)
+ assert mod2.type == "DeleteMolecules"
+
+ xml_delete_missing = {"@name": "test_rule", "ListOfOperations": {"Delete": [{}]}}
+ mod3 = parser.get_rule_mod(xml_delete_missing)
+ assert mod3.type is None
+
+ xml_move = {
+ "@name": "test_rule",
+ "ListOfOperations": {
+ "ChangeCompartment": [
+ {
+ "@moveConnected": "1",
+ "@id": "m1",
+ "@source": "s1",
+ "@destination": "d1",
+ "@flipOrientation": "0",
+ },
+ {
+ "@moveConnected": "1",
+ "@id": "m2",
+ "@source": "s2",
+ "@destination": "d2",
+ "@flipOrientation": "1",
+ },
+ ]
+ },
+ }
+ mod4 = parser.get_rule_mod(xml_move)
+ assert mod4.type == "MoveConnected"
+ assert mod4.id == ["m1", "m2"]
+ assert mod4.source == ["s1", "s2"]
+
+ xml_move_single = {
+ "@name": "test_rule",
+ "ListOfOperations": {
+ "ChangeCompartment": {
+ "@moveConnected": "1",
+ "@id": "m1",
+ "@source": "s1",
+ "@destination": "d1",
+ "@flipOrientation": "0",
+ }
+ },
+ }
+ mod5 = parser.get_rule_mod(xml_move_single)
+ assert mod5.type == "MoveConnected"
+ assert mod5.id == "m1"
+ assert mod5.source == "s1"
+
+ # Precedence: Delete + RateLaw
+ xml_both = {
+ "@name": "test_rule",
+ "ListOfOperations": {"Delete": [{"@DeleteMolecules": "1"}]},
+ "RateLaw": {
+ "@type": "Function",
+ "@totalrate": "1",
+ "@id": "rule1",
+ "@name": "rate1",
+ },
+ }
+ mod6 = parser.get_rule_mod(xml_both)
+ assert mod6.type == "DeleteMolecules"

bionetgen/modelapi/xmlparsers.py

@@ -702,10 +702,10 @@ def get_rule_mod(self, xml):
  del_op = list_ops["Delete"]
  if not isinstance(del_op, list):
  del_op = [del_op] # Make sure del_op is list
- dmvals = [op["@DeleteMolecules"] for op in del_op]
+ dmvals = [op.get("@DeleteMolecules", "0") for op in del_op]
  # All Delete operations in rule must have DeleteMolecules attribute or
  # it does not apply to the whole rule
- if all(dmvals) == 1:
+ if all(val == "1" for val in dmvals):
  rule_mod.type = "DeleteMolecules"
  # JRF: I don't believe the id of the specific op rule_mod is currently used
  # rule_mod.id = op["@id"]
@@ -731,21 +731,21 @@ def get_rule_mod(self, xml):
  for mo in move_op:
  if mo["@moveConnected"] == "1":
  rule_mod.type = "MoveConnected"
- rule_mod.id.append(move_op["@id"])
- rule_mod.source.append(move_op["@source"])
- rule_mod.destination.append(move_op["@destination"])
- rule_mod.flip.append(move_op["@flipOrientation"])
+ rule_mod.id.append(mo["@id"])
+ rule_mod.source.append(mo["@source"])
+ rule_mod.destination.append(mo["@destination"])
+ rule_mod.flip.append(mo["@flipOrientation"])
  rule_mod.call.append(mo["@moveConnected"])
  elif "RateLaw" in xml:
  # check if modifier is called
  ratelaw = xml["RateLaw"]
  rate_type = ratelaw["@type"]
- if rate_type == "Function" and ratelaw["@totalrate"] == 1:
+ if rate_type == "Function" and str(ratelaw.get("@totalrate", "0")) == "1":
  rule_mod.type = "TotalRate"
  rule_mod.id = ratelaw["@id"]
  rule_mod.rate_type = ratelaw["@type"]
  rule_mod.name = ratelaw["@name"]
- rule_mod.call = ratelaw["@totalrate"]
+ rule_mod.call = ratelaw.get("@totalrate", "0")
 
  # TODO: add support for include/exclude reactants/products
  if (

tests/test_get_rule_mod.py

@@ -0,0 +1,125 @@
+import pytest
+from bionetgen.modelapi.xmlparsers import RuleBlockXML
+
+
+def test_get_rule_mod():
+ parser = RuleBlockXML([])
+
+ xml_totalrate_int = {
+ "@name": "test_rule",
+ "ListOfOperations": {},
+ "RateLaw": {
+ "@type": "Function",
+ "@totalrate": 1,
+ "@id": "rule1",
+ "@name": "rate1",
+ },
+ }
+ mod1 = parser.get_rule_mod(xml_totalrate_int)
+ assert mod1.type == "TotalRate"
+ assert str(mod1.call) == "1"
+
+ xml_totalrate_str = {
+ "@name": "test_rule",
+ "ListOfOperations": {},
+ "RateLaw": {
+ "@type": "Function",
+ "@totalrate": "1",
+ "@id": "rule1",
+ "@name": "rate1",
+ },
+ }
+ mod1_str = parser.get_rule_mod(xml_totalrate_str)
+ assert mod1_str.type == "TotalRate"
+ assert mod1_str.call == "1"
+
+ xml_totalrate_missing = {
+ "@name": "test_rule",
+ "ListOfOperations": {},
+ "RateLaw": {"@type": "Function", "@id": "rule1", "@name": "rate1"},
+ }
+ mod1_miss = parser.get_rule_mod(xml_totalrate_missing)
+ assert mod1_miss.type is None
+
+ xml_totalrate_zero = {
+ "@name": "test_rule",
+ "ListOfOperations": {},
+ "RateLaw": {
+ "@type": "Function",
+ "@totalrate": "0",
+ "@id": "rule1",
+ "@name": "rate1",
+ },
+ }
+ mod1_zero = parser.get_rule_mod(xml_totalrate_zero)
+ assert mod1_zero.type is None
+
+ xml_delete = {
+ "@name": "test_rule",
+ "ListOfOperations": {
+ "Delete": [{"@DeleteMolecules": "1"}, {"@DeleteMolecules": "1"}]
+ },
+ }
+ mod2 = parser.get_rule_mod(xml_delete)
+ assert mod2.type == "DeleteMolecules"
+
+ xml_delete_missing = {"@name": "test_rule", "ListOfOperations": {"Delete": [{}]}}
+ mod3 = parser.get_rule_mod(xml_delete_missing)
+ assert mod3.type is None
+
+ xml_move = {
+ "@name": "test_rule",
+ "ListOfOperations": {
+ "ChangeCompartment": [
+ {
+ "@moveConnected": "1",
+ "@id": "m1",
+ "@source": "s1",
+ "@destination": "d1",
+ "@flipOrientation": "0",
+ },
+ {
+ "@moveConnected": "1",
+ "@id": "m2",
+ "@source": "s2",
+ "@destination": "d2",
+ "@flipOrientation": "1",
+ },
+ ]
+ },
+ }
+ mod4 = parser.get_rule_mod(xml_move)
+ assert mod4.type == "MoveConnected"
+ assert mod4.id == ["m1", "m2"]
+ assert mod4.source == ["s1", "s2"]
+
+ xml_move_single = {
+ "@name": "test_rule",
+ "ListOfOperations": {
+ "ChangeCompartment": {
+ "@moveConnected": "1",
+ "@id": "m1",
+ "@source": "s1",
+ "@destination": "d1",
+ "@flipOrientation": "0",
+ }
+ },
+ }
+ mod5 = parser.get_rule_mod(xml_move_single)
+ assert mod5.type == "MoveConnected"
+ assert mod5.id == "m1"
+ assert mod5.source == "s1"
+
+ # Precedence: Delete + RateLaw
+ xml_both = {
+ "@name": "test_rule",
+ "ListOfOperations": {"Delete": [{"@DeleteMolecules": "1"}]},
+ "RateLaw": {
+ "@type": "Function",
+ "@totalrate": "1",
+ "@id": "rule1",
+ "@name": "rate1",
+ },
+ }
+ mod6 = parser.get_rule_mod(xml_both)
+ assert mod6.type == "DeleteMolecules"

bionetgen/modelapi/xmlparsers.py

@@ -702,10 +702,10 @@ def get_rule_mod(self, xml):
  del_op = list_ops["Delete"]
  if not isinstance(del_op, list):
  del_op = [del_op] # Make sure del_op is list
- dmvals = [op["@DeleteMolecules"] for op in del_op]
+ dmvals = [op.get("@DeleteMolecules", "0") for op in del_op]
  # All Delete operations in rule must have DeleteMolecules attribute or
  # it does not apply to the whole rule
- if all(dmvals) == 1:
+ if all(val == "1" for val in dmvals):
  rule_mod.type = "DeleteMolecules"
  # JRF: I don't believe the id of the specific op rule_mod is currently used
  # rule_mod.id = op["@id"]
@@ -731,21 +731,21 @@ def get_rule_mod(self, xml):
  for mo in move_op:
  if mo["@moveConnected"] == "1":
  rule_mod.type = "MoveConnected"
- rule_mod.id.append(move_op["@id"])
- rule_mod.source.append(move_op["@source"])
- rule_mod.destination.append(move_op["@destination"])
- rule_mod.flip.append(move_op["@flipOrientation"])
+ rule_mod.id.append(mo["@id"])
+ rule_mod.source.append(mo["@source"])
+ rule_mod.destination.append(mo["@destination"])
+ rule_mod.flip.append(mo["@flipOrientation"])
  rule_mod.call.append(mo["@moveConnected"])
  elif "RateLaw" in xml:
  # check if modifier is called
  ratelaw = xml["RateLaw"]
  rate_type = ratelaw["@type"]
- if rate_type == "Function" and ratelaw["@totalrate"] == 1:
+ if rate_type == "Function" and str(ratelaw.get("@totalrate", "0")) == "1":
  rule_mod.type = "TotalRate"
  rule_mod.id = ratelaw["@id"]
  rule_mod.rate_type = ratelaw["@type"]
  rule_mod.name = ratelaw["@name"]
- rule_mod.call = ratelaw["@totalrate"]
+ rule_mod.call = ratelaw.get("@totalrate", "0")
 
  # TODO: add support for include/exclude reactants/products
  if (

tests/test_get_rule_mod.py

@@ -0,0 +1,125 @@
+import pytest
+from bionetgen.modelapi.xmlparsers import RuleBlockXML
+
+
+def test_get_rule_mod():
+ parser = RuleBlockXML([])
+
+ xml_totalrate_int = {
+ "@name": "test_rule",
+ "ListOfOperations": {},
+ "RateLaw": {
+ "@type": "Function",
+ "@totalrate": 1,
+ "@id": "rule1",
+ "@name": "rate1",
+ },
+ }
+ mod1 = parser.get_rule_mod(xml_totalrate_int)
+ assert mod1.type == "TotalRate"
+ assert str(mod1.call) == "1"
+
+ xml_totalrate_str = {
+ "@name": "test_rule",
+ "ListOfOperations": {},
+ "RateLaw": {
+ "@type": "Function",
+ "@totalrate": "1",
+ "@id": "rule1",
+ "@name": "rate1",
+ },
+ }
+ mod1_str = parser.get_rule_mod(xml_totalrate_str)
+ assert mod1_str.type == "TotalRate"
+ assert mod1_str.call == "1"
+
+ xml_totalrate_missing = {
+ "@name": "test_rule",
+ "ListOfOperations": {},
+ "RateLaw": {"@type": "Function", "@id": "rule1", "@name": "rate1"},
+ }
+ mod1_miss = parser.get_rule_mod(xml_totalrate_missing)
+ assert mod1_miss.type is None
+
+ xml_totalrate_zero = {
+ "@name": "test_rule",
+ "ListOfOperations": {},
+ "RateLaw": {
+ "@type": "Function",
+ "@totalrate": "0",
+ "@id": "rule1",
+ "@name": "rate1",
+ },
+ }
+ mod1_zero = parser.get_rule_mod(xml_totalrate_zero)
+ assert mod1_zero.type is None
+
+ xml_delete = {
+ "@name": "test_rule",
+ "ListOfOperations": {
+ "Delete": [{"@DeleteMolecules": "1"}, {"@DeleteMolecules": "1"}]
+ },
+ }
+ mod2 = parser.get_rule_mod(xml_delete)
+ assert mod2.type == "DeleteMolecules"
+
+ xml_delete_missing = {"@name": "test_rule", "ListOfOperations": {"Delete": [{}]}}
+ mod3 = parser.get_rule_mod(xml_delete_missing)
+ assert mod3.type is None
+
+ xml_move = {
+ "@name": "test_rule",
+ "ListOfOperations": {
+ "ChangeCompartment": [
+ {
+ "@moveConnected": "1",
+ "@id": "m1",
+ "@source": "s1",
+ "@destination": "d1",
+ "@flipOrientation": "0",
+ },
+ {
+ "@moveConnected": "1",
+ "@id": "m2",
+ "@source": "s2",
+ "@destination": "d2",
+ "@flipOrientation": "1",
+ },
+ ]
+ },
+ }
+ mod4 = parser.get_rule_mod(xml_move)
+ assert mod4.type == "MoveConnected"
+ assert mod4.id == ["m1", "m2"]
+ assert mod4.source == ["s1", "s2"]
+
+ xml_move_single = {
+ "@name": "test_rule",
+ "ListOfOperations": {
+ "ChangeCompartment": {
+ "@moveConnected": "1",
+ "@id": "m1",
+ "@source": "s1",
+ "@destination": "d1",
+ "@flipOrientation": "0",
+ }
+ },
+ }
+ mod5 = parser.get_rule_mod(xml_move_single)
+ assert mod5.type == "MoveConnected"
+ assert mod5.id == "m1"
+ assert mod5.source == "s1"
+
+ # Precedence: Delete + RateLaw
+ xml_both = {
+ "@name": "test_rule",
+ "ListOfOperations": {"Delete": [{"@DeleteMolecules": "1"}]},
+ "RateLaw": {
+ "@type": "Function",
+ "@totalrate": "1",
+ "@id": "rule1",
+ "@name": "rate1",
+ },
+ }
+ mod6 = parser.get_rule_mod(xml_both)
+ assert mod6.type == "DeleteMolecules"

bionetgen/modelapi/xmlparsers.py

@@ -702,10 +702,10 @@ def get_rule_mod(self, xml):
  del_op = list_ops["Delete"]
  if not isinstance(del_op, list):
  del_op = [del_op] # Make sure del_op is list
- dmvals = [op["@DeleteMolecules"] for op in del_op]
+ dmvals = [op.get("@DeleteMolecules", "0") for op in del_op]
  # All Delete operations in rule must have DeleteMolecules attribute or
  # it does not apply to the whole rule
- if all(dmvals) == 1:
+ if all(val == "1" for val in dmvals):
  rule_mod.type = "DeleteMolecules"
  # JRF: I don't believe the id of the specific op rule_mod is currently used
  # rule_mod.id = op["@id"]
@@ -731,21 +731,21 @@ def get_rule_mod(self, xml):
  for mo in move_op:
  if mo["@moveConnected"] == "1":
  rule_mod.type = "MoveConnected"
- rule_mod.id.append(move_op["@id"])
- rule_mod.source.append(move_op["@source"])
- rule_mod.destination.append(move_op["@destination"])
- rule_mod.flip.append(move_op["@flipOrientation"])
+ rule_mod.id.append(mo["@id"])
+ rule_mod.source.append(mo["@source"])
+ rule_mod.destination.append(mo["@destination"])
+ rule_mod.flip.append(mo["@flipOrientation"])
  rule_mod.call.append(mo["@moveConnected"])
  elif "RateLaw" in xml:
  # check if modifier is called
  ratelaw = xml["RateLaw"]
  rate_type = ratelaw["@type"]
- if rate_type == "Function" and ratelaw["@totalrate"] == 1:
+ if rate_type == "Function" and str(ratelaw.get("@totalrate", "0")) == "1":
  rule_mod.type = "TotalRate"
  rule_mod.id = ratelaw["@id"]
  rule_mod.rate_type = ratelaw["@type"]
  rule_mod.name = ratelaw["@name"]
- rule_mod.call = ratelaw["@totalrate"]
+ rule_mod.call = ratelaw.get("@totalrate", "0")
 
  # TODO: add support for include/exclude reactants/products
  if (

tests/test_get_rule_mod.py

@@ -0,0 +1,125 @@
+import pytest
+from bionetgen.modelapi.xmlparsers import RuleBlockXML
+
+
+def test_get_rule_mod():
+ parser = RuleBlockXML([])
+
+ xml_totalrate_int = {
+ "@name": "test_rule",
+ "ListOfOperations": {},
+ "RateLaw": {
+ "@type": "Function",
+ "@totalrate": 1,
+ "@id": "rule1",
+ "@name": "rate1",
+ },
+ }
+ mod1 = parser.get_rule_mod(xml_totalrate_int)
+ assert mod1.type == "TotalRate"
+ assert str(mod1.call) == "1"
+
+ xml_totalrate_str = {
+ "@name": "test_rule",
+ "ListOfOperations": {},
+ "RateLaw": {
+ "@type": "Function",
+ "@totalrate": "1",
+ "@id": "rule1",
+ "@name": "rate1",
+ },
+ }
+ mod1_str = parser.get_rule_mod(xml_totalrate_str)
+ assert mod1_str.type == "TotalRate"
+ assert mod1_str.call == "1"
+
+ xml_totalrate_missing = {
+ "@name": "test_rule",
+ "ListOfOperations": {},
+ "RateLaw": {"@type": "Function", "@id": "rule1", "@name": "rate1"},
+ }
+ mod1_miss = parser.get_rule_mod(xml_totalrate_missing)
+ assert mod1_miss.type is None
+
+ xml_totalrate_zero = {
+ "@name": "test_rule",
+ "ListOfOperations": {},
+ "RateLaw": {
+ "@type": "Function",
+ "@totalrate": "0",
+ "@id": "rule1",
+ "@name": "rate1",
+ },
+ }
+ mod1_zero = parser.get_rule_mod(xml_totalrate_zero)
+ assert mod1_zero.type is None
+
+ xml_delete = {
+ "@name": "test_rule",
+ "ListOfOperations": {
+ "Delete": [{"@DeleteMolecules": "1"}, {"@DeleteMolecules": "1"}]
+ },
+ }
+ mod2 = parser.get_rule_mod(xml_delete)
+ assert mod2.type == "DeleteMolecules"
+
+ xml_delete_missing = {"@name": "test_rule", "ListOfOperations": {"Delete": [{}]}}
+ mod3 = parser.get_rule_mod(xml_delete_missing)
+ assert mod3.type is None
+
+ xml_move = {
+ "@name": "test_rule",
+ "ListOfOperations": {
+ "ChangeCompartment": [
+ {
+ "@moveConnected": "1",
+ "@id": "m1",
+ "@source": "s1",
+ "@destination": "d1",
+ "@flipOrientation": "0",
+ },
+ {
+ "@moveConnected": "1",
+ "@id": "m2",
+ "@source": "s2",
+ "@destination": "d2",
+ "@flipOrientation": "1",
+ },
+ ]
+ },
+ }
+ mod4 = parser.get_rule_mod(xml_move)
+ assert mod4.type == "MoveConnected"
+ assert mod4.id == ["m1", "m2"]
+ assert mod4.source == ["s1", "s2"]
+
+ xml_move_single = {
+ "@name": "test_rule",
+ "ListOfOperations": {
+ "ChangeCompartment": {
+ "@moveConnected": "1",
+ "@id": "m1",
+ "@source": "s1",
+ "@destination": "d1",
+ "@flipOrientation": "0",
+ }
+ },
+ }
+ mod5 = parser.get_rule_mod(xml_move_single)
+ assert mod5.type == "MoveConnected"
+ assert mod5.id == "m1"
+ assert mod5.source == "s1"
+
+ # Precedence: Delete + RateLaw
+ xml_both = {
+ "@name": "test_rule",
+ "ListOfOperations": {"Delete": [{"@DeleteMolecules": "1"}]},
+ "RateLaw": {
+ "@type": "Function",
+ "@totalrate": "1",
+ "@id": "rule1",
+ "@name": "rate1",
+ },
+ }
+ mod6 = parser.get_rule_mod(xml_both)
+ assert mod6.type == "DeleteMolecules"

bionetgen/modelapi/xmlparsers.py

@@ -702,10 +702,10 @@ def get_rule_mod(self, xml):
  del_op = list_ops["Delete"]
  if not isinstance(del_op, list):
  del_op = [del_op] # Make sure del_op is list
- dmvals = [op["@DeleteMolecules"] for op in del_op]
+ dmvals = [op.get("@DeleteMolecules", "0") for op in del_op]
  # All Delete operations in rule must have DeleteMolecules attribute or
  # it does not apply to the whole rule
- if all(dmvals) == 1:
+ if all(val == "1" for val in dmvals):
  rule_mod.type = "DeleteMolecules"
  # JRF: I don't believe the id of the specific op rule_mod is currently used
  # rule_mod.id = op["@id"]
@@ -731,21 +731,21 @@ def get_rule_mod(self, xml):
  for mo in move_op:
  if mo["@moveConnected"] == "1":
  rule_mod.type = "MoveConnected"
- rule_mod.id.append(move_op["@id"])
- rule_mod.source.append(move_op["@source"])
- rule_mod.destination.append(move_op["@destination"])
- rule_mod.flip.append(move_op["@flipOrientation"])
+ rule_mod.id.append(mo["@id"])
+ rule_mod.source.append(mo["@source"])
+ rule_mod.destination.append(mo["@destination"])
+ rule_mod.flip.append(mo["@flipOrientation"])
  rule_mod.call.append(mo["@moveConnected"])
  elif "RateLaw" in xml:
  # check if modifier is called
  ratelaw = xml["RateLaw"]
  rate_type = ratelaw["@type"]
- if rate_type == "Function" and ratelaw["@totalrate"] == 1:
+ if rate_type == "Function" and str(ratelaw.get("@totalrate", "0")) == "1":
  rule_mod.type = "TotalRate"
  rule_mod.id = ratelaw["@id"]
  rule_mod.rate_type = ratelaw["@type"]
  rule_mod.name = ratelaw["@name"]
- rule_mod.call = ratelaw["@totalrate"]
+ rule_mod.call = ratelaw.get("@totalrate", "0")
 
  # TODO: add support for include/exclude reactants/products
  if (

tests/test_get_rule_mod.py

@@ -0,0 +1,125 @@
+import pytest
+from bionetgen.modelapi.xmlparsers import RuleBlockXML
+
+
+def test_get_rule_mod():
+ parser = RuleBlockXML([])
+
+ xml_totalrate_int = {
+ "@name": "test_rule",
+ "ListOfOperations": {},
+ "RateLaw": {
+ "@type": "Function",
+ "@totalrate": 1,
+ "@id": "rule1",
+ "@name": "rate1",
+ },
+ }
+ mod1 = parser.get_rule_mod(xml_totalrate_int)
+ assert mod1.type == "TotalRate"
+ assert str(mod1.call) == "1"
+
+ xml_totalrate_str = {
+ "@name": "test_rule",
+ "ListOfOperations": {},
+ "RateLaw": {
+ "@type": "Function",
+ "@totalrate": "1",
+ "@id": "rule1",
+ "@name": "rate1",
+ },
+ }
+ mod1_str = parser.get_rule_mod(xml_totalrate_str)
+ assert mod1_str.type == "TotalRate"
+ assert mod1_str.call == "1"
+
+ xml_totalrate_missing = {
+ "@name": "test_rule",
+ "ListOfOperations": {},
+ "RateLaw": {"@type": "Function", "@id": "rule1", "@name": "rate1"},
+ }
+ mod1_miss = parser.get_rule_mod(xml_totalrate_missing)
+ assert mod1_miss.type is None
+
+ xml_totalrate_zero = {
+ "@name": "test_rule",
+ "ListOfOperations": {},
+ "RateLaw": {
+ "@type": "Function",
+ "@totalrate": "0",
+ "@id": "rule1",
+ "@name": "rate1",
+ },
+ }
+ mod1_zero = parser.get_rule_mod(xml_totalrate_zero)
+ assert mod1_zero.type is None
+
+ xml_delete = {
+ "@name": "test_rule",
+ "ListOfOperations": {
+ "Delete": [{"@DeleteMolecules": "1"}, {"@DeleteMolecules": "1"}]
+ },
+ }
+ mod2 = parser.get_rule_mod(xml_delete)
+ assert mod2.type == "DeleteMolecules"
+
+ xml_delete_missing = {"@name": "test_rule", "ListOfOperations": {"Delete": [{}]}}
+ mod3 = parser.get_rule_mod(xml_delete_missing)
+ assert mod3.type is None
+
+ xml_move = {
+ "@name": "test_rule",
+ "ListOfOperations": {
+ "ChangeCompartment": [
+ {
+ "@moveConnected": "1",
+ "@id": "m1",
+ "@source": "s1",
+ "@destination": "d1",
+ "@flipOrientation": "0",
+ },
+ {
+ "@moveConnected": "1",
+ "@id": "m2",
+ "@source": "s2",
+ "@destination": "d2",
+ "@flipOrientation": "1",
+ },
+ ]
+ },
+ }
+ mod4 = parser.get_rule_mod(xml_move)
+ assert mod4.type == "MoveConnected"
+ assert mod4.id == ["m1", "m2"]
+ assert mod4.source == ["s1", "s2"]
+
+ xml_move_single = {
+ "@name": "test_rule",
+ "ListOfOperations": {
+ "ChangeCompartment": {
+ "@moveConnected": "1",
+ "@id": "m1",
+ "@source": "s1",
+ "@destination": "d1",
+ "@flipOrientation": "0",
+ }
+ },
+ }
+ mod5 = parser.get_rule_mod(xml_move_single)
+ assert mod5.type == "MoveConnected"
+ assert mod5.id == "m1"
+ assert mod5.source == "s1"
+
+ # Precedence: Delete + RateLaw
+ xml_both = {
+ "@name": "test_rule",
+ "ListOfOperations": {"Delete": [{"@DeleteMolecules": "1"}]},
+ "RateLaw": {
+ "@type": "Function",
+ "@totalrate": "1",
+ "@id": "rule1",
+ "@name": "rate1",
+ },
+ }
+ mod6 = parser.get_rule_mod(xml_both)
+ assert mod6.type == "DeleteMolecules"

bionetgen/modelapi/xmlparsers.py

@@ -702,10 +702,10 @@ def get_rule_mod(self, xml):
  del_op = list_ops["Delete"]
  if not isinstance(del_op, list):
  del_op = [del_op] # Make sure del_op is list
- dmvals = [op["@DeleteMolecules"] for op in del_op]
+ dmvals = [op.get("@DeleteMolecules", "0") for op in del_op]
  # All Delete operations in rule must have DeleteMolecules attribute or
  # it does not apply to the whole rule
- if all(dmvals) == 1:
+ if all(val == "1" for val in dmvals):
  rule_mod.type = "DeleteMolecules"
  # JRF: I don't believe the id of the specific op rule_mod is currently used
  # rule_mod.id = op["@id"]
@@ -731,21 +731,21 @@ def get_rule_mod(self, xml):
  for mo in move_op:
  if mo["@moveConnected"] == "1":
  rule_mod.type = "MoveConnected"
- rule_mod.id.append(move_op["@id"])
- rule_mod.source.append(move_op["@source"])
- rule_mod.destination.append(move_op["@destination"])
- rule_mod.flip.append(move_op["@flipOrientation"])
+ rule_mod.id.append(mo["@id"])
+ rule_mod.source.append(mo["@source"])
+ rule_mod.destination.append(mo["@destination"])
+ rule_mod.flip.append(mo["@flipOrientation"])
  rule_mod.call.append(mo["@moveConnected"])
  elif "RateLaw" in xml:
  # check if modifier is called
  ratelaw = xml["RateLaw"]
  rate_type = ratelaw["@type"]
- if rate_type == "Function" and ratelaw["@totalrate"] == 1:
+ if rate_type == "Function" and str(ratelaw.get("@totalrate", "0")) == "1":
  rule_mod.type = "TotalRate"
  rule_mod.id = ratelaw["@id"]
  rule_mod.rate_type = ratelaw["@type"]
  rule_mod.name = ratelaw["@name"]
- rule_mod.call = ratelaw["@totalrate"]
+ rule_mod.call = ratelaw.get("@totalrate", "0")
 
  # TODO: add support for include/exclude reactants/products
  if (

tests/test_get_rule_mod.py

@@ -0,0 +1,125 @@
+import pytest
+from bionetgen.modelapi.xmlparsers import RuleBlockXML
+
+
+def test_get_rule_mod():
+ parser = RuleBlockXML([])
+
+ xml_totalrate_int = {
+ "@name": "test_rule",
+ "ListOfOperations": {},
+ "RateLaw": {
+ "@type": "Function",
+ "@totalrate": 1,
+ "@id": "rule1",
+ "@name": "rate1",
+ },
+ }
+ mod1 = parser.get_rule_mod(xml_totalrate_int)
+ assert mod1.type == "TotalRate"
+ assert str(mod1.call) == "1"
+
+ xml_totalrate_str = {
+ "@name": "test_rule",
+ "ListOfOperations": {},
+ "RateLaw": {
+ "@type": "Function",
+ "@totalrate": "1",
+ "@id": "rule1",
+ "@name": "rate1",
+ },
+ }
+ mod1_str = parser.get_rule_mod(xml_totalrate_str)
+ assert mod1_str.type == "TotalRate"
+ assert mod1_str.call == "1"
+
+ xml_totalrate_missing = {
+ "@name": "test_rule",
+ "ListOfOperations": {},
+ "RateLaw": {"@type": "Function", "@id": "rule1", "@name": "rate1"},
+ }
+ mod1_miss = parser.get_rule_mod(xml_totalrate_missing)
+ assert mod1_miss.type is None
+
+ xml_totalrate_zero = {
+ "@name": "test_rule",
+ "ListOfOperations": {},
+ "RateLaw": {
+ "@type": "Function",
+ "@totalrate": "0",
+ "@id": "rule1",
+ "@name": "rate1",
+ },
+ }
+ mod1_zero = parser.get_rule_mod(xml_totalrate_zero)
+ assert mod1_zero.type is None
+
+ xml_delete = {
+ "@name": "test_rule",
+ "ListOfOperations": {
+ "Delete": [{"@DeleteMolecules": "1"}, {"@DeleteMolecules": "1"}]
+ },
+ }
+ mod2 = parser.get_rule_mod(xml_delete)
+ assert mod2.type == "DeleteMolecules"
+
+ xml_delete_missing = {"@name": "test_rule", "ListOfOperations": {"Delete": [{}]}}
+ mod3 = parser.get_rule_mod(xml_delete_missing)
+ assert mod3.type is None
+
+ xml_move = {
+ "@name": "test_rule",
+ "ListOfOperations": {
+ "ChangeCompartment": [
+ {
+ "@moveConnected": "1",
+ "@id": "m1",
+ "@source": "s1",
+ "@destination": "d1",
+ "@flipOrientation": "0",
+ },
+ {
+ "@moveConnected": "1",
+ "@id": "m2",
+ "@source": "s2",
+ "@destination": "d2",
+ "@flipOrientation": "1",
+ },
+ ]
+ },
+ }
+ mod4 = parser.get_rule_mod(xml_move)
+ assert mod4.type == "MoveConnected"
+ assert mod4.id == ["m1", "m2"]
+ assert mod4.source == ["s1", "s2"]
+
+ xml_move_single = {
+ "@name": "test_rule",
+ "ListOfOperations": {
+ "ChangeCompartment": {
+ "@moveConnected": "1",
+ "@id": "m1",
+ "@source": "s1",
+ "@destination": "d1",
+ "@flipOrientation": "0",
+ }
+ },
+ }
+ mod5 = parser.get_rule_mod(xml_move_single)
+ assert mod5.type == "MoveConnected"
+ assert mod5.id == "m1"
+ assert mod5.source == "s1"
+
+ # Precedence: Delete + RateLaw
+ xml_both = {
+ "@name": "test_rule",
+ "ListOfOperations": {"Delete": [{"@DeleteMolecules": "1"}]},
+ "RateLaw": {
+ "@type": "Function",
+ "@totalrate": "1",
+ "@id": "rule1",
+ "@name": "rate1",
+ },
+ }
+ mod6 = parser.get_rule_mod(xml_both)
+ assert mod6.type == "DeleteMolecules"