From 29357eccde69a00a889034882c7c38d771ff1042 Mon Sep 17 00:00:00 2001
From: cjarmstrong97 <cjarmstrong97@gmail.com>
Date: Tue, 21 Sep 2021 13:21:19 -0400
Subject: [PATCH 1/2] Beginning of parsing branch

---
 bionetgen/modelapi/pattern.py    |  4 ++++
 bionetgen/modelapi/xmlparsers.py | 22 +++++++++++++++++-----
 tests/models/hybrid_test.bngl    |  7 +++++--
 3 files changed, 26 insertions(+), 7 deletions(-)

diff --git a/bionetgen/modelapi/pattern.py b/bionetgen/modelapi/pattern.py
index 0205453..810233b 100644
--- a/bionetgen/modelapi/pattern.py
+++ b/bionetgen/modelapi/pattern.py
@@ -31,6 +31,8 @@ def __init__(self, molecules=[], bonds=None, compartment=None, label=None):
         self._label = label
         self.fixed = False
         self.MatchOnce = False
+        self.relation = None
+        self.quantity = None
 
     @property
     def compartment(self):
@@ -73,6 +75,8 @@ def __str__(self):
             if imol > 0:
                 sstr += "."
             sstr += str(mol)
+        if self.relation is not None:
+            sstr += f"{self.relation}{self.quantity}"
         return sstr
 
     def __repr__(self):
diff --git a/bionetgen/modelapi/xmlparsers.py b/bionetgen/modelapi/xmlparsers.py
index ff9f9e3..f607098 100644
--- a/bionetgen/modelapi/xmlparsers.py
+++ b/bionetgen/modelapi/xmlparsers.py
@@ -151,17 +151,29 @@ def parse_xml(self, xml) -> Pattern:
             bonds = BondsXML()
             pattern._bonds = bonds
             self._bonds = bonds
-        #
+        # check for compartment and add if exists
         if "@compartment" in xml:
             pattern.compartment = xml["@compartment"]
-        #
+        # check for label and add if exists
         if "@label" in xml:
             pattern.label = xml["@label"]
-        #
+        # check to see if pattern is fixed
         if "@Fixed" in xml:
             if xml["@Fixed"] == "1":
                 pattern.fixed = True
-        #
+        # check for relation & quantity, add if exist
+        if ("@relation" in xml) and ("@quantity" in xml):
+            relation = xml["@relation"]
+            quantity = xml["@quantity"]
+            pattern.relation = relation
+            try:
+                n = int(pattern.quantity)
+                f = float(pattern.quantity)
+                if n == f:
+                    pattern.quantity = quantity
+            except ValueError as e:
+                print("Quantity needs to be an integer")
+        # check for either list of molecules or single molecule, add if exist
         mols = xml["ListOfMolecules"]["Molecule"]
         molecules = []
         if isinstance(mols, list):
@@ -262,7 +274,7 @@ def parse_xml(self, xml) -> list:
         return patterns
 
 
-###### Parsers  ######
+###### Parsers ######
 class ParameterBlockXML(XMLObj):
     """
     PatternBlock XML parser, derived from XMLObj. Creates
diff --git a/tests/models/hybrid_test.bngl b/tests/models/hybrid_test.bngl
index a8bf61a..6887904 100644
--- a/tests/models/hybrid_test.bngl
+++ b/tests/models/hybrid_test.bngl
@@ -31,6 +31,9 @@ begin observables
 	Species    R3       R==3
 	Species    R4       R==4
     Species    R5       R>4
+	Species    R5le		R<=4
+	Species	   R5l		R<4
+	Species	   R5ge		R>=4
 end observables
 begin reaction rules
 	R(l!1).L(r!1)          ->  R(l)  +  L(r)          koff
@@ -45,5 +48,5 @@ end population maps
 end model
 
 ## actions ##
-generate_hybrid_model({overwrite=>1, execute=>1, verbose=>1, safe=>0, actions=>["writeXML()"]})
-
+#generate_hybrid_model({overwrite=>1, execute=>1, verbose=>1, safe=>0, actions=>["writeXML()"]})
+writeXML()

From 2de69a1dd70070970d092c8ebfe3d8b466a3b5a2 Mon Sep 17 00:00:00 2001
From: cjarmstrong97 <cjarmstrong97@gmail.com>
Date: Tue, 21 Sep 2021 15:10:04 -0400
Subject: [PATCH 2/2] Ensured parsing of every element of PatternQuantifier

---
 bionetgen/modelapi/xmlparsers.py | 4 ++--
 tests/models/hybrid_test.bngl    | 8 ++------
 2 files changed, 4 insertions(+), 8 deletions(-)

diff --git a/bionetgen/modelapi/xmlparsers.py b/bionetgen/modelapi/xmlparsers.py
index f607098..2f3f5fa 100644
--- a/bionetgen/modelapi/xmlparsers.py
+++ b/bionetgen/modelapi/xmlparsers.py
@@ -167,8 +167,8 @@ def parse_xml(self, xml) -> Pattern:
             quantity = xml["@quantity"]
             pattern.relation = relation
             try:
-                n = int(pattern.quantity)
-                f = float(pattern.quantity)
+                n = int(quantity)
+                f = float(quantity)
                 if n == f:
                     pattern.quantity = quantity
             except ValueError as e:
diff --git a/tests/models/hybrid_test.bngl b/tests/models/hybrid_test.bngl
index 6887904..ba381de 100644
--- a/tests/models/hybrid_test.bngl
+++ b/tests/models/hybrid_test.bngl
@@ -30,10 +30,7 @@ begin observables
 	Species    R2       R==2
 	Species    R3       R==3
 	Species    R4       R==4
-    Species    R5       R>4
-	Species    R5le		R<=4
-	Species	   R5l		R<4
-	Species	   R5ge		R>=4
+    Species    R5       R<4
 end observables
 begin reaction rules
 	R(l!1).L(r!1)          ->  R(l)  +  L(r)          koff
@@ -48,5 +45,4 @@ end population maps
 end model
 
 ## actions ##
-#generate_hybrid_model({overwrite=>1, execute=>1, verbose=>1, safe=>0, actions=>["writeXML()"]})
-writeXML()
+generate_hybrid_model({overwrite=>1, execute=>1, verbose=>1, safe=>0, actions=>["writeXML()"]})
\ No newline at end of file