From d85f33903d59d18a2966ff9e092bf4a644a7ac40 Mon Sep 17 00:00:00 2001
From: Marketa Opichalova <514349@mail.muni.cz>
Date: Tue, 16 Apr 2024 16:06:53 +0200
Subject: [PATCH 1/6] tests for observables

---
 Testing/objects_testing.py          |  2 ++
 Testing/parsing/test_observables.py | 49 +++++++++++++++++++++++++++++
 2 files changed, 51 insertions(+)
 create mode 100644 Testing/parsing/test_observables.py

diff --git a/Testing/objects_testing.py b/Testing/objects_testing.py
index a324d26..bd1b9dd 100644
--- a/Testing/objects_testing.py
+++ b/Testing/objects_testing.py
@@ -22,6 +22,8 @@
 rule_parser = Parser("rule")
 rules_parser = Parser("rules")
 model_parser = Parser("model")
+observables_parser = Parser("observables")
+observable_parser = Parser("observable")
 
 # atomic
 a1 = AtomicAgent("T", "s")
diff --git a/Testing/parsing/test_observables.py b/Testing/parsing/test_observables.py
new file mode 100644
index 0000000..2a01224
--- /dev/null
+++ b/Testing/parsing/test_observables.py
@@ -0,0 +1,49 @@
+import pytest
+
+import Testing.objects_testing as objects
+
+
+def test_parser():
+    observable_expr1 = "abc: A()::cell"
+    assert objects.observable_parser.parse(observable_expr1)
+
+    observable_expr2 = "efg: E()"
+    assert objects.observable_parser.parse(observable_expr2)
+
+    observable_expr3 = "hij: $H()::cell"
+    assert objects.observable_parser.parse(observable_expr3)
+
+    observable_expr4 = "klm: {matchOnce}K()"
+    assert objects.observable_parser.parse(observable_expr4)
+
+    observable_expr5 = "nop: N()::cell > 2"
+    assert objects.observable_parser.parse(observable_expr5).success
+
+    observable_expr6 = "qrs: Q().R().S()::cell > 2"
+    assert objects.observable_parser.parse(observable_expr6).success
+
+    observable_expr7 = "tuv: T(U{v})"
+    assert objects.observable_parser.parse(observable_expr7).success
+
+    observables_expr = (
+        "#! observables\n"
+        + observable_expr1
+        + "\n"
+        + observable_expr2
+        + "\n"
+        + observable_expr3
+        + "\n"
+        + observable_expr4
+        + "\n"
+        + observable_expr5
+        + "\n"
+        + observable_expr6
+    )
+    assert objects.observables_parser.parse(observables_expr).success
+
+
+    assert not objects.observable_parser.parse("A()::cell > 2").success
+    assert not objects.observable_parser.parse("a: A(::cell").success
+    assert not objects.observable_parser.parse("a: b: A():cell > 2").success
+    assert not objects.observable_parser.parse("a: 2 > A():cell").success
+    assert not objects.observable_parser.parse("a: A()::cell$").success

From 8722fccc380f7a53e18ba57399951ccc6a608fe4 Mon Sep 17 00:00:00 2001
From: Marketa Opichalova <514349@mail.muni.cz>
Date: Tue, 16 Apr 2024 16:07:20 +0200
Subject: [PATCH 2/6] observable grammar added

---
 eBCSgen/Parsing/ParseBCSL.py | 24 +++++++++++++++++++++++-
 1 file changed, 23 insertions(+), 1 deletion(-)

diff --git a/eBCSgen/Parsing/ParseBCSL.py b/eBCSgen/Parsing/ParseBCSL.py
index 4bb2843..c7eff83 100644
--- a/eBCSgen/Parsing/ParseBCSL.py
+++ b/eBCSgen/Parsing/ParseBCSL.py
@@ -106,13 +106,14 @@ def to_side(self):
 
 GRAMMAR = r"""
     model: (sections)* rules (sections | rules)*
-    sections: inits | definitions | complexes | regulation
+    sections: inits | definitions | complexes | regulation | observables
 
     rules: RULES_START _NL+ (rule _NL+)* rule _NL*
     inits: INITS_START _NL+ (init _NL+)* init _NL*
     definitions: DEFNS_START _NL+ (definition _NL+)* definition _NL*
     complexes: COMPLEXES_START _NL+ (cmplx_dfn _NL+)* cmplx_dfn _NL*
     regulation: REGULATION_START _NL+ regulation_def _NL*
+    observables: OBSERVABLES_START _NL+ (observable _NL+)* observable _NL*
 
     init: const? rate_complex 
     definition: def_param "=" number
@@ -138,6 +139,7 @@ def to_side(self):
     DEFNS_START: "#! definitions"
     COMPLEXES_START: "#! complexes"
     REGULATION_START: "#! regulation"
+    OBSERVABLES_START: "#! observables"
     _NL: /(\r?\n[\t ]*)+/
 
     !label: CNAME "~"
@@ -239,6 +241,13 @@ def to_side(self):
     REGEX_CHAR: /[^\\^$().*+?{}\[\]|]/
 """
 
+OBSERVABLES_GRAMMAR = """
+    observable: CNAME ":" ("0" | basic_observable)
+    basic_observable: pattern_mod? (rate_complex | value) pattern_quantified?
+    !pattern_quantified: (">" | "<" | ">=" | "<=" | "==" | "!=") INT
+    !pattern_mod: "$" | "{matchOnce}"
+"""
+
 
 class TransformRegulations(Transformer):
     def regulation(self, matches):
@@ -702,6 +711,15 @@ def inits(self, matches):
             else:
                 result[init[0].children[0]] = 1
         return {"inits": result}
+    
+    def observable(self, matches):
+        return {str(matches[0]): matches[1].children}
+    
+    def observables(self, matches):
+        result = dict()
+        for observable in matches[1:]:
+            result.update(observable)
+        return {"observables": result}
 
     def param(self, matches):
         self.params.add(str(matches[0]))
@@ -712,6 +730,7 @@ def model(self, matches):
         definitions = dict()
         regulation = None
         inits = collections.Counter()
+        observables = dict()
         for match in matches:
             if type(match) == dict:
                 key, value = list(match.items())[0]
@@ -728,6 +747,8 @@ def model(self, matches):
                 inits.update(value)
             elif key == "definitions":
                 definitions.update(value)
+            elif key == "observables":
+                observables.update(value)
             elif key == "regulation":
                 if regulation:
                     raise UnspecifiedParsingError("Multiple regulations")
@@ -749,6 +770,7 @@ def __init__(self, start):
             + EXTENDED_GRAMMAR
             + REGULATIONS_GRAMMAR
             + REGEX_GRAMMAR
+            + OBSERVABLES_GRAMMAR
         )
         self.parser = Lark(
             grammar, parser="earley", propagate_positions=False, maybe_placeholders=False

From 8b509d0846570a9995a340f6f8a89c409d6ca620 Mon Sep 17 00:00:00 2001
From: Marketa Opichalova <514349@mail.muni.cz>
Date: Tue, 16 Apr 2024 16:25:48 +0200
Subject: [PATCH 3/6] observable tests extended

---
 Testing/parsing/test_observables.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/Testing/parsing/test_observables.py b/Testing/parsing/test_observables.py
index 2a01224..4b03232 100644
--- a/Testing/parsing/test_observables.py
+++ b/Testing/parsing/test_observables.py
@@ -7,7 +7,7 @@ def test_parser():
     observable_expr1 = "abc: A()::cell"
     assert objects.observable_parser.parse(observable_expr1)
 
-    observable_expr2 = "efg: E()"
+    observable_expr2 = "efg: E(F{_})"
     assert objects.observable_parser.parse(observable_expr2)
 
     observable_expr3 = "hij: $H()::cell"
@@ -47,3 +47,4 @@ def test_parser():
     assert not objects.observable_parser.parse("a: b: A():cell > 2").success
     assert not objects.observable_parser.parse("a: 2 > A():cell").success
     assert not objects.observable_parser.parse("a: A()::cell$").success
+    assert not objects.observable_parser.parse("a: A{}::cell").success

From 11aebbb1e7e4d6aaee16269b95753e5b24d35e35 Mon Sep 17 00:00:00 2001
From: Marketa Opichalova <514349@mail.muni.cz>
Date: Tue, 23 Apr 2024 10:41:39 +0200
Subject: [PATCH 4/6] observables extended and scaling implemented

---
 Testing/parsing/test_observables.py | 13 ++++++++++++-
 eBCSgen/Parsing/ParseBCSL.py        |  6 ++++--
 2 files changed, 16 insertions(+), 3 deletions(-)

diff --git a/Testing/parsing/test_observables.py b/Testing/parsing/test_observables.py
index 4b03232..8a71900 100644
--- a/Testing/parsing/test_observables.py
+++ b/Testing/parsing/test_observables.py
@@ -25,6 +25,18 @@ def test_parser():
     observable_expr7 = "tuv: T(U{v})"
     assert objects.observable_parser.parse(observable_expr7).success
 
+    observable_expr8 = "wx: 2W{x}"
+    assert objects.observable_parser.parse(observable_expr8).success
+
+    observable_expr9 = "z: Y{z} + Z{y}"
+    assert objects.observable_parser.parse(observable_expr9).success
+
+    observable_expr10 = "z: 2 * Y{z} + Z{y}"
+    assert objects.observable_parser.parse(observable_expr10).success
+
+    observable_expr10 = "z: Y{z} + Z{y} / 2.1 ** 10"
+    assert objects.observable_parser.parse(observable_expr10).success
+
     observables_expr = (
         "#! observables\n"
         + observable_expr1
@@ -41,7 +53,6 @@ def test_parser():
     )
     assert objects.observables_parser.parse(observables_expr).success
 
-
     assert not objects.observable_parser.parse("A()::cell > 2").success
     assert not objects.observable_parser.parse("a: A(::cell").success
     assert not objects.observable_parser.parse("a: b: A():cell > 2").success
diff --git a/eBCSgen/Parsing/ParseBCSL.py b/eBCSgen/Parsing/ParseBCSL.py
index c7eff83..73ffb0f 100644
--- a/eBCSgen/Parsing/ParseBCSL.py
+++ b/eBCSgen/Parsing/ParseBCSL.py
@@ -242,10 +242,12 @@ def to_side(self):
 """
 
 OBSERVABLES_GRAMMAR = """
-    observable: CNAME ":" ("0" | basic_observable)
-    basic_observable: pattern_mod? (rate_complex | value) pattern_quantified?
+    observable: CNAME ":" pattern_mod? (basic_observable | scaled_observable) pattern_quantified?
+    basic_observable: side | (const? observable_complex "+")* (const? observable_complex)?
+    !scaled_observable: const | observable_complex | scaled_observable "+" scaled_observable | scaled_observable "-" scaled_observable | scaled_observable "*" scaled_observable | scaled_observable "/" scaled_observable | scaled_observable POW const | "(" scaled_observable ")"
     !pattern_quantified: (">" | "<" | ">=" | "<=" | "==" | "!=") INT
     !pattern_mod: "$" | "{matchOnce}"
+    observable_complex: (abstract_sequence|value|cmplx_name)
 """
 
 

From 6da78d948ae0d57a525081c424f50b25b652295c Mon Sep 17 00:00:00 2001
From: Marketa Opichalova <514349@mail.muni.cz>
Date: Tue, 23 Apr 2024 19:54:33 +0200
Subject: [PATCH 5/6] scaling complexes with compartments corrected

---
 Testing/parsing/test_observables.py | 10 ++++++--
 eBCSgen/Parsing/ParseBCSL.py        | 38 +++++++++++++++++------------
 2 files changed, 30 insertions(+), 18 deletions(-)

diff --git a/Testing/parsing/test_observables.py b/Testing/parsing/test_observables.py
index 8a71900..1f5ac7e 100644
--- a/Testing/parsing/test_observables.py
+++ b/Testing/parsing/test_observables.py
@@ -25,7 +25,7 @@ def test_parser():
     observable_expr7 = "tuv: T(U{v})"
     assert objects.observable_parser.parse(observable_expr7).success
 
-    observable_expr8 = "wx: 2W{x}"
+    observable_expr8 = "wx: 2 W{x}"
     assert objects.observable_parser.parse(observable_expr8).success
 
     observable_expr9 = "z: Y{z} + Z{y}"
@@ -34,9 +34,15 @@ def test_parser():
     observable_expr10 = "z: 2 * Y{z} + Z{y}"
     assert objects.observable_parser.parse(observable_expr10).success
 
-    observable_expr10 = "z: Y{z} + Z{y} / 2.1 ** 10"
+    observable_expr10 = "z: (Y{z} + Z{y}) / 2.1 ** 10"
     assert objects.observable_parser.parse(observable_expr10).success
 
+    observable_expr11 = "scaled_A: 1000 * A{i}::cell"
+    assert objects.observable_parser.parse(observable_expr11).success
+
+    observable_expr12 = "obs_A_all: A{i}::cell + A{a}::cell"
+    assert objects.observable_parser.parse(observable_expr12).success
+
     observables_expr = (
         "#! observables\n"
         + observable_expr1
diff --git a/eBCSgen/Parsing/ParseBCSL.py b/eBCSgen/Parsing/ParseBCSL.py
index 73ffb0f..3529772 100644
--- a/eBCSgen/Parsing/ParseBCSL.py
+++ b/eBCSgen/Parsing/ParseBCSL.py
@@ -243,11 +243,10 @@ def to_side(self):
 
 OBSERVABLES_GRAMMAR = """
     observable: CNAME ":" pattern_mod? (basic_observable | scaled_observable) pattern_quantified?
-    basic_observable: side | (const? observable_complex "+")* (const? observable_complex)?
-    !scaled_observable: const | observable_complex | scaled_observable "+" scaled_observable | scaled_observable "-" scaled_observable | scaled_observable "*" scaled_observable | scaled_observable "/" scaled_observable | scaled_observable POW const | "(" scaled_observable ")"
+    basic_observable: const? (value | abstract_sequence) (DOUBLE_COLON compartment)?
+    !scaled_observable: const | basic_observable | scaled_observable "+" scaled_observable | scaled_observable "-" scaled_observable | scaled_observable "*" scaled_observable | scaled_observable "/" scaled_observable | scaled_observable POW const | "(" scaled_observable ")"
     !pattern_quantified: (">" | "<" | ">=" | "<=" | "==" | "!=") INT
     !pattern_mod: "$" | "{matchOnce}"
-    observable_complex: (abstract_sequence|value|cmplx_name)
 """
 
 
@@ -674,15 +673,19 @@ def rule(self, matches):
         reversible = False
         if arrow == "<=>":
             reversible = True
-        return reversible, Rule(
-            agents,
-            mid,
-            compartments,
-            complexes,
-            pairs,
-            Rate(rate1) if rate1 else None,
-            label,
-        ), Rate(rate2) if rate2 else None
+        return (
+            reversible,
+            Rule(
+                agents,
+                mid,
+                compartments,
+                complexes,
+                pairs,
+                Rate(rate1) if rate1 else None,
+                label,
+            ),
+            Rate(rate2) if rate2 else None,
+        )
 
     def rules(self, matches):
         rules = []
@@ -713,10 +716,10 @@ def inits(self, matches):
             else:
                 result[init[0].children[0]] = 1
         return {"inits": result}
-    
+
     def observable(self, matches):
         return {str(matches[0]): matches[1].children}
-    
+
     def observables(self, matches):
         result = dict()
         for observable in matches[1:]:
@@ -775,7 +778,10 @@ def __init__(self, start):
             + OBSERVABLES_GRAMMAR
         )
         self.parser = Lark(
-            grammar, parser="earley", propagate_positions=False, maybe_placeholders=False
+            grammar,
+            parser="earley",
+            propagate_positions=False,
+            maybe_placeholders=False,
         )
 
         self.terminals = dict((v, k) for k, v in _TERMINAL_NAMES.items())
@@ -880,7 +886,7 @@ def syntax_check(self, expression: str) -> Result:
             return Result(
                 False,
                 {
-                    "unexpected": str(u.token), 
+                    "unexpected": str(u.token),
                     "expected": self.replace(u.expected),
                     "line": u.line,
                     "column": u.column,

From fde3ff9f691a4f3b2b9d6be775517943b97589ee Mon Sep 17 00:00:00 2001
From: Marketa Opichalova <514349@mail.muni.cz>
Date: Wed, 24 Apr 2024 13:19:29 +0200
Subject: [PATCH 6/6] observables - remove modifiers, quantifiers and
 stoichiometry

---
 Testing/parsing/test_observables.py | 20 ++++++++++----------
 eBCSgen/Parsing/ParseBCSL.py        |  7 ++-----
 2 files changed, 12 insertions(+), 15 deletions(-)

diff --git a/Testing/parsing/test_observables.py b/Testing/parsing/test_observables.py
index 1f5ac7e..75340a9 100644
--- a/Testing/parsing/test_observables.py
+++ b/Testing/parsing/test_observables.py
@@ -7,34 +7,34 @@ def test_parser():
     observable_expr1 = "abc: A()::cell"
     assert objects.observable_parser.parse(observable_expr1)
 
-    observable_expr2 = "efg: E(F{_})"
+    observable_expr2 = "efg: E(F{_})::cell"
     assert objects.observable_parser.parse(observable_expr2)
 
-    observable_expr3 = "hij: $H()::cell"
+    observable_expr3 = "hij: H()::cell"
     assert objects.observable_parser.parse(observable_expr3)
 
-    observable_expr4 = "klm: {matchOnce}K()"
+    observable_expr4 = "klm: K()::cyt * L()::cell + M()::cell"
     assert objects.observable_parser.parse(observable_expr4)
 
-    observable_expr5 = "nop: N()::cell > 2"
+    observable_expr5 = "nop: N()::cell"
     assert objects.observable_parser.parse(observable_expr5).success
 
-    observable_expr6 = "qrs: Q().R().S()::cell > 2"
+    observable_expr6 = "qrs: Q().R().S()::cell"
     assert objects.observable_parser.parse(observable_expr6).success
 
-    observable_expr7 = "tuv: T(U{v})"
+    observable_expr7 = "tuv: T(U{v})::cell "
     assert objects.observable_parser.parse(observable_expr7).success
 
-    observable_expr8 = "wx: 2 W{x}"
+    observable_expr8 = "wx: 2 * W{x}::cell"
     assert objects.observable_parser.parse(observable_expr8).success
 
-    observable_expr9 = "z: Y{z} + Z{y}"
+    observable_expr9 = "z: Y{z}::cyt + Z{y}::ext"
     assert objects.observable_parser.parse(observable_expr9).success
 
-    observable_expr10 = "z: 2 * Y{z} + Z{y}"
+    observable_expr10 = "z: 2 * Y{z}::cyt + Z{y}::ext ** 2"
     assert objects.observable_parser.parse(observable_expr10).success
 
-    observable_expr10 = "z: (Y{z} + Z{y}) / 2.1 ** 10"
+    observable_expr10 = "z: (Y{z}::cell + Z{y}::cyt) / 2.1 ** 10"
     assert objects.observable_parser.parse(observable_expr10).success
 
     observable_expr11 = "scaled_A: 1000 * A{i}::cell"
diff --git a/eBCSgen/Parsing/ParseBCSL.py b/eBCSgen/Parsing/ParseBCSL.py
index 3529772..8a3973c 100644
--- a/eBCSgen/Parsing/ParseBCSL.py
+++ b/eBCSgen/Parsing/ParseBCSL.py
@@ -242,11 +242,8 @@ def to_side(self):
 """
 
 OBSERVABLES_GRAMMAR = """
-    observable: CNAME ":" pattern_mod? (basic_observable | scaled_observable) pattern_quantified?
-    basic_observable: const? (value | abstract_sequence) (DOUBLE_COLON compartment)?
-    !scaled_observable: const | basic_observable | scaled_observable "+" scaled_observable | scaled_observable "-" scaled_observable | scaled_observable "*" scaled_observable | scaled_observable "/" scaled_observable | scaled_observable POW const | "(" scaled_observable ")"
-    !pattern_quantified: (">" | "<" | ">=" | "<=" | "==" | "!=") INT
-    !pattern_mod: "$" | "{matchOnce}"
+    observable: CNAME ":" observable_pattern
+    !observable_pattern: const | complex | observable_pattern "+" observable_pattern | observable_pattern "-" observable_pattern | observable_pattern "*" observable_pattern | observable_pattern "/" observable_pattern | observable_pattern POW const | "(" observable_pattern ")"
 """