From e1fb066d8e932de1a2b721295b1a465c94183701 Mon Sep 17 00:00:00 2001
From: Marketa Opichalova <514349@mail.muni.cz>
Date: Wed, 31 Jan 2024 09:50:03 +0100
Subject: [PATCH 1/4] enable direct usage of complexes

---
 eBCSgen/Parsing/ParseBCSL.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/eBCSgen/Parsing/ParseBCSL.py b/eBCSgen/Parsing/ParseBCSL.py
index 69915b4..1e4c43a 100644
--- a/eBCSgen/Parsing/ParseBCSL.py
+++ b/eBCSgen/Parsing/ParseBCSL.py
@@ -137,9 +137,9 @@ def to_side(self):
 
 EXTENDED_GRAMMAR = """
     abstract_sequence: atomic_complex | atomic_structure_complex | structure_complex
-    atomic_complex: atomic ":" (cmplx_name|VAR)
-    atomic_structure_complex: atomic ":" structure ":" (cmplx_name|VAR)
-    structure_complex: structure ":" (cmplx_name|VAR)
+    atomic_complex: atomic ":" (VAR | value)
+    atomic_structure_complex: atomic ":" structure ":" (VAR | value)
+    structure_complex: structure ":" (VAR | value)
 
     variable: VAR "=" "{" cmplx_name ("," cmplx_name)+ "}"
     VAR: "?"

From dcd488aee43f39a9a7e8b4c41507a675433511bb Mon Sep 17 00:00:00 2001
From: Marketa Opichalova <514349@mail.muni.cz>
Date: Tue, 13 Feb 2024 09:50:10 +0100
Subject: [PATCH 2/4] zooming inserting

---
 eBCSgen/Parsing/ParseBCSL.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/eBCSgen/Parsing/ParseBCSL.py b/eBCSgen/Parsing/ParseBCSL.py
index 1e4c43a..406cf8f 100644
--- a/eBCSgen/Parsing/ParseBCSL.py
+++ b/eBCSgen/Parsing/ParseBCSL.py
@@ -348,6 +348,10 @@ def insert_struct_to_complex(self, struct, complex):
             if self.get_name(struct) == self.get_name(complex.children[i].children[0]):
                 complex.children[i] = Tree('agent', [struct])
                 break
+            elif isinstance(complex.children[0].children[0].children[0].children[0], Tree):
+                complex.children[i].children[0] = Tree('agent', [struct])
+                break
+
         return complex
 
     def insert_atomic_to_complex(self, atomic, complex):

From 7432dd57a692ae0064cce46be4fa5f0ffce01f83 Mon Sep 17 00:00:00 2001
From: Marketa Opichalova <514349@mail.muni.cz>
Date: Tue, 13 Feb 2024 09:59:29 +0100
Subject: [PATCH 3/4] test cases for complexes in abstract sequence

---
 Testing/models/model_cmplx_in_abstr_seq1.txt |  5 +++++
 Testing/models/model_cmplx_in_abstr_seq2.txt |  2 ++
 Testing/parsing/test_cmplx_in_abstr_seq.py   | 17 +++++++++++++++++
 3 files changed, 24 insertions(+)
 create mode 100644 Testing/models/model_cmplx_in_abstr_seq1.txt
 create mode 100644 Testing/models/model_cmplx_in_abstr_seq2.txt
 create mode 100644 Testing/parsing/test_cmplx_in_abstr_seq.py

diff --git a/Testing/models/model_cmplx_in_abstr_seq1.txt b/Testing/models/model_cmplx_in_abstr_seq1.txt
new file mode 100644
index 0000000..f03c61d
--- /dev/null
+++ b/Testing/models/model_cmplx_in_abstr_seq1.txt
@@ -0,0 +1,5 @@
+#! rules
+S{i}:A():A2::cell  => A()::cell
+
+#! complexes
+A2 = A().A()
diff --git a/Testing/models/model_cmplx_in_abstr_seq2.txt b/Testing/models/model_cmplx_in_abstr_seq2.txt
new file mode 100644
index 0000000..801026b
--- /dev/null
+++ b/Testing/models/model_cmplx_in_abstr_seq2.txt
@@ -0,0 +1,2 @@
+#! rules
+S{i}:A():A().A()::cell => A()::cell
diff --git a/Testing/parsing/test_cmplx_in_abstr_seq.py b/Testing/parsing/test_cmplx_in_abstr_seq.py
new file mode 100644
index 0000000..068f47d
--- /dev/null
+++ b/Testing/parsing/test_cmplx_in_abstr_seq.py
@@ -0,0 +1,17 @@
+import pytest
+
+from Testing.models.get_model_str import get_model_str
+import Testing.objects_testing as objects
+
+
+def test_complexes_in_abstract_sequence():
+    # is allowed
+    model = get_model_str("model_cmplx_in_abstr_seq1")
+    ret1 = objects.model_parser.parse(model)
+    assert ret1.success
+
+    # should be allowed
+    model = get_model_str("model_cmplx_in_abstr_seq2")
+    ret2 = objects.model_parser.parse(model)
+    assert ret2.success
+    assert ret1.data == ret2.data

From ef609a7c007b001c082b3d83d97c6065b36701e3 Mon Sep 17 00:00:00 2001
From: Marketa Opichalova <514349@mail.muni.cz>
Date: Mon, 26 Feb 2024 20:37:36 +0100
Subject: [PATCH 4/4] fix incorrect parsed object comparison in
 TransformAbstractSyntax

---
 eBCSgen/Parsing/ParseBCSL.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/eBCSgen/Parsing/ParseBCSL.py b/eBCSgen/Parsing/ParseBCSL.py
index 651494c..e70646c 100644
--- a/eBCSgen/Parsing/ParseBCSL.py
+++ b/eBCSgen/Parsing/ParseBCSL.py
@@ -412,12 +412,12 @@ def insert_struct_to_complex(self, struct, complex):
                 # search same name structs - if they contain atomics with matching names, they are considered incompatible
                 for j in range(len(struct.children[1].children)):
                     for k in range(
-                        len(complex.children[i].children[0].children[1].children)
+                        len(search.children[i].children[0].children[1].children)
                     ):
                         if self.get_name(
                             struct.children[1].children[j]
                         ) == self.get_name(
-                            complex.children[i].children[0].children[1].children[k]
+                            search.children[i].children[0].children[1].children[k]
                         ):
                             struct_found = False
                             break