Added 1 missing validation rule (layout)

validation/error-test-files/AF/af10115-fail.sbgn

@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
+<sbgn xmlns="http://sbgn.org/libsbgn/0.3">
+    <map id="map1" language="activity flow">
+        <glyph id="glyph1" class="biological activity">
+            <label text="A"/>
+            <bbox x="26.0" y="30.0" w="108.0" h="60.0"/>
+        </glyph>
+        <glyph id="glyph2" class="biological activity">
+            <label text="B"/>
+            <bbox x="80.0" y="30.0" w="108.0" h="60.0"/>
+        </glyph>
+    </map>
+</sbgn>

validation/error-test-files/AF/af10115-pass.sbgn

@@ -0,0 +1,26 @@
+<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
+<sbgn xmlns="http://sbgn.org/libsbgn/0.3">
+    <map id="map1" language="activity flow">
+        <glyph id="glyph2" class="biological activity">
+            <label text="A"/>
+            <bbox y="30.0" x="26.0" h="60.0" w="108.0"/>
+        </glyph>
+        <glyph id="glyph3" class="biological activity">
+            <label text="B"/>
+            <bbox y="20.0" x="286.0" h="60.0" w="108.0"/>
+        </glyph>
+        <glyph id="glyph4" class="not">
+            <bbox y="89.0" x="179.0" h="42.0" w="42.0"/>
+            <port y="110.0" x="158.0" id="glyph4.1"/>
+            <port y="110.0" x="242.0" id="glyph4.2"/>
+        </glyph>
+        <arc target="glyph4.1" source="glyph2" id="arc0" class="logic arc">
+            <start y="90.0" x="126.8"/>
+            <end y="110.0" x="158.0"/>
+        </arc>
+        <arc target="glyph3" source="glyph4.2" id="arc2" class="positive influence">
+            <start y="110.0" x="242.0"/>
+            <end y="73.14286" x="286.0"/>
+        </arc>
+    </map>
+</sbgn>

validation/rules/sbgn_af.sch

@@ -32,6 +32,7 @@ Schematron validation for SBGN AF
 		<iso:active pattern="af10112"/>
 		<iso:active pattern="af10113"/>
 		<iso:active pattern="af10114"/>
+		<iso:active pattern="af10115"/>
 	</iso:phase>
 
 	<iso:pattern id="00000">
@@ -259,6 +260,43 @@ Schematron validation for SBGN AF
 			</iso:assert>
 		</iso:rule> 
 	</iso:pattern> 
+
+	<iso:pattern id="af10115">
+		<iso:rule context="sbgn:map/sbgn:glyph[
+			@class= 'biological activity' or 
+		@class = 'phenotype' or 
+		@class = 'submap' or 
+		@class = 'and' or 
+		@class = 'or' or 
+		@class = 'not' or 
+		@class = 'delay'
+		]">
+			<iso:let name="id" value="@id"/>
+			<iso:assert
+				id="af10115"
+				name="check-overlapping-nodes"
+				role="error"
+				test="not(following-sibling::sbgn:glyph[
+					(@class= 'biological activity' or
+				@class = 'phenotype' or
+				@class = 'submap' or
+				@class = 'and' or
+				@class = 'or' or
+				@class = 'not' or
+				@class = 'delay')
+				and (
+  						(number(sbgn:bbox/@x) &lt;= number(current()/sbgn:bbox/@x) + number(current()/sbgn:bbox/@w)) and
+ 					(number(sbgn:bbox/@x) + number(sbgn:bbox/@w) >= number(current()/sbgn:bbox/@x)) and
+  					(number(sbgn:bbox/@y) &lt;= number(current()/sbgn:bbox/@y) + number(current()/sbgn:bbox/@h)) and
+  					(number(sbgn:bbox/@y) + number(sbgn:bbox/@h) >= number(current()/sbgn:bbox/@y))
+					)
+
+				]
+				)"
+				diagnostics="id">Illegal overlapping nodes are not allowed in SBGN AF.
+			</iso:assert>
+		</iso:rule> 
+	</iso:pattern> 
 
 	<iso:diagnostics>
 		<iso:diagnostic id="id"><iso:value-of select="$id"/></iso:diagnostic> 		

validation/validate.py

@@ -0,0 +1,124 @@
+import subprocess
+from pathlib import Path
+
+# --------------------
+# Global configuration
+# --------------------
+
+SAXON_JAR = Path("lib/saxon9he.jar")
+SCHEMATRON_DIR = Path("schematron")
+RULES_DIR = Path("rules")
+TESTS_DIR = Path("error-test-files")
+SVRL_ROOT = Path("svrl")
+
+
+# --------------------
+# Utility
+# --------------------
+
+def run(cmd):
+    print("▶", " ".join(cmd))
+    subprocess.run(cmd, check=True)
+
+
+# --------------------
+# Compile step
+# --------------------
+
+def compile_schematron(language: str):
+    """
+    Compile Schematron rules for a given SBGN language (pd / er / af)
+    into an XSLT validator.
+    """
+    language = language.lower()
+
+    sch_file = RULES_DIR / f"sbgn_{language}.sch"
+    step1 = Path(f"sbgn_{language}.step1.sch")
+    step2 = Path(f"sbgn_{language}.step2.sch")
+    validator = Path(f"sbgn_{language}_validator.xsl")
+
+    print(f"\n=== Compiling Schematron for {language.upper()} ===")
+
+    # Step 1: expand includes
+    run([
+        "java", "-jar", str(SAXON_JAR),
+        "-s:" + str(sch_file),
+        "-xsl:" + str(SCHEMATRON_DIR / "iso_dsdl_include.xsl"),
+        "-o:" + str(step1)
+    ])
+
+    # Step 2: expand abstract patterns
+    run([
+        "java", "-jar", str(SAXON_JAR),
+        "-s:" + str(step1),
+        "-xsl:" + str(SCHEMATRON_DIR / "iso_abstract_expand.xsl"),
+        "-o:" + str(step2)
+    ])
+
+    # Step 3: compile to SVRL-producing XSLT
+    run([
+        "java", "-jar", str(SAXON_JAR),
+        "-s:" + str(step2),
+        "-xsl:" + str(SCHEMATRON_DIR / "iso_svrl_for_xslt1.xsl"),
+        "-o:" + str(validator)
+    ])
+
+    print(f" Validator created: {validator}")
+    return validator
+
+
+# --------------------
+# Validation step
+# --------------------
+
+def validate_sbgn(language: str, sbgn_file: Path):
+    """
+    Validate a single SBGN file and write SVRL output.
+    """
+    language = language.upper()
+
+    validator = Path(f"sbgn_{language.lower()}_validator.xsl")
+    svrl_dir = SVRL_ROOT / language
+    svrl_dir.mkdir(parents=True, exist_ok=True)
+
+    output = svrl_dir / (sbgn_file.stem + ".svrl")
+
+    print(f"\n=== Validating {sbgn_file.name} ({language}) ===")
+
+    run([
+        "java", "-jar", str(SAXON_JAR),
+        "-s:" + str(sbgn_file),
+        "-xsl:" + str(validator),
+        "-o:" + str(output)
+    ])
+
+    print(f"SVRL written to {output}")
+
+
+# --------------------
+# Batch validation
+# --------------------
+
+def validate_all(language: str):
+    """
+    Validate all test files for a given language.
+    """
+    language = language.upper()
+    test_dir = TESTS_DIR / language
+
+    for sbgn in sorted(test_dir.glob("*.sbgn")):
+        validate_sbgn(language, sbgn)
+
+
+# --------------------
+# Entry point
+# --------------------
+
+if __name__ == "__main__":
+
+    pd = "pd"
+    af = "af"
+    er = "er"
+    #compile_schematron(pd)
+    compile_schematron(af)
+    validate_all(af)