Merge pull request #1645 from virtualcell/AddPythonExpressionSyntax

Add python expression syntax

Author: CodeByDrescher

.github/workflows/ci_cd.yml

@@ -85,6 +85,14 @@ jobs:
           java -version
           mvn --batch-mode clean install dependency:copy-dependencies -DskipTests=true
 
+      - name: Add jython
+        shell: bash
+        run: |
+          curl https://repo1.maven.org/maven2/org/python/jython-installer/2.7.4/jython-installer-2.7.4.jar -o jython-installer.jar
+          mkdir .temp_holding
+          mv /home/runner/.m2/repository/org/python/jython/2.7.4/* .temp_holding
+          java -jar jython-installer.jar -s -d /home/runner/.m2/repository/org/python/jython/2.7.4
+
       - name: Test building of docker image
         run: |
           docker build \
@@ -170,6 +178,14 @@ jobs:
           java-version: '17'
           cache: 'maven'
 
+      - name: Add jython
+        shell: bash
+        run: |
+          curl https://repo1.maven.org/maven2/org/python/jython-installer/2.7.4/jython-installer-2.7.4.jar -o jython-installer.jar
+          mkdir .temp_holding
+          mv /home/runner/.m2/repository/org/python/jython/2.7.4/* .temp_holding
+          java -jar jython-installer.jar -s -d /home/runner/.m2/repository/org/python/jython/2.7.4 
+
       - name: Maven Build and run Test group ${{ matrix.test-group }}
         shell: bash
         run: |

.gitignore

@@ -28,6 +28,7 @@ ziptool
 vcell-client/UserDocumentation/originalXML/helpSearchConfig.txt
 *.iml
 .metadata/
+.jython_cache
 
 ### Eclipse ###
 .metadata

vcell-math/pom.xml

@@ -121,6 +121,18 @@
 				</exclusion>
 			</exclusions>
 		</dependency>
+        <dependency>
+            <groupId>org.python</groupId>
+            <artifactId>jython</artifactId>
+            <version>2.7.4</version>
+            <scope>compile</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.commons</groupId>
+            <artifactId>commons-math4-core</artifactId>
+            <version>4.0-beta1</version>
+            <scope>compile</scope>
+        </dependency>
 		<dependency>
 			<groupId>org.eclipse.microprofile.openapi</groupId>
 			<artifactId>microprofile-openapi-api</artifactId>

vcell-math/src/main/java/cbit/vcell/parser/ASTAndNode.java

@@ -31,6 +31,10 @@ public boolean isBoolean() {
 	  return true;
 }
 
+public boolean isLogical() {
+	  return true;
+}
+
   public void bind(SymbolTable symbolTable) throws ExpressionBindingException
   {
 	  super.bind(symbolTable);
@@ -167,6 +171,13 @@ public String infixString(int lang)
 			  buffer.append(jjtGetChild(i).infixString(lang));
 			  buffer.append(")");
 		  }
+	  }else if(lang == LANGUAGE_PYTHON){
+		  buffer.append("float(bool(");
+		  for (int i=0;i<jjtGetNumChildren();i++){
+			  if (i>0) buffer.append(" and ");
+			  buffer.append(jjtGetChild(i).infixString(lang));
+		  }
+		  buffer.append("))");
 	  }else{
 		  for (int i=0;i<jjtGetNumChildren();i++){
 			if (i>0) {

vcell-math/src/main/java/cbit/vcell/parser/ASTFloatNode.java

@@ -142,7 +142,11 @@ public String infixString(int lang)
 					  return "("+ value +")";
 				  }
 			  }
-		  } else {
+		  } else if (lang == LANGUAGE_PYTHON) {
+              if (value == Double.POSITIVE_INFINITY) return "float('inf')";
+              if (value == Double.NEGATIVE_INFINITY) return "float('-inf')";
+              return value.toString();
+          } else {
 		      return value.toString();
 		  }
 	  }