report part 1 done

extract_feature_vectors.py

@@ -85,12 +85,16 @@ def parse(path: str):
         # consider only the class matching the input file name, to skip inner classes
         if path.endswith(node.name + '.java'):
             fqdn = package_name + '.' + node.name
+            print(fqdn)
 
             fields = get_fields(node)
             methods = get_methods(node)
 
             cols = sorted(fields.union(methods))
 
+            print("# Attributes", len(cols))
+            print("# Feature vectors", len(node.methods))
+            
             df = pd.DataFrame(columns=cols, dtype=int)
             for m in node.methods:
                 # make sure method is included in csv file
@@ -100,9 +104,6 @@ def parse(path: str):
                 m_methods = get_methods_accessed_by_method(m, methods)
 
                 for member in m_fields.union(m_methods):
-                    if member not in fields and member not in methods:
-                        print(member)
-
                     df.loc[m.name, member] = 1
             df = df.fillna(0)
 

feature_vectors/org.apache.xerces.dom.CoreDocumentImpl.csv

@@ -1,4 +1,4 @@
-,abort,actualEncoding,addEventListener,adoptNode,allowGrammarAccess,callUserDataHandlers,canRenameElements,changed,changes,checkDOMNSErr,checkNamespaceWF,checkQName,clearIdentifiers,clone,cloneNode,copyEventListeners,createAttribute,createAttributeNS,createCDATASection,createComment,createDocumentFragment,createDocumentType,createElement,createElementDefinition,createElementNS,createEntity,createEntityReference,createNotation,createProcessingInstruction,createTextNode,deletedText,dispatchEvent,docElement,docType,documentNumber,domNormalizer,encoding,errorChecking,fConfiguration,fDocumentURI,fFreeNLCache,fXPathEvaluator,freeNodeListCache,getAsync,getBaseURI,getDoctype,getDocumentElement,getDocumentURI,getDomConfig,getElementById,getElementsByTagName,getElementsByTagNameNS,getEncoding,getErrorChecking,getFeature,getIdentifier,getIdentifiers,getImplementation,getInputEncoding,getMutationEvents,getNodeListCache,getNodeName,getNodeNumber,getNodeType,getOwnerDocument,getStandalone,getStrictErrorChecking,getTextContent,getUserData,getUserDataRecord,getVersion,getXmlEncoding,getXmlStandalone,getXmlVersion,identifiers,importNode,insertBefore,insertedNode,insertedText,insertingNode,isKidOK,isNormalizeDocRequired,isValidQName,isXML11Version,isXMLName,isXMLVersionChanged,kidOK,load,loadXML,modifiedAttrValue,modifiedCharacterData,modifyingCharacterData,nodeCounter,nodeTable,normalizeDocument,putIdentifier,readObject,removeChild,removeEventListener,removeIdentifier,removeUserDataTable,removedAttrNode,removedNode,removingNode,renameNode,renamedAttrNode,renamedElement,replaceChild,replaceRenameElement,replacedCharacterData,replacedNode,replacedText,replacingData,replacingNode,saveXML,serialVersionUID,setAsync,setAttrNode,setDocumentURI,setEncoding,setErrorChecking,setInputEncoding,setMutationEvents,setStandalone,setStrictErrorChecking,setTextContent,setUserData,setUserDataTable,setVersion,setXmlEncoding,setXmlStandalone,setXmlVersion,standalone,undeferChildren,userData,version,writeObject,xml11Version,xmlVersionChanged,Node,UserDataHandler,kid,DOMMessageFormatter,DOMException,NamespaceContext
+,abort,actualEncoding,addEventListener,adoptNode,allowGrammarAccess,callUserDataHandlers,canRenameElements,changed,changes,checkDOMNSErr,checkNamespaceWF,checkQName,clearIdentifiers,clone,cloneNode,copyEventListeners,createAttribute,createAttributeNS,createCDATASection,createComment,createDocumentFragment,createDocumentType,createElement,createElementDefinition,createElementNS,createEntity,createEntityReference,createNotation,createProcessingInstruction,createTextNode,deletedText,dispatchEvent,docElement,docType,documentNumber,domNormalizer,encoding,errorChecking,fConfiguration,fDocumentURI,fFreeNLCache,fXPathEvaluator,freeNodeListCache,getAsync,getBaseURI,getDoctype,getDocumentElement,getDocumentURI,getDomConfig,getElementById,getElementsByTagName,getElementsByTagNameNS,getEncoding,getErrorChecking,getFeature,getIdentifier,getIdentifiers,getImplementation,getInputEncoding,getMutationEvents,getNodeListCache,getNodeName,getNodeNumber,getNodeType,getOwnerDocument,getStandalone,getStrictErrorChecking,getTextContent,getUserData,getUserDataRecord,getVersion,getXmlEncoding,getXmlStandalone,getXmlVersion,identifiers,importNode,insertBefore,insertedNode,insertedText,insertingNode,isKidOK,isNormalizeDocRequired,isValidQName,isXML11Version,isXMLName,isXMLVersionChanged,kidOK,load,loadXML,modifiedAttrValue,modifiedCharacterData,modifyingCharacterData,nodeCounter,nodeTable,normalizeDocument,putIdentifier,readObject,removeChild,removeEventListener,removeIdentifier,removeUserDataTable,removedAttrNode,removedNode,removingNode,renameNode,renamedAttrNode,renamedElement,replaceChild,replaceRenameElement,replacedCharacterData,replacedNode,replacedText,replacingData,replacingNode,saveXML,serialVersionUID,setAsync,setAttrNode,setDocumentURI,setEncoding,setErrorChecking,setInputEncoding,setMutationEvents,setStandalone,setStrictErrorChecking,setTextContent,setUserData,setUserDataTable,setVersion,setXmlEncoding,setXmlStandalone,setXmlVersion,standalone,undeferChildren,userData,version,writeObject,xml11Version,xmlVersionChanged,Node,UserDataHandler,kid,DOMException,DOMMessageFormatter,NamespaceContext
 getOwnerDocument,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
 getNodeType,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0
 getNodeName,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0

report/main.md

@@ -1,6 +1,7 @@
 ---
 author: Claudio Maggioni
 title: Information Modelling & Analysis -- Project 1
+geometry: margin=2.5cm,bottom=3cm
 ---
 
 <!--
@@ -31,6 +32,29 @@ Commit ID: **TBD**
 
 ## God Classes
 
+The first part of the project requires to label some classes of the _Xerces_ 
+project as "God classes" based on the number of methods each class has.
+Specifically, I label "God classes" the classes that have a number of methods
+six times the standard deviation above the the mean number of methods, i.e. where
+the condition
+
+$$|M(C)| > \mu(M) + 6\sigma(M)$$
+
+holds.
+
+To scan and compute the number of methods of each class I use the Python library `javalang`, which implements the Java AST and parser. The Python script
+`./find_god_classes.py` uses this library to parse each file in the project and 
+compute the number of methods of each class. Note that only non-constructor methods are counted (specifically the code counts the number of `method` nodes in each `ClassDeclaration` node).
+
+Then, the script computes mean and standard 
+deviation of the number of methods and filters the list of classes according to the 
+condition described above. The file `god_classes/god_classes.csv` then is outputted
+listing all the god classes found.
+
+The god classes I identified, and their corresponding number of methods
+can be found in Table [1](#tab:god_classes){reference-type="ref"
+reference="tab:god_classes"}. 
+
 ::: {#tab:god_classes}
   ---------------------------------------------- ---------------
   **Class Name**                                  **\# Methods**
@@ -43,11 +67,6 @@ Commit ID: **TBD**
   : Identified God Classes
 :::
 
-The god classes I identified, and their corresponding number of methods
-can be found in Table [1](#tab:god_classes){reference-type="ref"
-reference="tab:god_classes"}. 
-
-Note: the number of methods was computed by considering only methods and not constructors.
 
 ## Feature Vectors