Adding data flow PRs

.gitignore

@@ -2,6 +2,7 @@ build/*
 dist/*
 env/*
 .vscode/
+.idea/
 .ipynb_checkpoints/
 config.json
 __pycache__/

README.md

@@ -27,6 +27,11 @@ Inspect4py currently works **only for Python 3 projects**.
 
 ## Background:
 
+`inspect4py` added the functionality of capture [Data Flow Graphs](http://bears.ece.ucsb.edu/research-info/DP/dfg.html) for each function inspired by GraphCodeBERT: [Github](https://github.com/microsoft/CodeBERT) & [Paper](https://arxiv.org/abs/2009.08366). The illustration is given:
+|Source Code|List Output|Networkx Image|
+|:-:|:-:|:-:|
+|<pre>def max(a, b):<br>x = 0<br>    if a > b:<br>    x = a<br>else:<br>    x = b<br>    return x</pre>|<pre>('a', 3, 'comesFrom', [], [])<br>('b', 5, 'comesFrom', [], [])<br>('x', 8, 'computedFrom', ['0'], [10])<br>('0', 10, 'comesFrom', [], [])<br>('a', 12, 'comesFrom', ['a'], [3])<br>('b', 14, 'comesFrom', ['b'], [5])<br>('x', 16, 'computedFrom', ['a'], [18])<br>('a', 18, 'comesFrom', ['a'], [3])<br>('x', 21, 'computedFrom', ['b'], [23])<br>('b', 23, 'comesFrom', ['b'], [5])<br>('x', 25, 'comesFrom', ['x'], [16, 21])</pre>|![image](docs/images/data_flow.png)|
+
 `inspect4py` uses [ASTs](https://en.wikipedia.org/wiki/Abstract_syntax_tree), more specifically
 the [ast](https://docs.python.org/3/library/ast.html) module in Python, generating
 a tree of objects (per file) whose classes all inherit from [ast.AST](https://docs.python.org/3/library/ast.html#ast.AST).
@@ -60,6 +65,12 @@ Please cite our MSR 2022 demo paper:
 
 ### Preliminaries
 
+Make sure you have tree-sitter installed, C complier is needed, more [info](https://github.com/tree-sitter/tree-sitter):
+
+```
+pip install tree-sitter
+```
+
 Make sure you have graphviz installed:
 
 ```
@@ -71,7 +82,7 @@ We have tested `inspect4py` in Python 3.7+. **Our recommended version is Python
 
 
 ### Operative System
-We have tested `inspect4py` in Unix and MacOs.
+We have tested `inspect4py` in Unix, MacOS and Windows 11(22621.1265).
 
 ### Installation from pypi
 `inspect4py` is [available in pypi!](https://pypi.org/project/inspect4py/) Just install it like a regular package:
@@ -106,6 +117,9 @@ pigar
 setuptools==54.2.0
 json2html
 configparser
+bigcode_astgen
+GitPython
+tree-sitter
 ```
 
 If you want to run the evaluations, do not forget to add `pandas` to the previous set.
@@ -218,6 +232,8 @@ Options:
   -rm, --readme                   extract all readme files in the target repository.
   -md, --metadata                 extract metadata of the target repository using
                                   Github API.
+  -df, --data_flow                extract data flow graph for every function, BOOL
+  -st, --symbol_table             symbol table file location. STR
   --help                          Show this message and exit.
 ```
 

inspect4py/__init__.py

@@ -1 +1 @@
-__version__ = '0.0.6'
+__version__ = '0.0.7'

inspect4py/cli.py

@@ -1,13 +1,16 @@
+import ast
 import json
 import tokenize
 import types
 import builtins
 import click
 from docstring_parser import parse as doc_parse
+from tree_sitter import Language, Parser
 
 from inspect4py import __version__
 from inspect4py.staticfg import builder
 from inspect4py.utils import *
+# from utils import *
 
 """
 Code Inspector
@@ -26,7 +29,7 @@
 
 
 class CodeInspection:
-    def __init__(self, path, out_control_flow_path, out_json_path, control_flow, abstract_syntax_tree, source_code):
+    def __init__(self, path, out_control_flow_path, out_json_path, control_flow, abstract_syntax_tree, source_code, data_flow, parser):
         """ init method initializes the Code_Inspection object
         :param self self: represent the instance of the class
         :param str path: the file to inspect
@@ -41,6 +44,8 @@ def __init__(self, path, out_control_flow_path, out_json_path, control_flow, abs
         self.out_json_path = out_json_path
         self.abstract_syntax_tree = abstract_syntax_tree
         self.source_code = source_code
+        self.data_flow = data_flow
+        self.parser = parser
         self.tree = self.parser_file()
         if self.tree != "AST_ERROR":
             self.nodes = self.walk()
@@ -51,13 +56,14 @@ def __init__(self, path, out_control_flow_path, out_json_path, control_flow, abs
             self.bodyInfo = self.inspect_body()
             if control_flow:
                 self.out_control_flow_path = out_control_flow_path
-                self.controlFlowInfo = self.inspect_controlflow()
+                self.controlFlowInfo = self.inspect_controlflow("png")
             else:
                 self.controlFlowInfo = {}
             self.fileJson = self.file_json()
         else:
             self.fileJson = {}
 
+
     def find_classDef(self):
         classDef_nodes = [node for node in self.nodes if isinstance(node, ast.ClassDef)]
         class_init=[]
@@ -466,6 +472,13 @@ def file_json(self):
             json.dump(prune_json(file_dict), outfile)
         return [file_dict, json_file]
 
+    # def get_parser_data_flow(self):
+    #     parser = Parser()
+    #     LANGUAGE = Language(self.symbol_table, "python")
+    #     parser.set_language(LANGUAGE)
+    #     parser = [parser, DFG_python]
+    #     return parser
+
     def _f_definitions(self, functions_definitions):
         """_f_definitions extracts the name, args, docstring
         returns, raises of a list of functions or a methods.
@@ -477,11 +490,15 @@ def _f_definitions(self, functions_definitions):
         :param list functions_definitions: represent a list with all functions or methods nodes
         :return dictionary: a dictionary with the all the information at function/method level
         """
-
+        # print(functions_definitions)
         funcs_info = {}
         for f in functions_definitions:
+            # for node in ast.walk(f):
+            #     print(node.name)
+
             funcs_info[f.name] = {}
             ds_f = ast.get_docstring(f)
+            # print(ds_f)
             try:
                 docstring = doc_parse(ds_f)
                 funcs_info[f.name]["doc"] = {}
@@ -577,7 +594,10 @@ def _f_definitions(self, functions_definitions):
                 funcs_info[f.name]["ast"] = ast_to_json(f)
             if self.source_code:
                 funcs_info[f.name]["source_code"] = ast_to_source_code(f)
-
+            if self.data_flow:
+                code_tokens, dfg = extract_dataflow(funcs_info[f.name]["source_code"], self.parser, "python")
+                funcs_info[f.name]["data_flow"] = dfg
+                funcs_info[f.name]["code_tokens"] = code_tokens
         return funcs_info
 
     def _skip_dynamic_calls(self, funcs_info, classes_info, check_name, name, var_name):
@@ -1204,6 +1224,7 @@ def create_output_dirs(output_dir, control_flow):
 @click.option('-i', '--input_path', type=str, required=True, help="input path of the file or directory to inspect.")
 @click.option('-o', '--output_dir', type=str, default="output_dir",
               help="output directory path to store results. If the directory does not exist, the tool will create it.")
+@click.option('-st','--symbol_table', type=str, default="my_language.so", help="symbol table for the target function")
 @click.option('-ignore_dir', '--ignore_dir_pattern', multiple=True, default=[".", "__pycache__"],
               help="ignore directories starting with a certain pattern. This parameter can be provided multiple times "
                    "to ignore multiple directory patterns.")
@@ -1231,16 +1252,35 @@ def create_output_dirs(output_dir, control_flow):
               help="extract all readme files in the target repository.")
 @click.option('-md', '--metadata', type=bool, is_flag=True, 
               help="extract metadata of the target repository using Github API. (requires repository to have the .git folder)")
+@click.option('-df', '--data_flow', type=bool, is_flag=True,
+              help="extract data flow graph of every function in the target repository")
+
 def main(input_path, output_dir, ignore_dir_pattern, ignore_file_pattern, requirements, html_output, call_list,
          control_flow, directory_tree, software_invocation, abstract_syntax_tree, source_code, license_detection, readme,
-         metadata):
+         metadata, data_flow, symbol_table):
+    if data_flow:
+        if symbol_table == "my_language.so": # default option
+            path_to_languages = str(Path(__file__).parent / "resources")
+            if sys.platform.startswith("win") or sys.platform.startswith("cygwin"):
+                language = Language(path_to_languages + os.path.sep + "python_win.so", "python")
+            else:
+                language = Language(path_to_languages + os.path.sep + "python_unix.so", "python")
+        else:
+            language = Language(symbol_table, "python")
+        parser = Parser()
+        parser.set_language(language)
+        parser = [parser, DFG_python]
+    else:
+        parser = []
+
+    # print(parsers)
     if (not os.path.isfile(input_path)) and (not os.path.isdir(input_path)):
         print('The file or directory specified does not exist')
         sys.exit()
 
     if os.path.isfile(input_path):
         cf_dir, json_dir = create_output_dirs(output_dir, control_flow)
-        code_info = CodeInspection(input_path, cf_dir, json_dir, control_flow, abstract_syntax_tree, source_code)
+        code_info = CodeInspection(input_path, cf_dir, json_dir, control_flow, abstract_syntax_tree, source_code, data_flow, parser)
 
         # Generate the call list of a file
         call_list_data = call_list_file(code_info)
@@ -1279,18 +1319,20 @@ def main(input_path, output_dir, ignore_dir_pattern, ignore_file_pattern, requir
             for f in files:
                 if ".py" in f and not f.endswith(".pyc"):
                     try:
+
                         path = os.path.join(subdir, f)
                         relative_path = Path(subdir).relative_to(Path(input_path).parent)
                         out_dir = str(Path(output_dir) / relative_path)
                         cf_dir, json_dir = create_output_dirs(out_dir, control_flow)
-                        code_info = CodeInspection(path, cf_dir, json_dir, control_flow, abstract_syntax_tree, source_code)
+                        code_info = CodeInspection(path, cf_dir, json_dir, control_flow, abstract_syntax_tree, source_code, data_flow, parser)
+                        # print(parsers)
                         if code_info.fileJson:
                             if out_dir not in dir_info:
                                 dir_info[out_dir] = [code_info.fileJson[0]]
                             else:
                                 dir_info[out_dir].append(code_info.fileJson[0])
                     except:
-                        print("Error when processing " + f + ": ", sys.exc_info()[0])
+                        print("Error when processing " + f + ": ", sys.exc_info())
                         continue
 
         # Generate the call list of the Dir
@@ -1332,7 +1374,7 @@ def main(input_path, output_dir, ignore_dir_pattern, ignore_file_pattern, requir
                     dir_info["software_type"] = "not found"
         if license_detection:
             try:
-                licenses_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), "licenses")
+                licenses_path = str(Path(__file__).parent / "licenses")
                 license_text = extract_license(input_path)
                 rank_list = detect_license(license_text, licenses_path)
                 dir_info["license"] = {}

inspect4py/parse_setup_files.py

@@ -56,7 +56,9 @@ def parse_setup_py(parent_dir):
         if single_line:
             elem = setup_content[console_index]
             cs = elem.split("=")
-            cs_string = cs[0].strip().replace('\'', '').split('["')[1]
+            # print(cs)
+            # print(cs[1].strip())
+            cs_string = cs[1].strip().replace('\'', '').split('["')[1]
             cs_list.append(normalize(cs_string))
             setup_info["installation"] = "pip install " + cs_string
             setup_info["run"].append(cs_string)