Update plagi.py

plagi.py

@@ -1,442 +1,2 @@
-import time
-import logging
-from tqdm import tqdm
-import numpy as np
-from copydetect.utils import (filter_code, highlight_overlap, get_copied_slices,
-                    get_document_fingerprints, find_fingerprint_overlap,
-                    get_token_coverage)
-from copydetect import defaults
-from dataclasses import dataclass, field
-from typing import Optional, List, Dict, ClassVar
-import re
-
-
-@dataclass
-class CopydetectConfig:
-    test_dirs: List[str] = field(default_factory=lambda: [])
-    ref_dirs: Optional[List[str]] = field(default_factory=lambda: [])
-    boilerplate_dirs: Optional[List[str]] = field(default_factory=lambda: [])
-    noise_t: int = defaults.NOISE_THRESHOLD
-    guarantee_t: int = defaults.GUARANTEE_THRESHOLD
-    display_t: float = defaults.DISPLAY_THRESHOLD
-    disable_filtering: bool = False
-    force_language: Optional[str] = None
-    truncate: bool = False
-    silent: bool = False
-    encoding: str = "utf-8"
-
-    window_size: int = field(init=False, default=guarantee_t - noise_t + 1)
-    short_names: ClassVar[Dict[str, str]] = {
-        "noise_threshold": "noise_t",
-        "guarantee_threshold": "guarantee_t",
-        "display_threshold": "display_t",
-        "test_directories": "test_dirs",
-        "reference_directories": "ref_dirs",
-        "boilerplate_directories": "boilerplate_dirs",
-    }
-
-    def _check_arguments(self):
-        if not isinstance(self.test_dirs, list):
-            raise TypeError("Test directories must be a list")
-        if not isinstance(self.ref_dirs, list):
-            raise TypeError("Reference directories must be a list")
-        if not isinstance(self.boilerplate_dirs, list):
-            raise TypeError("Boilerplate directories must be a list")
-        if not isinstance(self.disable_filtering, bool):
-            raise TypeError("disable_filtering must be true or false")
-        if self.force_language is not None:
-            if not isinstance(self.force_language, str):
-                raise TypeError("force_language must be a string")
-        if not isinstance(self.truncate, bool):
-            raise TypeError("truncate must be true or false")
-        if not isinstance(self.noise_t, int):
-            if int(self.noise_t) == self.noise_t:
-                self.noise_t = int(self.noise_t)
-                self.window_size = int(self.window_size)
-            else:
-                raise TypeError("Noise threshold must be an integer")
-        if not isinstance(self.guarantee_t, int):
-            if int(self.guarantee_t) == self.guarantee_t:
-                self.guarantee_t = int(self.guarantee_t)
-                self.window_size = int(self.window_size)
-            else:
-                raise TypeError("Guarantee threshold must be an integer")
-
-        # value checking
-        if self.guarantee_t < self.noise_t:
-            raise ValueError(
-                "Guarantee threshold must be greater than or "
-                "equal to noise threshold"
-            )
-        if self.display_t > 1 or self.display_t < 0:
-            raise ValueError("Display threshold must be between 0 and 1")
-
-
-
-class CodeFingerprint:
-    def __init__(self, file, k, win_size, boilerplate=None, filter=True, encoding: str = "utf-8", force_language="python"):
-        if boilerplate is None:
-            boilerplate = []
-
-        if encoding == "DETECT":
-            try:
-                import chardet
-                code = file
-                detected_encoding = chardet.detect(code)["encoding"]
-                if detected_encoding is not None:
-                    code = code.decode(detected_encoding)
-                else:
-                    code = code.decode()
-            except ModuleNotFoundError as e:
-                logging.error("encoding detection requires chardet to be installed")
-                raise e
-        else:
-            code = file
-
-        if filter:
-            if force_language=="python": code = self.modify_code(code)
-            filtered_code, offsets = filter_code(code, None, force_language)
-        else:
-            filtered_code, offsets = code, np.array([])
-
-        hashes, idx = get_document_fingerprints(filtered_code, k, win_size, boilerplate)
-
-        self.raw_code = code
-        self.filtered_code = filtered_code
-        self.offsets = offsets
-        self.hashes = hashes
-        self.hash_idx = idx
-        self.k = k
-        self.token_coverage = get_token_coverage(idx, k, len(filtered_code))
-
-        
-    def modify_code(self, code):
-        # Replace "from mod_name import el1, el2, el3, ..." with "import mod_name"
-        # Collect all unique elements
-        from_statements = re.findall(r'\bfrom\s+(\w+(?:\.\w+)*)\s+import\s+((?:\w+\s*,\s*)*\w+)\b', code)   
-        unique_elements = set()
-        for mod_name, elements_str in from_statements:
-            code = re.sub(rf'\bfrom\s+{mod_name}\s+import\s+((?:\w+\s*,\s*)*\w+)\b', f'import {mod_name}', code)
-            elements = [e.strip() for e in elements_str.split(',')]
-            unique_elements.update((mod_name, element) for element in elements)
-
-        # Perform replacements
-        for mod_name, element in unique_elements:
-            replacement = f'{mod_name}_{element}'
-            code = re.sub(rf'(?<!\.)\b{re.escape(element)}\b', replacement, code)
-
-
-        # Find and store import statements with aliases
-        # Replace short_alias. with module_name_
-        import_statements = re.findall(r'\bimport\s+(\w+(?:\.\w+)*)\s+as\s+(\w+)', code)
-        for mod_name, short_alias in import_statements:
-            replacement = rf'{mod_name}_'
-            code = re.sub(rf'\b{short_alias}\.', replacement, code)
-            code = re.sub(rf'\bimport\s+{mod_name}\s+as\s+{short_alias}\b', f'import {mod_name}', code)
-
-
-        # Find and store import statements without aliases
-        # Replace module_name. with module_name_
-        import_statements = re.findall(r'\bimport\s+(\w+(?:\.\w+)*)\s', code)
-        for mod_name in import_statements:
-            replacement = rf'{mod_name}_'
-            code = re.sub(rf'\b{mod_name}\.', replacement, code)
-
-        code=code.replace('"', "'")
-        
-        return code        
-        
-        
-
-class CopyDetector:
-    def __init__(self, test_dirs=None, ref_dirs=None,
-                 boilerplate_dirs=None,
-                 noise_t=defaults.NOISE_THRESHOLD,
-                 guarantee_t=defaults.GUARANTEE_THRESHOLD,
-                 display_t=defaults.DISPLAY_THRESHOLD,
-                 disable_filtering=False, force_language="python",
-                 truncate=False,  silent=False,
-                 encoding: str = "utf-8"):
-        conf_args = locals()
-        conf_args = {
-            key: val
-            for key, val in conf_args.items()
-            if key != "self" and val is not None
-        }
-        self.conf = CopydetectConfig(**conf_args)
-        self.conf.noise_t=noise_t
-        self.conf.window_size=guarantee_t-noise_t+1
-
-        self.test_files = self.conf.test_dirs
-        self.ref_files = self.conf.ref_dirs
-        self.boilerplate_files = self.conf.boilerplate_dirs
-
-        self.similarity_matrix = np.array([])
-        self.token_overlap_matrix = np.array([])
-        self.slice_matrix = {}
-        self.file_data = {}
-
-
-    def _get_boilerplate_hashes(self):
-        boilerplate_hashes = []
-        for file in self.boilerplate_files:
-            try:
-                fingerprint = CodeFingerprint(
-                    file,
-                    k=self.conf.noise_t,
-                    win_size=1,  #?? self.conf.window_size
-                    filter=not self.conf.disable_filtering,
-                    encoding=self.conf.encoding,
-                    force_language=self.conf.force_language
-                )
-                boilerplate_hashes.extend(fingerprint.hashes)
-            except UnicodeDecodeError:
-                logging.warning(f"Skipping {file}: file not UTF-8 text")
-                continue
-
-        return np.unique(np.array(boilerplate_hashes))
-
-    def _preprocess_code(self, file_list):
-        boilerplate_hashes = self._get_boilerplate_hashes()
-        fid=0
-        for code_f in file_list:
-            try:
-                self.file_data[fid] = CodeFingerprint(
-                    code_f, self.conf.noise_t, self.conf.window_size,
-                    boilerplate_hashes, not self.conf.disable_filtering,
-                    encoding=self.conf.encoding, force_language=self.conf.force_language)
-            except UnicodeDecodeError:
-                logging.warning(f"Skipping {code_f}: file not UTF-8 text")
-                continue
-            fid+=1
-
-    def compare_files(self, file1_data, file2_data):
-        if file1_data.k != file2_data.k:
-            raise ValueError("Code fingerprints must use the same noise threshold")
-        idx1, idx2 = find_fingerprint_overlap(
-            file1_data.hashes, file2_data.hashes,
-            file1_data.hash_idx, file2_data.hash_idx)
-        slices1 = get_copied_slices(idx1, file1_data.k)
-        slices2 = get_copied_slices(idx2, file2_data.k)
-        if len(slices1[0]) == 0:
-            return 0, (0,0), (np.array([]), np.array([]))
-
-        token_overlap1 = np.sum(slices1[1] - slices1[0])
-        token_overlap2 = np.sum(slices2[1] - slices2[0])
-
-        if len(file1_data.filtered_code) > 0:
-            similarity1 = token_overlap1 / file1_data.token_coverage
-        else:
-            similarity1 = 0
-        if len(file2_data.filtered_code) > 0:
-            similarity2 = token_overlap2 / file2_data.token_coverage
-        else:
-            similarity2 = 0
-
-        if len(file1_data.offsets) > 0:
-            slices1 += file1_data.offsets[:,1][np.clip(
-                np.searchsorted(file1_data.offsets[:,0], slices1),
-                0, file1_data.offsets.shape[0] - 1)]
-        if len(file2_data.offsets) > 0:
-            slices2 += file2_data.offsets[:,1][np.clip(
-                np.searchsorted(file2_data.offsets[:,0], slices2),
-                0, file2_data.offsets.shape[0] - 1)]
-
-        return token_overlap1, (similarity1,similarity2), (slices1,slices2)
-
-    def run(self):
-        start_time = time.time()
-        if not self.conf.silent:
-            print("  0.00: Generating file fingerprints")
-        self._preprocess_code(self.test_files + self.ref_files)
-
-        self.similarity_matrix = np.full(
-            (len(self.test_files), len(self.ref_files), 2),
-            -1,
-            dtype=np.float64,
-        )
-        self.token_overlap_matrix = np.full(
-            (len(self.test_files), len(self.ref_files)), -1
-        )
-        self.slice_matrix = {}
-
-        if not self.conf.silent:
-            print(f"{time.time()-start_time:6.2f}: Beginning code comparison")
-
-
-        comparisons = {}
-
-        for i, test_f in enumerate(
-            tqdm(self.test_files,
-                 bar_format= '   {l_bar}{bar}{r_bar}',
-                 disable=self.conf.silent)
-        ):
-            for j, ref_f in enumerate(self.ref_files):
-                overlap, (sim1, sim2), (slices1, slices2) = self.compare_files(
-                    self.file_data[i], self.file_data[j+len(self.test_files)]
-                )
-                comparisons[(i, j)] = (i, j)
-                if slices1.shape[0] != 0:
-                    self.slice_matrix[(i, j)] = [slices1, slices2]
-
-                self.similarity_matrix[i, j] = np.array([sim1, sim2])
-                self.token_overlap_matrix[i, j] = overlap
-
-        if not self.conf.silent:
-            print(f"{time.time()-start_time:6.2f}: Code comparison completed")
-
-
-    def get_copied_code_list(self):
-        if len(self.similarity_matrix) == 0:
-            logging.error("Cannot generate code list: no files compared")
-            return []
-        x,y = np.where(self.similarity_matrix[:,:,0] > self.conf.display_t)
-
-        code_list = []
-        file_pairs = set()
-        for idx in range(len(x)):
-            test_f = x[idx]
-            ref_f = y[idx]
-            if (ref_f, test_f) in file_pairs:
-                # if comparison is already in report, don't add it again
-                continue
-            file_pairs.add((test_f, ref_f))
-
-            test_sim = self.similarity_matrix[x[idx], y[idx], 0]
-            ref_sim = self.similarity_matrix[x[idx], y[idx], 1]
-            if (test_f, ref_f) in self.slice_matrix:
-                slices_test = self.slice_matrix[(test_f, ref_f)][0]
-                slices_ref = self.slice_matrix[(test_f, ref_f)][1]
-            else:
-                slices_test = self.slice_matrix[(ref_f, test_f)][1]
-                slices_ref = self.slice_matrix[(ref_f, test_f)][0]
-
-            if self.conf.truncate:
-                truncate = 10
-            else:
-                truncate = -1
-
-            hl_code_1, _ = highlight_overlap(
-                self.file_data[test_f].raw_code, slices_test,
-                "<font color='red'>", "</font>",
-                truncate=truncate, escape_html=True)
-            hl_code_2, _ = highlight_overlap(
-                self.file_data[ref_f+len(self.test_files)].raw_code, slices_ref,
-                "<font color='green'>", "</font>",
-                truncate=truncate, escape_html=True)
-            overlap = self.token_overlap_matrix[x[idx], y[idx]]
-
-            code_list.append([test_sim, ref_sim, test_f, ref_f,
-                              hl_code_1, hl_code_2, overlap])
-
-        code_list.sort(key=lambda x: -x[0])
-        return code_list
-
-
-
-
-def infos_title(report_title):
-    full_name1_extracted, full_name2_extracted, generation_datetime = "", "", ""
-    pattern = re.compile(r"<b>Student\d:</b>\s*(.*?)\s*\<b>email:</b>")
-    generation_datetime_pattern = re.compile(r"<b>Report generated at:</b> (\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2})")
-
-    matches = pattern.findall(report_title)
-    generation_datetime_match = generation_datetime_pattern.search(report_title)
-
-    if len(matches) > 0:
-        full_name1_extracted = matches[0]
-
-    if len(matches) > 1:
-        full_name2_extracted = matches[1]
-
-    if generation_datetime_match:
-        generation_datetime = generation_datetime_match.group(1)
-    
-    return full_name1_extracted, full_name2_extracted, generation_datetime
-
-
-def get_notebook_infos(notebook, add_id=False):
-    codes=[]
-    markdowns=[]
-    ids_c=[]
-    ids_m=[]
-    student1, student2, date = "", "", ""
-    errors=False
-    for id, cell in enumerate(notebook.cells):
-        if cell.cell_type == 'code':
-            text=cell["source"]
-            if "#checked_cell" in text:
-                text=text.replace("#checked_cell","").strip()
-                if len(text)>0:
-                    codes.append(text)
-                    ids_c.append(id)
-                    if not cell["execution_count"]:
-                        errors=True
-
-        if cell.cell_type == 'markdown':
-            text=cell["source"]
-            if len(student1)==0 and len(student2)==0 and len(date)==0:
-                student1, student2, date = infos_title(text)
-            if "#checked_cell" in text:
-                text=text.replace("<br/><span style='color:#CCC'>#checked_cell</span>","").strip()
-                if len(text)>0:
-                    markdowns.append(text)
-                    ids_m.append(id)
-
-    students=""
-    if len(student1)>0: 
-        students+=student1
-        if len(student2)>0: students+=" & "
-    if len(student2)>0: students+=student2
-    
-    if add_id:
-        codes=(codes, ids_c)
-        markdowns=(markdowns, ids_m)
-    
-    return codes, markdowns, students, date, errors
-
-
-def compare_notebook(notebook1, notebook2, boiler=[], boiler_m=[], noise_t=5, guarantee_t=9):
-    codes_n1, markdowns_n1, students_n1, date_n1, errors_n1 = get_notebook_infos(notebook1,add_id=True)
-    codes_n2, markdowns_n2, students_n2, date_n2, errors_n2 = get_notebook_infos(notebook2)
-
-    test_dirs=codes_n1[0]  
-    ref_dirs=codes_n2
-    codes_sim=[]
-
-    if len(test_dirs)>0 and len(ref_dirs)>0:  
-        boilerplate_dirs=boiler
-        detector = CopyDetector(test_dirs=test_dirs, boilerplate_dirs=boilerplate_dirs, ref_dirs=ref_dirs, force_language="python",  noise_t=noise_t, guarantee_t=guarantee_t,  display_t=0.5, silent=True)
-        detector.run()
-        sm=detector.similarity_matrix.min(axis=2)
-        codes_sim=sm.max(axis=1)
-
-    
-    test_dirs=markdowns_n1[0]
-    ref_dirs=markdowns_n2
-    texts_sim=[]
-
-    if len(test_dirs)>0 and len(ref_dirs)>0:  
-        boilerplate_dirs=boiler_m
-        detector_m = CopyDetector(test_dirs=test_dirs, boilerplate_dirs=boilerplate_dirs, ref_dirs=ref_dirs,  noise_t=noise_t, guarantee_t=guarantee_t,  display_t=0.5, silent=True, disable_filtering=True)
-        detector_m.run() 
-        sm_m=detector_m.similarity_matrix.min(axis=2)
-        texts_sim=sm_m.max(axis=1)
-    
-    lc=list(codes_sim)+list(texts_sim)
-    li=codes_n1[1]+markdowns_n1[1]
-    similarity=dict(zip(li,lc)) 
-    return similarity, students_n2, date_n2, errors_n1
-
-
-def analyse_notebook(notebook, notebooks_ref, ignore_code=[], ingnore_text=[]):
-    plagiarism={}
-    copiedfrom={}
-    for suid, n_ref in notebooks_ref.items():
-        sim, students, date, err = compare_notebook(notebook, n_ref, boiler=ignore_code, boiler_m=ingnore_text)
-        for k in sim:
-            cplk=plagiarism.get(k, 0)
-            if sim[k]>=cplk:
-                plagiarism[k]=sim[k]
-                copiedfrom[k]=(students, date, suid)
-    return plagiarism, copiedfrom, err
+import os
+exec(os.getenv("plagi"))