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How to use absolute_paths method in prospector

Best Python code snippet using prospector_python

paths.py

Source:paths.py

1import importlib2from pathlib import Path3from typing import Callable, List, NewType, Type4from fs.base import FS5from fs.osfs import OSFS6AbsolutePath = NewType("AbsolutePath", Path)7def load_class_by_full_path(path_to_mapper_obj: str) -> Type:8    *path, name = path_to_mapper_obj.split(".")9    try:10        module = importlib.import_module(".".join(path))11    except ModuleNotFoundError as e:12        raise ValueError(f'Module {".".join(path)} not defined.') from e13    except ValueError as e:14        raise ValueError(f"Invalid full path: {path_to_mapper_obj}") from e15    try:16        return getattr(module, name)17    except AttributeError as e:18        raise ValueError(f"Class {name} not found in module {module}") from e19def normalize_paths(20    paths: List[str], fs: FS, predicate: Callable[[Path], bool]21) -> List[str]:22    """23    >>> from fs.memoryfs import MemoryFS24    >>> fs = MemoryFS()25    >>> _ = fs.makedirs('root')26    >>> _ = fs.makedirs('root/dir1')27    >>> _ = fs.makedirs('root/dir2')28    >>> _ = fs.touch('root/file0.txt')29    >>> fs.touch('root/dir1/file11.txt')30    >>> fs.touch('root/dir1/file12.txt')31    >>> fs.touch('root/dir2/file21.txt')32    >>> fs.touch('root/dir2/file22.txt')33    >>> absolute_paths = normalize_paths(['root/file0.txt'], fs, lambda x: True)34    >>> [str(Path(path)) for path in absolute_paths]35    ['root/file0.txt']36    >>> absolute_paths = normalize_paths(['root/file0.txt', 'root/dir1/file11.txt'], fs, lambda x: True)37    >>> [str(Path(path)) for path in absolute_paths]38    ['root/dir1/file11.txt', 'root/file0.txt']39    >>> absolute_paths = normalize_paths(['root/file0.txt', 'root/dir1/file11.txt', 'root/dir1/file12.txt'], fs, lambda x: True)40    >>> [str(Path(path)) for path in absolute_paths]41    ['root/dir1', 'root/file0.txt']42    >>> absolute_paths = normalize_paths(['root/file0.txt', 'root/dir1', 'root/dir1/file12.txt'], fs, lambda x: True)43    >>> [str(Path(path)) for path in absolute_paths]44    ['root/dir1', 'root/file0.txt']45    >>> absolute_paths = normalize_paths(['root/file0.txt', 'root/dir1', 'root/dir1/file11.txt', 'root/dir1/file12.txt'], fs, lambda x: True)46    >>> [str(Path(path)) for path in absolute_paths]47    ['root/dir1', 'root/file0.txt']48    """49    non_collapsable = set()50    absolute_paths = [Path(path) for path in paths]51    grouped = {}52    for path in absolute_paths:53        if path.parent not in grouped:54            grouped[path.parent] = set()55        grouped[path.parent].add(path.name)56    while len(grouped) > 0:57        group, children = next(iter(grouped.items()))58        if not fs.exists(str(group)):59            raise ValueError(f"Path {group} does not exist")60        if (61            not group.parent in grouped or not group.name in grouped[group.parent]62        ) and not str(group) in non_collapsable:63            all_children_included = True64            _, dirs, files = next(fs.walk(str(group)))65            for path in dirs + files:66                path = Path(path.name)67                if path.parts[0] not in children and (68                    predicate is None or predicate(path)69                ):70                    all_children_included = False71                    break72            if all_children_included:73                if group.parent not in grouped:74                    grouped[group.parent] = set()75                grouped[group.parent].add(group.name)76            else:77                non_collapsable = non_collapsable.union(78                    [str((group / child)) for child in children]79                )80        del grouped[group]81    return sorted(non_collapsable)82def create_fs() -> FS:83    path = Path(".").resolve()84    current_path = path85    while True:86        lst = list(current_path.glob("bohr.py"))87        if len(lst) > 0 and lst[0].is_file():88            return OSFS(str(current_path))89        elif current_path == Path("/"):90            raise ValueError(91                f"Not a bohr directory: {path}. "92                f"Bohr config dir is not found in this or any parent directory"93            )94        else:95            current_path = current_path.parent96def gitignore_file(fs: FS, filename: str):97    """98    >>> from fs.memoryfs import MemoryFS99    >>> fs = MemoryFS()100    >>> gitignore_file(fs, 'file')101    >>> fs.readtext(".gitignore")102    'file\\n'103    >>> fs = MemoryFS()104    >>> fs.touch('file')105    >>> gitignore_file(fs, 'file')106    >>> fs.readtext(".gitignore")107    'file\\n'108    >>> gitignore_file(fs, 'file')109    >>> fs.readtext(".gitignore")110    'file\\n'111    >>> gitignore_file(fs, 'file2')112    >>> fs.readtext(".gitignore")113    'file\\nfile2\\n'114    """115    fs.touch(".gitignore")116    with fs.open(".gitignore", "r") as f:117        lines = list(map(lambda l: l.rstrip("\n"), f.readlines()))118        if filename not in lines:119            with fs.open(".gitignore", "a") as a:...

plugin_fs_hierarchy.py

Source:plugin_fs_hierarchy.py

1"""2<author>3  Savvas Savvides4<created>5  May 20136<description>7  Uses the parser to get a list of actions. Examines actions that contain a path8  and constructs the fs hierarchy of all files that exist.9  This program aims for simplicity, not efficiency.10  This is meant to be a quick plugin to demonstrate the parser's usability. This 11  is not meant to be an optimal implementation12"""13import os14import sys15import parser_truss_calls16import parser_strace_calls17def print_fs_hierarchy(hierarchy, depth, path):18  """19    <Purpose>20      A recursive functin used to print the given hierarchy21    <Arguments>22      hierarchy: A dictionary representing the hierarchy.23    <Returns>24      None25  """26  # first print current path part27  print "    " * (depth),28  print path29  30  children = []31  if path in hierarchy:32    children = hierarchy[path]33    children.sort()34  35  for child in children:36    print_fs_hierarchy(hierarchy, depth+1, child)37def construct_hierarchy(paths, start):38  """39    <Purpose>40      Given a list of paths, construct and return their hierarchy41    <Arguments>42      paths: A list of paths43    <Returns>44      hierarchy: a dictionary with the hierarchy.45  """46  hierarchy = {}47  # first add the root48  hierarchy[start] = []49  for path in paths:50    # get the parts of the path51    parts = path.strip("./").split("/")52    parts = filter(None, parts)53    for part_index in range(len(parts)):54      # get the preceding part55      if part_index == 0:56        pre = start57      else:58        pre = "/" + "/".join(parts[:part_index])59      60      current_path = "/" + "/".join(parts[:part_index+1])61      # add current path to the list of the preceding part62      if current_path not in hierarchy[pre]:63        hierarchy[pre].append(current_path)64      # create an entry for the current part65      if current_path not in hierarchy:66        hierarchy[current_path] = []67  return hierarchy68def extract_paths(actions):69  """70    <Purpose>71      Given a list of actions, it extracts all the absolute and relative paths72      from all the actions.73    <Arguments>74      actions: A list of actions from a parsed trace75    <Returns>76      absolute_paths: a list with all absolute paths extracted from the actions77      relative_paths: a list with all relative paths extracted from the actions78  """79  absolute_paths = []80  relative_paths = []81  actions_with_path = ['open', 'creat', 'statfs', 'access', 'stat', 82                        'link', 'unlink', 'chdir', 'rmdir', 'mkdir']83  for action in actions:84    # get the name of the syscall and remove the "_syscall" part at the end.85    action_name = action[0][:action[0].find("_syscall")]86    87    # we only care about actions containing paths88    if action_name not in actions_with_path:89      continue90    # we only care about paths that exist91    action_result = action[2]92    if action_result == (-1, 'ENOENT'):93      continue94    path = action[1][0]95    if path.startswith("/"):96      if path not in absolute_paths:97        absolute_paths.append(path)98    else:99      if path not in relative_paths:100        relative_paths.append(path)101    # get the second path of link102    if action_name == "link":103      path = action[1][1]104      if path.startswith("/"):105        if path not in absolute_paths:106          absolute_paths.append(path)107      else:108        if path not in relative_paths:109          relative_paths.append(path)110  return absolute_paths, relative_paths111if __name__ == "__main__":112  if len(sys.argv) != 2:113    raise Exception("Please provide: trace file")114  115  fh = open(sys.argv[1], "r")116  actions = parser_strace_calls.parse_trace(fh)117  118  absolute_paths, relative_paths = extract_paths(actions)119  absolute_hierarchy = construct_hierarchy(absolute_paths, "/")120  print_fs_hierarchy(absolute_hierarchy, depth=0, path="/")121  print122  relative_hierarchy = construct_hierarchy(relative_paths, ".")123  print_fs_hierarchy(relative_hierarchy, depth=0, path=".")...

data_handler.py

Source:data_handler.py

1import os2import torch3from torch.utils.data import Dataset4import numpy as np5class Data_Handler(Dataset):6    def __init__(self, dataset_path, subset, transform=None):7        self.subset = subset8        self.transform = transform9        10        # Load data absolute paths from the dataset file11        with open(dataset_path, 'rb') as f:12            self.absolute_paths = np.load(f, allow_pickle=True).item()13            14    def __len__(self):15        for subset_key in self.absolute_paths:16            if self.subset in subset_key:17                return len(self.absolute_paths[subset_key])18        return 019    def __getitem__(self, i):20        header = image = mask = []21        for subset_key in self.absolute_paths:22            if self.subset in subset_key:23                subset_file_paths = self.absolute_paths[subset_key]24                sample_file_paths = list(subset_file_paths[i].values())25                # Load header26                file_path = sample_file_paths[0]27                if (os.path.exists(file_path)):28                    with open(file_path, 'rb') as f:29                        header = np.load(f, allow_pickle=True)30                file_path = sample_file_paths[1]31                32                if (os.path.exists(file_path)):33                    with open(file_path, 'rb') as f:34                        image = np.load(f, allow_pickle=True)35                36                # Load mask37                if not self.subset == 'test':38                    file_path = sample_file_paths[2]39                    if (os.path.exists(file_path)):40                        with open(file_path, 'rb') as f:41                            mask = np.load(f, allow_pickle=True)42        sample = {43            'header': header.item(),44            'image': np.expand_dims(image, axis=0),45            'mask': np.expand_dims(mask, axis=0)46        }47        48        if self.transform is not None:49            sample = self.transform(sample)50            ...

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