diff --git a/requirements-swh.txt b/requirements-swh.txt index 850ffb6..c34a185 100644 --- a/requirements-swh.txt +++ b/requirements-swh.txt @@ -1,3 +1,3 @@ # Add here internal Software Heritage dependencies, one per line. swh.core >= 0.3 -swh.model >= 0.3.8 +swh.model >= 2.3.0 diff --git a/swh/scanner/benchmark_algos.py b/swh/scanner/benchmark_algos.py index 6a1d0dd..4523c66 100644 --- a/swh/scanner/benchmark_algos.py +++ b/swh/scanner/benchmark_algos.py @@ -1,417 +1,412 @@ # Copyright (C) 2020 The Software Heritage developers # See the AUTHORS file at the top-level directory of this distribution # License: GNU General Public License version 3, or any later version # See top-level LICENSE file for more information import collections import itertools import json import logging import os from pathlib import Path import random +import time from typing import Dict, Iterable, List, Optional import requests from requests.adapters import HTTPAdapter from requests.packages.urllib3.util.retry import Retry from swh.model.from_disk import Content, Directory, accept_all_directories -from swh.model.identifiers import CONTENT, DIRECTORY, swhid +from swh.model.identifiers import CONTENT, DIRECTORY, CoreSWHID, ObjectType from .exceptions import APIError from .model import Status, Tree from .scanner import directory_filter, extract_regex_objs session = requests.Session() retries_rule = Retry(total=5, backoff_factor=1) session.mount("http://", HTTPAdapter(max_retries=retries_rule)) def query_swhids( swhids: List[Tree], api_url: str, counter: Optional[collections.Counter] = None ) -> Dict[str, Dict[str, bool]]: """ Returns: A dictionary with: key(str): persistent identifier value(dict): value['known'] = True if pid is found value['known'] = False if pid is not found """ endpoint = api_url + "known/" chunk_size = 1000 if counter: counter["queries"] += len(swhids) def make_request(swhids): swhids = [swhid.swhid for swhid in swhids] req = session.post(endpoint, json=swhids) if req.status_code != 200: error_message = "%s with given values %s" % (req.text, str(swhids)) raise APIError(error_message) if counter: counter["api_calls"] += 1 resp = req.text return json.loads(resp) def get_chunk(swhids): for i in range(0, len(swhids), chunk_size): yield swhids[i : i + chunk_size] if len(swhids) > chunk_size: return dict( itertools.chain.from_iterable( make_request(swhids_chunk).items() for swhids_chunk in get_chunk(swhids) ) ) else: return make_request(swhids) def stopngo(source_tree: Tree, api_url: str, counter: collections.Counter): nodes = [] nodes.append(source_tree) while len(nodes) > 0: parsed_nodes = query_swhids(nodes, api_url, counter) for node in nodes.copy(): nodes.remove(node) node.known = parsed_nodes[node.swhid]["known"] node.status = Status.queried if node.otype == DIRECTORY: if not node.known: nodes.extend(list(node.children.values())) else: set_children_status(node, [CONTENT, DIRECTORY], True) def set_father_status(node, known): """ Recursively change father known and visited status of a given node """ parent = node.father if parent is None: return if parent.status != Status.unset: return parent.known = known set_father_status(parent, known) def set_children_status( node: Tree, node_types: Iterable[str], known: bool, status: Status = Status.unset ): """ Recursively change the status of the children of the provided node """ for child_node in node.iterate(): if child_node.otype in node_types and child_node.status == status: child_node.known = known def file_priority(source_tree: Tree, api_url: str, counter: collections.Counter): # get all the files all_contents = list( filter(lambda node: node.otype == CONTENT, source_tree.iterate_bfs()) ) all_contents.reverse() # we check nodes from the deepest # query the backend to get all file contents status parsed_contents = query_swhids(all_contents, api_url, counter) # set all the file contents status for cnt in all_contents: cnt.known = parsed_contents[cnt.swhid]["known"] cnt.status = Status.queried # set all the upstream directories of unknown file contents to unknown if not cnt.known: set_father_status(cnt, False) # get all unset directories and check their status # (update children directories accordingly) unset_dirs = list( filter( lambda node: node.otype == DIRECTORY and node.status == Status.unset, source_tree.iterate(), ) ) if source_tree.status == Status.unset: unset_dirs.append(source_tree) # check unset directories for dir_ in unset_dirs: if dir_.status == Status.unset: # update directory status dir_.known = query_swhids([dir_], api_url, counter)[dir_.swhid]["known"] dir_.status = Status.queried if dir_.known: set_children_status(dir_, [DIRECTORY], True) def directory_priority(source_tree: Tree, api_url: str, counter: collections.Counter): # get all directory contents that have at least one file content unset_dirs = list( filter( lambda dir_: dir_.otype == DIRECTORY and dir_.has_contents, source_tree.iterate_bfs(), ) ) unset_dirs.reverse() for dir_ in unset_dirs: # if the directory is known set all the downstream file contents to known if dir_.status == Status.unset: dir_.known = query_swhids([dir_], api_url, counter)[dir_.swhid]["known"] dir_.status = Status.queried if dir_.known: set_children_status(dir_, [CONTENT], True) else: set_father_status(dir_, False) # get remaining directories that have no file contents unset_dirs_no_cnts = list( filter( lambda node: node.otype == DIRECTORY and not node.has_contents, source_tree.iterate_bfs(), ) ) parsed_dirs_no_cnts = query_swhids(unset_dirs_no_cnts, api_url, counter) # update status of directories that have no file contents for dir_ in unset_dirs_no_cnts: dir_.known = parsed_dirs_no_cnts[dir_.swhid]["known"] dir_.status = Status.queried # check unknown file contents unset_files = list( filter( lambda node: node.otype == CONTENT and node.status == Status.unset, source_tree.iterate(), ) ) parsed_unset_files = query_swhids(unset_files, api_url, counter) for file_ in unset_files: file_.known = parsed_unset_files[file_.swhid]["known"] file_.status = Status.queried def random_( source_tree: Tree, api_url: str, counter: collections.Counter, seed: Optional[int] = None, ): if seed: random.seed(seed) # get all directory/file contents all_nodes = [node for node in source_tree.iterate()] + [source_tree] # shuffle contents random.shuffle(all_nodes) while len(all_nodes): node = all_nodes.pop() if node.status != Status.unset: continue node.known = query_swhids([node], api_url, counter)[node.swhid]["known"] node.status = Status.queried if node.otype == DIRECTORY and node.known: for child_node in node.iterate(): child_node.known = True elif node.otype == CONTENT and not node.known: set_father_status(node, False) -def algo_min(source_tree: Tree, api_url: str): +def algo_min(source_tree: Tree, api_url: str, counter: collections.Counter): """ The minimal number of queries knowing the known/unknown status of every node """ def change_parent_status(node, status): parent = node.father if parent is None: return parent.status = status change_parent_status(parent, status) def change_children_status(node, status): for child_node in node.iterate(): child_node.status = status all_nodes = [node for node in source_tree.iterate_bfs()] parsed_nodes = query_swhids(all_nodes, api_url) for node in all_nodes: node.known = parsed_nodes[node.swhid]["known"] unknown_cnts = list( filter(lambda node: node.known is False, source_tree.iterate_bfs()) ) unknown_cnts.reverse() for node in unknown_cnts: change_parent_status(node, Status.unset) known_dirs = list( filter( lambda node: node.otype == DIRECTORY and node.known is True, source_tree.iterate(), ) ) if source_tree.known: known_dirs += [source_tree] for dir_ in known_dirs: change_children_status(dir_, Status.unset) unset_cnts = list( filter(lambda node: node.status == Status.unset, source_tree.iterate_bfs()) ) - return len(source_tree) - len(unset_cnts) + counter["api_calls"] = -1 + counter["queries"] = len(source_tree) - len(unset_cnts) def get_swhids(paths: Iterable[Path], exclude_patterns): def swhid_of(path): if path.is_dir(): if exclude_patterns: def dir_filter(dirpath, *args): return directory_filter(dirpath, exclude_patterns) else: dir_filter = accept_all_directories obj = Directory.from_disk( path=bytes(path), dir_filter=dir_filter ).get_data() - return swhid(DIRECTORY, obj) + return str(CoreSWHID(object_type=ObjectType.DIRECTORY, object_id=obj["id"])) else: obj = Content.from_file(path=bytes(path)).get_data() - return swhid(CONTENT, obj) + return str( + CoreSWHID(object_type=ObjectType.CONTENT, object_id=obj["sha1_git"]) + ) for path in paths: yield str(path), swhid_of(path) def load_source(root, sre_patterns): """ Load the source code inside the Tree data structure """ def _scan(root_path, source_tree, sre_patterns): files = [] dirs = [] for elem in os.listdir(root_path): cnt = Path(root_path).joinpath(elem) if not os.path.islink(cnt): if os.path.isfile(cnt): files.append(cnt) elif os.path.isdir(cnt): dirs.append(cnt) if files: parsed_file_swhids = dict(get_swhids(files, sre_patterns)) for path, swhid_ in parsed_file_swhids.items(): source_tree.add_node(Path(path), swhid_) if dirs: parsed_dirs_swhids = dict(get_swhids(dirs, sre_patterns)) for path, swhid_ in parsed_dirs_swhids.items(): if not directory_filter(path, sre_patterns): continue source_tree.add_node(Path(path), swhid_) _scan(path, source_tree, sre_patterns) source_tree = Tree(root) root_swhid = dict(get_swhids([root], sre_patterns)) source_tree.swhid = root_swhid[str(root)] _scan(root, source_tree, sre_patterns) return source_tree def run( root: str, api_url: str, backend_name: str, exclude_patterns: Iterable[str], algo: str, origin: str, commit: str, seed: Optional[int] = None, ): sre_patterns = set() if exclude_patterns: sre_patterns = { reg_obj for reg_obj in extract_regex_objs(Path(root), exclude_patterns) } # temporary directory prefix repo_id = Path(root).parts[-1].split("_")[0] counter: collections.Counter = collections.Counter() counter["api_calls"] = 0 counter["queries"] = 0 source_tree = load_source(Path(root), sre_patterns) logging.info( f'started processing repo "{repo_id}" with algorithm ' f'"{algo}" and knowledge base "{backend_name}"' ) + tstart = time.time() if algo == "random": if seed: random_(source_tree, api_url, counter, seed) else: random_(source_tree, api_url, counter) elif algo == "algo_min": - min_queries = algo_min(source_tree, api_url) - min_result = ( - repo_id, - origin, - commit, - backend_name, - len(source_tree), - algo, - -1, - min_queries, - ) - print(*min_result, sep=",") - return + algo_min(source_tree, api_url, counter) elif algo == "stopngo": stopngo(source_tree, api_url, counter) elif algo == "file_priority": file_priority(source_tree, api_url, counter) elif algo == "directory_priority": directory_priority(source_tree, api_url, counter) else: raise Exception(f'Algorithm "{algo}" not found') + tend = time.time() result = ( repo_id, origin, commit, backend_name, len(source_tree), algo, counter["api_calls"], counter["queries"], + tend - tstart, ) logging.info( f'finished processing repo "{repo_id}" with algorithm ' f'"{algo}" and knowledge base "{backend_name}"' ) print(*result, sep=",") diff --git a/swh/scanner/plot.py b/swh/scanner/plot.py index ff14125..1f942a8 100644 --- a/swh/scanner/plot.py +++ b/swh/scanner/plot.py @@ -1,278 +1,278 @@ # Copyright (C) 2020 The Software Heritage developers # See the AUTHORS file at the top-level directory of this distribution # License: GNU General Public License version 3, or any later version # See top-level LICENSE file for more information """ The purpose of this module is to display and to interact with the result of the scanner contained in the model. The `sunburst` function generates a navigable sunburst chart from the directories information retrieved from the model. The chart displays for each directory the total number of files and the percentage of file known. The size of the directory is defined by the total number of contents whereas the color gradient is generated relying on the percentage of contents known. """ from pathlib import Path from typing import Dict, List, Tuple -import numpy as np # type: ignore +import numpy as np import pandas as pd # type: ignore import plotly.graph_objects as go from plotly.offline import offline def build_hierarchical_df( dirs_dataframe: pd.DataFrame, levels: List[str], metrics_columns: List[str], root_name: str, ) -> pd.DataFrame: """ Build a hierarchy of levels for Sunburst or Treemap charts. For each directory the new dataframe will have the following information: id: the directory name parent: the parent directory of id contents: the total number of contents of the directory id and the relative subdirectories known: the percentage of contents known relative to computed 'contents' Example: Given the following dataframe: .. code-block:: none lev0 lev1 contents known '' '' 20 2 //root kernel kernel/subdirker 5 0 telnet telnet/subdirtel 10 4 The output hierarchical dataframe will be like the following: .. code-block:: none id parent contents known 20 10.00 kernel/subdirker kernel 5 0.00 telnet/subdirtel telnet 10 40.00 total 20 10.00 kernel total 5 0.00 telnet total 10 40.00 total 35 17.14 To create the hierarchical dataframe we need to iterate through the dataframe given in input relying on the number of levels. Based on the previous example we have to do two iterations: iteration 1 The generated dataframe 'df_tree' will be: .. code-block:: none id parent contents known 20 10.0 kernel/subdirker kernel 5 0.0 telnet/subdirtel telnet 10 40.0 iteration 2 The generated dataframe 'df_tree' will be: .. code-block:: none id parent contents known total 20 10.0 kernel total 5 0.0 telnet total 10 40.0 Note that since we have reached the last level, the parent given to the directory id is the directory root. The 'total' row il computed by adding the number of contents of the dataframe given in input and the average of the contents known on the total number of contents. """ def compute_known_percentage(contents: pd.Series, known: pd.Series) -> pd.Series: """This function compute the percentage of known contents and generate the new known column with the percentage values. It also assures that if there is no contents inside a directory the percentage is zero """ known_values = [] for idx, content_val in enumerate(contents): if content_val == 0: known_values.append(0) else: percentage = known[idx] / contents[idx] * 100 known_values.append(percentage) return pd.Series(np.array(known_values)) complete_df = pd.DataFrame(columns=["id", "parent", "contents", "known"]) # revert the level order to start from the deepest levels = [level for level in reversed(levels)] contents_col = metrics_columns[0] known_col = metrics_columns[1] df_tree_list = [] for i, level in enumerate(levels): df_tree = pd.DataFrame(columns=["id", "parent", "contents", "known"]) dfg = dirs_dataframe.groupby(levels[i:]).sum() dfg = dfg.reset_index() df_tree["id"] = dfg[level].copy() if i < len(levels) - 1: # copy the parent directories (one level above) df_tree["parent"] = dfg[levels[i + 1]].copy() else: # last level reached df_tree["parent"] = root_name # copy the contents column df_tree["contents"] = dfg[contents_col] # compute the percentage relative to the contents df_tree["known"] = compute_known_percentage(dfg[contents_col], dfg[known_col]) df_tree_list.append(df_tree) complete_df = complete_df.append(df_tree_list, ignore_index=True) # create the main parent total_contents = dirs_dataframe[contents_col].sum() total_known = dirs_dataframe[known_col].sum() total_avg = total_known / total_contents * 100 total = pd.Series( dict(id=root_name, parent="", contents=total_contents, known=total_avg) ) complete_df = complete_df.append(total, ignore_index=True) return complete_df def compute_max_depth(dirs_path: List[Path], root: Path) -> int: """Compute the maximum depth level of the given directory paths. Example: for `var/log/kernel/` the depth level is 3 """ max_depth = 0 for dir_path in dirs_path: if dir_path == root: continue dir_depth = len(dir_path.parts) if dir_depth > max_depth: max_depth = dir_depth return max_depth def generate_df_from_dirs( dirs: Dict[Path, Tuple[int, int]], columns: List[str], root: Path, max_depth: int, ) -> pd.DataFrame: """Generate a dataframe from the directories given in input. Example: given the following directories as input .. code-block:: python dirs = { '/var/log/': (23, 2), '/var/log/kernel': (5, 0), '/var/log/telnet': (10, 3) } The generated dataframe will be: .. code-block:: none lev0 lev1 lev2 contents known 'var' 'var/log' '' 23 2 'var' 'var/log' 'var/log/kernel' 5 0 'var' 'var/log' 'var/log/telnet' 10 3 """ def get_parents(path: Path): parts = path.parts[1:] if path.parts[0] == "/" else path.parts for i in range(1, len(parts) + 1): yield "/".join(parts[0:i]) def get_dirs_array(): for dir_path, contents_info in dirs.items(): empty_lvl = max_depth - len(dir_path.parts) if dir_path == root: # ignore the root but store contents information yield [""] * (max_depth) + list(contents_info) else: yield list(get_parents(dir_path)) + [""] * empty_lvl + list( contents_info ) df = pd.DataFrame( np.array([dir_array for dir_array in get_dirs_array()]), columns=columns ) df["contents"] = pd.to_numeric(df["contents"]) df["known"] = pd.to_numeric(df["known"]) return df def generate_sunburst( directories: Dict[Path, Tuple[int, int]], root: Path ) -> go.Sunburst: """Generate a sunburst chart from the directories given in input. """ max_depth = compute_max_depth(list(directories.keys()), root) metrics_columns = ["contents", "known"] levels_columns = ["lev" + str(i) for i in range(max_depth)] df_columns = levels_columns + metrics_columns dirs_df = generate_df_from_dirs(directories, df_columns, root, max_depth) hierarchical_df = build_hierarchical_df( dirs_df, levels_columns, metrics_columns, str(root) ) sunburst = go.Sunburst( labels=hierarchical_df["id"], parents=hierarchical_df["parent"], values=hierarchical_df["contents"], branchvalues="total", marker=dict( colors=hierarchical_df["known"], colorscale="matter", cmid=50, showscale=True, ), hovertemplate="""%{label}
Files: %{value}
Known: %{color:.2f}%""", name="", ) return sunburst def offline_plot(graph_object: go): """Plot a graph object to an html file """ fig = go.Figure() fig.add_trace(graph_object) offline.plot(fig, filename="chart.html") diff --git a/swh/scanner/scanner.py b/swh/scanner/scanner.py index 903b87c..8abe331 100644 --- a/swh/scanner/scanner.py +++ b/swh/scanner/scanner.py @@ -1,245 +1,249 @@ # Copyright (C) 2020 The Software Heritage developers # See the AUTHORS file at the top-level directory of this distribution # License: GNU General Public License version 3, or any later version # See top-level LICENSE file for more information import asyncio import fnmatch import glob import itertools import os from pathlib import Path import re from typing import Any, Dict, Iterable, Iterator, List, Pattern, Tuple, Union import aiohttp from swh.model.from_disk import Content, Directory, accept_all_directories -from swh.model.identifiers import CONTENT, DIRECTORY, parse_swhid, swhid +from swh.model.identifiers import CoreSWHID, ObjectType from .dashboard.dashboard import run_app from .exceptions import InvalidDirectoryPath, error_response from .model import Tree from .plot import generate_sunburst async def swhids_discovery( swhids: List[str], session: aiohttp.ClientSession, api_url: str, ) -> Dict[str, Dict[str, bool]]: """API Request to get information about the SoftWare Heritage persistent IDentifiers (SWHIDs) given in input. Args: swhids: a list of SWHIDS api_url: url for the API request Returns: A dictionary with: key: SWHID searched value: value['known'] = True if the SWHID is found value['known'] = False if the SWHID is not found """ endpoint = api_url + "known/" chunk_size = 1000 requests = [] def get_chunk(swhids): for i in range(0, len(swhids), chunk_size): yield swhids[i : i + chunk_size] async def make_request(swhids): async with session.post(endpoint, json=swhids) as resp: if resp.status != 200: error_response(resp.reason, resp.status, endpoint) return await resp.json() if len(swhids) > chunk_size: for swhids_chunk in get_chunk(swhids): requests.append(asyncio.create_task(make_request(swhids_chunk))) res = await asyncio.gather(*requests) # concatenate list of dictionaries return dict(itertools.chain.from_iterable(e.items() for e in res)) else: return await make_request(swhids) def directory_filter( path_name: Union[str, bytes], exclude_patterns: Iterable[Pattern[str]] ) -> bool: """It checks if the path_name is matching with the patterns given in input. It is also used as a `dir_filter` function when generating the directory object from `swh.model.from_disk` Returns: False if the directory has to be ignored, True otherwise """ path = Path(path_name.decode() if isinstance(path_name, bytes) else path_name) for sre_pattern in exclude_patterns: if sre_pattern.match(str(path)): return False return True def get_subpaths( path: Path, exclude_patterns: Iterable[Pattern[str]] ) -> Iterator[Tuple[Path, str]]: """Find the SoftWare Heritage persistent IDentifier (SWHID) of the directories and files under a given path. Args: path: the root path Yields: pairs of: path, the relative SWHID """ def swhid_of(path): if path.is_dir(): if exclude_patterns: def dir_filter(dirpath, *args): return directory_filter(dirpath, exclude_patterns) else: dir_filter = accept_all_directories obj = Directory.from_disk( path=bytes(path), dir_filter=dir_filter ).get_data() - return swhid(DIRECTORY, obj) + return str(CoreSWHID(object_type=ObjectType.DIRECTORY, object_id=obj["id"])) else: obj = Content.from_file(path=bytes(path)).get_data() - return swhid(CONTENT, obj) + return str( + CoreSWHID(object_type=ObjectType.CONTENT, object_id=obj["sha1_git"]) + ) dirpath, dnames, fnames = next(os.walk(path)) for node in itertools.chain(dnames, fnames): sub_path = Path(dirpath).joinpath(node) yield (sub_path, swhid_of(sub_path)) async def parse_path( path: Path, session: aiohttp.ClientSession, api_url: str, exclude_patterns: Iterable[Pattern[str]], ) -> Iterator[Tuple[str, str, bool]]: """Check if the sub paths of the given path are present in the archive or not. Args: path: the source path api_url: url for the API request Returns: a map containing tuples with: a subpath of the given path, the SWHID of the subpath and the result of the api call """ parsed_paths = dict(get_subpaths(path, exclude_patterns)) parsed_swhids = await swhids_discovery( list(parsed_paths.values()), session, api_url ) def unpack(tup): subpath, swhid = tup return (subpath, swhid, parsed_swhids[swhid]["known"]) return map(unpack, parsed_paths.items()) async def run( config: Dict[str, Any], root: str, source_tree: Tree, exclude_patterns: Iterable[Pattern[str]], ) -> None: """Start scanning from the given root. It fills the source tree with the path discovered. Args: root: the root path to scan api_url: url for the API request """ api_url = config["web-api"]["url"] async def _scan(root, session, api_url, source_tree, exclude_patterns): for path, obj_swhid, known in await parse_path( root, session, api_url, exclude_patterns ): - obj_type = parse_swhid(obj_swhid).object_type + obj_type = CoreSWHID.from_string(obj_swhid).object_type - if obj_type == CONTENT: + if obj_type == ObjectType.CONTENT: source_tree.add_node(path, obj_swhid, known) - elif obj_type == DIRECTORY and directory_filter(path, exclude_patterns): + elif obj_type == ObjectType.DIRECTORY and directory_filter( + path, exclude_patterns + ): source_tree.add_node(path, obj_swhid, known) if not known: await _scan(path, session, api_url, source_tree, exclude_patterns) if config["web-api"]["auth-token"]: headers = {"Authorization": f"Bearer {config['web-api']['auth-token']}"} else: headers = {} async with aiohttp.ClientSession(headers=headers, trust_env=True) as session: await _scan(root, session, api_url, source_tree, exclude_patterns) def extract_regex_objs( root_path: Path, patterns: Iterable[str] ) -> Iterator[Pattern[str]]: """Generates a regex object for each pattern given in input and checks if the path is a subdirectory or relative to the root path. Yields: an SRE_Pattern object """ for pattern in patterns: for path in glob.glob(pattern): dirpath = Path(path) if root_path not in dirpath.parents: error_msg = ( f'The path "{dirpath}" is not a subdirectory or relative ' f'to the root directory path: "{root_path}"' ) raise InvalidDirectoryPath(error_msg) regex = fnmatch.translate((pattern)) yield re.compile(regex) def scan( config: Dict[str, Any], root_path: str, exclude_patterns: Iterable[str], out_fmt: str, interactive: bool, ): """Scan a source code project to discover files and directories already present in the archive""" sre_patterns = set() if exclude_patterns: sre_patterns = { reg_obj for reg_obj in extract_regex_objs(Path(root_path), exclude_patterns) } source_tree = Tree(Path(root_path)) loop = asyncio.get_event_loop() loop.run_until_complete(run(config, root_path, source_tree, sre_patterns)) if interactive: root = Path(root_path) directories = source_tree.get_directories_info(root) figure = generate_sunburst(directories, root) run_app(figure, source_tree) else: source_tree.show(out_fmt)