From 7bd8dca3519a26744a13039c0e23469ccb92ee08 Mon Sep 17 00:00:00 2001 From: Yossi Mosbacher Date: Sat, 19 Aug 2023 11:41:31 +0300 Subject: [PATCH 1/3] load only relavent files if pattern given --- poetry.lock | 14 +++- pyproject.toml | 1 + xedocs/data_locations/data_folder.py | 59 ++++++--------- xedocs/data_locations/github.py | 5 +- xedocs/utils.py | 107 ++++++++++++++++++++++++++- 5 files changed, 146 insertions(+), 40 deletions(-) diff --git a/poetry.lock b/poetry.lock index 9e54415..fc1c172 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1981,6 +1981,18 @@ all = ["aiohttp", "coverage", "flake8", "graphviz", "ipython (!=8.7.0)", "myst-n doc = ["aiohttp", "graphviz", "ipython (!=8.7.0)", "myst-nb (==0.12.2)", "myst-parser", "nbconvert", "nbsite (==0.8.0rc2)", "pandas", "panel", "pydata-sphinx-theme (<0.9.0)", "pygraphviz", "sphinx-copybutton"] tests = ["coverage", "flake8", "pytest"] +[[package]] +name = "parse" +version = "1.19.1" +description = "parse() is the opposite of format()" +category = "main" +optional = false +python-versions = "*" +files = [ + {file = "parse-1.19.1-py2.py3-none-any.whl", hash = "sha256:371ed3800dc63983832159cc9373156613947707bc448b5215473a219dbd4362"}, + {file = "parse-1.19.1.tar.gz", hash = "sha256:cc3a47236ff05da377617ddefa867b7ba983819c664e1afe46249e5b469be464"}, +] + [[package]] name = "pathspec" version = "0.11.1" @@ -3551,4 +3563,4 @@ db = ["pymongo"] [metadata] lock-version = "2.0" python-versions = ">=3.8,<4.0" -content-hash = "675b40039808e69bb8c27f7614a614e05e6a29b93babe76b655d25cc9c65d60e" +content-hash = "a59eb3ace5a1850f3e01baebb3a75ef334d3a09f36b4c3fd65bf61a93edfa067" diff --git a/pyproject.toml b/pyproject.toml index b56c949..223cc91 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -30,6 +30,7 @@ tinydb = "^4.7.0" tqdm = "^4.64.1" xeauth = "^0.2.3" pyyaml = "^6.0" +parse = "^1.19.1" [tool.poetry.extras] db = ["pymongo"] diff --git a/xedocs/data_locations/data_folder.py b/xedocs/data_locations/data_folder.py index 4768f5b..1d08e48 100644 --- a/xedocs/data_locations/data_folder.py +++ b/xedocs/data_locations/data_folder.py @@ -1,43 +1,20 @@ import os -from typing import List, Union -import fsspec -from pydantic import BaseSettings, root_validator import yaml -from plum import dispatch -from ..dispatchers import read_files -from ..utils import Database, LazyDataAccessor -from ..json_records import JsonLoader - +import fsspec +from pydantic import BaseSettings -class FileLoader: - def __init__(self, paths: Union[str, List[str]], **kwargs) -> None: - if not isinstance(paths, (list, str)): - raise ValueError(f"Invalid path: {paths}") - if isinstance(paths, str): - paths = [paths] - self.paths = paths - self.kwargs = kwargs - - def load(self) -> List[dict]: - docs = [] - for path in self.paths: - docs.extend(read_files(path, **self.kwargs)) - return docs - - def __call__(self) -> List[dict]: - return self.load() +from ..utils import Database, LazyFileAccessor class DataFolder(BaseSettings): - __loader_class__ = FileLoader - class Config: env_prefix = "XEDOCS_DATA_FOLDER_" - + root: str = None + protocol: str = "file" config_path: str = "datasets.yml" @@ -47,10 +24,11 @@ def storage_kwargs(self, path): def abs_path(self, path): if isinstance(path, list): return [self.abs_path(p) for p in path] - if not os.path.isabs(path): + if not os.path.isabs(path) and self.root is not None: path = os.path.join(self.root, path) + path = "file://" + path if not path.startswith("file://") else path return path - + @property def datasets_config(self): return self.read_config() @@ -59,18 +37,27 @@ def get_datasets(self): import xedocs dsets = {} - for _, cfg in self.datasets_config.items(): - schema = xedocs.find_schema(cfg['schema']) - path = self.abs_path(cfg['path']) + schema = cfg.get('schema', None) + if schema is None: + continue + schema = xedocs.find_schema(schema) + path = cfg.get('path', None) + if path is None: + continue + path = self.abs_path(path) + pattern = cfg.get('pattern', None) kwargs = self.storage_kwargs(path) - datasource = self.__loader_class__(path, **kwargs) - dsets[schema._ALIAS] = LazyDataAccessor(schema, datasource=datasource) + dsets[schema._ALIAS] = LazyFileAccessor(schema, path, + root=self.root, + protocol=self.protocol, + pattern=pattern, **kwargs) return Database(dsets) - + def read_config(self): path = self.abs_path(self.config_path) kwargs = self.storage_kwargs(path) + with fsspec.open(path, **kwargs) as f: config = yaml.safe_load(f) return config diff --git a/xedocs/data_locations/github.py b/xedocs/data_locations/github.py index 11f7b54..490de15 100644 --- a/xedocs/data_locations/github.py +++ b/xedocs/data_locations/github.py @@ -69,7 +69,9 @@ def from_login(cls): class GithubRepo(DataFolder): class Config: env_prefix = "XEDOCS_GITHUB_REPO_" - + + protocol: str = "github" + root: str = "" org: str = "XENONnT" repo: str = "xedocs-data" username: str = "__token__" @@ -100,4 +102,3 @@ def get_token(cls, values): @property def datasets_config(self): return self.read_config() - diff --git a/xedocs/utils.py b/xedocs/utils.py index 7b0dd7a..7194903 100644 --- a/xedocs/utils.py +++ b/xedocs/utils.py @@ -1,12 +1,17 @@ -from typing import Any, Union +import parse +import fsspec + import pandas as pd +from typing import Any, Union from collections import UserDict from pydantic import ValidationError from rframe.data_accessor import DataAccessor from typing import List from plum import dispatch +from .dispatchers import read_files + def docs_to_wiki(schema, docs, title=None, columns=None): """Convert a list of documents to a dokuwiki table @@ -85,6 +90,106 @@ def storage(self, value): self.get_storage = value +def remove_prefix(text, prefix, sep="/"): + if text.startswith(prefix): + text = text[len(prefix):] + if sep is not None and text.startswith(sep): + text = text[len(sep):] + return text + + +class LazyFileAccessor(DataAccessor): + loaded: set + pattern: str + root: str + urlpaths: List[str] + storage_options: dict + + def __init__(self, schema, urlpaths, root=None, pattern=None, **kwargs): + if isinstance(urlpaths, str): + urlpaths = [urlpaths] + self.urlpaths = urlpaths + self.root = root + self.pattern = pattern + self.loaded = set() + self.storage_options = kwargs + storage = schema.empty_dframe() + super().__init__(schema, storage, False) + + def load_files(self, **labels): + dfs = [] + index_fields = list(self.schema.get_index_fields()) + if len(index_fields) == 1: + index_fields = index_fields[0] + for urlpath in self.urlpaths: + fs, _, paths = fsspec.get_fs_token_paths(urlpath, storage_options=self.storage_options) + for path in self.filter_paths(paths, **labels): + if path in self.loaded: + continue + records = read_files(path, **self.storage_options) + df = pd.json_normalize(records).set_index(index_fields) + dfs.append(df) + self.loaded.add(path) + self.storage = pd.concat([self.storage] + dfs).sort_values(index_fields) + + def _find(self, skip=None, limit=None, sort=None, **labels): + self.load_files(**labels) + return super()._find(skip=skip, limit=limit, sort=sort, **labels) + + def filter_paths(self, paths, **kwargs): + if self.pattern is None: + return paths + if self.root is not None and self.pattern.startswith(self.root): + self.pattern = remove_prefix(self.pattern, self.root) + pattern = parse.compile(self.pattern) + result = [] + for path in paths: + if self.root is not None and path.startswith(self.root): + p = remove_prefix(path, self.root) + else: + p = path + r = pattern.parse(p) + if r is None: + continue + for k,v in kwargs.items(): + if not isinstance(v, list): + v = [v] + label = r.named.get(k, None) + if label is None: + continue + if k in self.schema.__fields__: + index = self.schema.index_for(k) + label = index.validate_label(label) + v = index.validate_label(v) + if label not in v: + break + else: + result.append(path) + return result + + def _min(self, **kwargs): + self.load_files() + return super()._min() + + def _max(self, **kwargs): + self.load_files() + return super()._max(**kwargs) + + def _count(self, **kwargs): + self.load_files() + return super()._count(**kwargs) + + def _unique(self, **kwargs): + self.load_files() + return super()._unique(**kwargs) + + def insert(self, docs, raise_on_error=True, dry=False): + raise NotImplementedError + + def delete(self, docs, raise_on_error=True): + raise NotImplementedError + + class Database(UserDict): def __getattr__(self, attr): if attr in self.keys(): From 1af9c1fdbf0279ce46b3609fcf266d11462519f3 Mon Sep 17 00:00:00 2001 From: Yossi Mosbacher Date: Sun, 20 Aug 2023 19:52:01 +0300 Subject: [PATCH 2/3] use paths as patterns --- xedocs/data_locations/data_folder.py | 10 +- xedocs/data_locations/github.py | 5 +- xedocs/utils.py | 153 ++++++++++++++++++--------- 3 files changed, 112 insertions(+), 56 deletions(-) diff --git a/xedocs/data_locations/data_folder.py b/xedocs/data_locations/data_folder.py index 1d08e48..a5e373d 100644 --- a/xedocs/data_locations/data_folder.py +++ b/xedocs/data_locations/data_folder.py @@ -26,7 +26,6 @@ def abs_path(self, path): return [self.abs_path(p) for p in path] if not os.path.isabs(path) and self.root is not None: path = os.path.join(self.root, path) - path = "file://" + path if not path.startswith("file://") else path return path @property @@ -46,12 +45,11 @@ def get_datasets(self): if path is None: continue path = self.abs_path(path) - pattern = cfg.get('pattern', None) + kwargs = self.storage_kwargs(path) - dsets[schema._ALIAS] = LazyFileAccessor(schema, path, - root=self.root, - protocol=self.protocol, - pattern=pattern, **kwargs) + dsets[schema._ALIAS] = LazyFileAccessor(schema, + path, + **kwargs) return Database(dsets) def read_config(self): diff --git a/xedocs/data_locations/github.py b/xedocs/data_locations/github.py index 490de15..51cfad4 100644 --- a/xedocs/data_locations/github.py +++ b/xedocs/data_locations/github.py @@ -71,7 +71,6 @@ class Config: env_prefix = "XEDOCS_GITHUB_REPO_" protocol: str = "github" - root: str = "" org: str = "XENONnT" repo: str = "xedocs-data" username: str = "__token__" @@ -81,10 +80,12 @@ class Config: def abs_path(self, path): if isinstance(path, list): return [self.abs_path(p) for p in path] - return f"github://{self.org}:{self.repo}@/{path.lstrip('/')}" + return f"github://{path.lstrip('/')}" def storage_kwargs(self, path): return { + "org": self.org, + "repo": self.repo, "username": self.username, "token": self.token, "sha": self.branch, diff --git a/xedocs/utils.py b/xedocs/utils.py index 7194903..327e9c1 100644 --- a/xedocs/utils.py +++ b/xedocs/utils.py @@ -1,3 +1,4 @@ +import os import parse import fsspec @@ -101,75 +102,91 @@ def remove_prefix(text, prefix, sep="/"): class LazyFileAccessor(DataAccessor): loaded: set pattern: str + protocol: str root: str urlpaths: List[str] storage_options: dict - def __init__(self, schema, urlpaths, root=None, pattern=None, **kwargs): + def __init__(self, schema, urlpaths, **kwargs): if isinstance(urlpaths, str): urlpaths = [urlpaths] - self.urlpaths = urlpaths - self.root = root - self.pattern = pattern self.loaded = set() self.storage_options = kwargs + self.urlpaths = urlpaths storage = schema.empty_dframe() super().__init__(schema, storage, False) + def _find(self, skip=None, limit=None, sort=None, **labels): + self.load_files(**labels) + return super()._find(skip=skip, limit=limit, sort=sort, **labels) + + def format_to_glob(self, path): + for field in self.schema.__fields__: + test_cases = ["{" + field + "}", "{ " + field + " }", "{" + field + ":s}", "{" + field + ":d}"] + for test_case in test_cases: + if test_case in path: + path = path.replace(test_case, "*") + return path + + def glob_to_format(self, path): + return path.replace("*", "{}") + def load_files(self, **labels): dfs = [] index_fields = list(self.schema.get_index_fields()) if len(index_fields) == 1: index_fields = index_fields[0] - for urlpath in self.urlpaths: - fs, _, paths = fsspec.get_fs_token_paths(urlpath, storage_options=self.storage_options) - for path in self.filter_paths(paths, **labels): - if path in self.loaded: - continue - records = read_files(path, **self.storage_options) - df = pd.json_normalize(records).set_index(index_fields) - dfs.append(df) - self.loaded.add(path) - self.storage = pd.concat([self.storage] + dfs).sort_values(index_fields) - def _find(self, skip=None, limit=None, sort=None, **labels): - self.load_files(**labels) - return super()._find(skip=skip, limit=limit, sort=sort, **labels) - - def filter_paths(self, paths, **kwargs): - if self.pattern is None: - return paths - if self.root is not None and self.pattern.startswith(self.root): - self.pattern = remove_prefix(self.pattern, self.root) - pattern = parse.compile(self.pattern) - result = [] - for path in paths: - if self.root is not None and path.startswith(self.root): - p = remove_prefix(path, self.root) - else: - p = path - r = pattern.parse(p) - if r is None: - continue - for k,v in kwargs.items(): - if not isinstance(v, list): - v = [v] - label = r.named.get(k, None) - if label is None: + for path in self.urlpaths: + + glob_patttern = self.format_to_glob(path) + fs, _, fpaths = fsspec.get_fs_token_paths(glob_patttern, + storage_options=self.storage_options) + pattern = path.replace(f"{fs.protocol}://", "") + pattern = parse.compile(self.glob_to_format(pattern)) + for fpath in fpaths: + if fpath in self.loaded: continue - if k in self.schema.__fields__: - index = self.schema.index_for(k) - label = index.validate_label(label) - v = index.validate_label(v) - if label not in v: - break - else: - result.append(path) - return result + r = pattern.parse(fpath) + if r is None: + continue + for k,vs in labels.items(): + + if vs is None: + continue + if not isinstance(vs, list): + vs = [vs] + elif not len(vs): + continue + label = r.named.get(k, None) + if label is None: + continue + if k in self.schema.__fields__: + index = self.schema.index_for(k) + label = index.validate_label(label) + vs = [index.validate_label(v) for v in vs] + if label not in vs: + break + else: + records = read_files(fpath, protocol=fs.protocol, **fs.storage_options) + docs = [] + for doc in records: + if not isinstance(doc, dict): + continue + try: + doc = self.schema(**doc).pandas_dict() + docs.append(doc) + except ValidationError as e: + continue + df = pd.DataFrame(docs, columns=list(self.schema.__fields__)) + df = df.set_index(index_fields) + dfs.append(df) + self.loaded.add(fpath) + self.storage = pd.concat([self.storage] + dfs).sort_values(index_fields) def _min(self, **kwargs): self.load_files() - return super()._min() + return super()._min(**kwargs) def _max(self, **kwargs): self.load_files() @@ -189,6 +206,46 @@ def insert(self, docs, raise_on_error=True, dry=False): def delete(self, docs, raise_on_error=True): raise NotImplementedError +class FileLoader: + root: str = None + protocol: str = "file" + loaded: set + pattern: str + root: str + urlpaths: List[str] + storage_options: dict + + @property + def prefix(self): + return f"{self.protocol}://{self.root}/" + + def abs_path(self, path): + if path.startswith(self.prefix): + return path + return f"{self.prefix}{path}" + + def rel_path(self, path): + if path.startswith(self.prefix): + return path[len(self.prefix):] + return path + + def load_files(self, **labels): + dfs = [] + index_fields = list(self.schema.get_index_fields()) + if len(index_fields) == 1: + index_fields = index_fields[0] + for urlpath in self.urlpaths: + fs, _, paths = fsspec.get_fs_token_paths(urlpath, storage_options=self.storage_options) + for path in self.filter_paths(paths, **labels): + if path in self.loaded: + continue + records = read_files(path, **self.storage_options) + df = pd.json_normalize(records).set_index(index_fields) + dfs.append(df) + self.loaded.add(path) + self.storage = pd.concat([self.storage] + dfs).sort_values(index_fields) + + class Database(UserDict): def __getattr__(self, attr): From 8d4194cbf7529542fa97a4a69dd1e2fe7b4b8761 Mon Sep 17 00:00:00 2001 From: Yossi Mosbacher Date: Sun, 20 Aug 2023 20:04:43 +0300 Subject: [PATCH 3/3] update deps --- poetry.lock | 1397 ++++++++++++++++++++++++++------------------------- 1 file changed, 712 insertions(+), 685 deletions(-) diff --git a/poetry.lock b/poetry.lock index fc1c172..d0fc67c 100644 --- a/poetry.lock +++ b/poetry.lock @@ -48,23 +48,24 @@ files = [ [[package]] name = "argon2-cffi" -version = "21.3.0" -description = "The secure Argon2 password hashing algorithm." +version = "23.1.0" +description = "Argon2 for Python" category = "dev" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" files = [ - 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