From a0ca71ea87a7f2bdd2ab851b6a75e398d07b4f0c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Florian=20F=C3=B6rster?= Date: Thu, 7 Nov 2024 17:30:33 +0100 Subject: [PATCH] major changes in several aspects --- lang-main.code-workspace | 8 + notebooks/dummy_data_generation.ipynb | 2 +- notebooks/misc.ipynb | 247 ++++- pdm.lock | 1315 +++++++++++++++++------ pyproject.toml | 26 +- scripts/dash_timeline_static.py | 2 +- scripts/lang_main_config.old.toml | 58 + scripts/lang_main_config.toml | 13 +- src/lang_main/__init__.py | 151 ++- src/lang_main/analysis/graphs.py | 4 +- src/lang_main/analysis/preprocessing.py | 13 +- src/lang_main/analysis/shared.py | 10 +- src/lang_main/analysis/tokens.py | 22 +- src/lang_main/constants.py | 51 +- src/lang_main/errors.py | 22 + src/lang_main/lang_main_config.toml | 5 + src/lang_main/loggers.py | 63 +- src/lang_main/model_loader.py | 25 +- src/lang_main/pipelines/base.py | 22 +- src/lang_main/pipelines/predefined.py | 12 +- src/lang_main/render/__init__.py | 7 + src/lang_main/types.py | 29 +- 22 files changed, 1628 insertions(+), 479 deletions(-) create mode 100644 lang-main.code-workspace create mode 100644 scripts/lang_main_config.old.toml diff --git a/lang-main.code-workspace b/lang-main.code-workspace new file mode 100644 index 0000000..876a149 --- /dev/null +++ b/lang-main.code-workspace @@ -0,0 +1,8 @@ +{ + "folders": [ + { + "path": "." + } + ], + "settings": {} +} \ No newline at end of file diff --git a/notebooks/dummy_data_generation.ipynb b/notebooks/dummy_data_generation.ipynb index 4ebf4c7..c794466 100644 --- a/notebooks/dummy_data_generation.ipynb +++ b/notebooks/dummy_data_generation.ipynb @@ -1236,7 +1236,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.11.9" + "version": "3.11.10" } }, "nbformat": 4, diff --git a/notebooks/misc.ipynb b/notebooks/misc.ipynb index 1a3e8dd..ec37419 100644 --- a/notebooks/misc.ipynb +++ b/notebooks/misc.ipynb @@ -11,6 +11,251 @@ "%autoreload 2" ] }, + { + "cell_type": "code", + "execution_count": null, + "id": "6e1c76cc-6f99-484a-b73c-c99d9d567bbd", + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": 10, + "id": "f34b343b-a7b6-4a6d-8db4-7f2f71addc54", + "metadata": {}, + "outputs": [], + "source": [ + "from importlib.util import find_spec" + ] + }, + { + "cell_type": "code", + "execution_count": 11, + "id": "59c32d49-5bad-4f48-b91f-f069487ff543", + "metadata": {}, + "outputs": [], + "source": [ + "importlib.util.find_spec('nunpy')" + ] + }, + { + "cell_type": "code", + "execution_count": 14, + "id": "dd3d9434-374d-42a4-9c08-230495d0f5a6", + "metadata": {}, + "outputs": [], + "source": [ + "_has_dash: bool = True if (find_spec('dash') and find_spec('kalido')) else False" + ] + }, + { + "cell_type": "code", + "execution_count": 15, + "id": "4da22bea-d086-4097-86f6-37784b59e02b", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "False" + ] + }, + "execution_count": 15, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "_has_dash" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "id": "dfc51145-759e-43ee-a850-580149679c5b", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "False" + ] + }, + "execution_count": 9, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "_has_py4cyto" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "dbdbc7c1-4dd6-49d6-b570-3fc7eb60938f", + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": 18, + "id": "36aa5c9c-c29a-4a05-8854-30b086a9240e", + "metadata": {}, + "outputs": [], + "source": [ + "from pathlib import Path" + ] + }, + { + "cell_type": "code", + "execution_count": 20, + "id": "b8afbf49-e61c-49ce-af53-694b01f90702", + "metadata": {}, + "outputs": [], + "source": [ + "curr_path = Path.cwd()" + ] + }, + { + "cell_type": "code", + "execution_count": 28, + "id": "c353967a-2702-4370-b4f2-914ac3b950a3", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[]" + ] + }, + "execution_count": 28, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "list(curr_path.glob('./lang_main_consdfig.toml'))" + ] + }, + { + "cell_type": "code", + "execution_count": 27, + "id": "48ee9b11-60fa-43d4-87de-c9a2172a563b", + "metadata": {}, + "outputs": [], + "source": [ + "pkg_dir = curr_path" + ] + }, + { + "cell_type": "code", + "execution_count": 36, + "id": "02d404e1-a352-44f6-a4e9-96b6aed0c3a3", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "WindowsPath('A:/Arbeitsaufgaben/lang-main/notebooks')" + ] + }, + "execution_count": 36, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "pkg_dir" + ] + }, + { + "cell_type": "code", + "execution_count": 44, + "id": "fc9142c2-9e59-4113-811c-7a03068857f2", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[WindowsPath('A:/Arbeitsaufgaben/lang-main/notebooks'),\n", + " WindowsPath('A:/Arbeitsaufgaben/lang-main'),\n", + " WindowsPath('A:/Arbeitsaufgaben'),\n", + " WindowsPath('A:/')]" + ] + }, + "execution_count": 44, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "list((pkg_dir/'home.py').parents)" + ] + }, + { + "cell_type": "code", + "execution_count": 40, + "id": "ac1312bf-332f-4008-8951-c53e35f37990", + "metadata": {}, + "outputs": [], + "source": [ + "cfg_found = False\n", + "for it in range(len(pkg_dir.parents)):\n", + " search_path = pkg_dir.parents[it]\n", + " res = tuple(search_path.glob(f'lang_main*.toml'))\n", + " if res:\n", + " cfg_found = True\n", + " target = res[0]\n", + " break\n", + " if search_path.name == 'python':\n", + " break" + ] + }, + { + "cell_type": "code", + "execution_count": 41, + "id": "a9bb96cc-f8a7-4749-ae2b-62e363d18f54", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "True" + ] + }, + "execution_count": 41, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "cfg_found" + ] + }, + { + "cell_type": "code", + "execution_count": 30, + "id": "58472aba-e887-4c50-857a-894c1c5c9003", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "WindowsPath('A:/Arbeitsaufgaben/lang-main/lang_main_config.toml')" + ] + }, + "execution_count": 30, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "target" + ] + }, { "cell_type": "code", "execution_count": 2, @@ -11562,7 +11807,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - 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b/scripts/lang_main_config.old.toml new file mode 100644 index 0000000..c85635d --- /dev/null +++ b/scripts/lang_main_config.old.toml @@ -0,0 +1,58 @@ +# lang_main: Config file + +[paths] +inputs = './inputs/' +# results = './results/dummy_N_1000/' +# dataset = '../data/Dummy_Dataset_N_1000.csv' +results = './results/test_20240807/' +dataset = '../data/02_202307/Export4.csv' + +# only debugging features, production-ready pipelines should always +# be fully executed +[control] +preprocessing_skip = true +token_analysis_skip = true +graph_postprocessing_skip = false +graph_rescaling_skip = false +graph_static_rendering_skip = true +time_analysis_skip = true + +[preprocess] +date_cols = [ + "VorgangsDatum", + "ErledigungsDatum", + "Arbeitsbeginn", + "ErstellungsDatum", +] +threshold_amount_characters = 5 +threshold_similarity = 0.8 + +[graph_postprocessing] +threshold_edge_number = 330 +# threshold_edge_weight = 150 + +[time_analysis.uniqueness] +threshold_unique_texts = 4 +criterion_feature = 'HObjektText' +feature_name_obj_id = 'ObjektID' + +[time_analysis.preparation] +name_delta_feat_to_repair = 'Zeitspanne bis zur Behebung [Tage]' +name_delta_feat_to_next_failure = 'Zeitspanne bis zum nächsten Ereignis [Tage]' + +[time_analysis.model_input] +# input_features = [ +# 'VorgangsTypName', +# 'VorgangsArtText', +# 'VorgangsBeschreibung', +# ] +input_features = [ + 'VorgangsBeschreibung', +] +activity_feature = 'VorgangsTypName' +activity_types = [ + 'Reparaturauftrag (Portal)', + 'Störungsmeldung', +] +threshold_num_acitivities = 1 +threshold_similarity = 0.8 \ No newline at end of file diff --git a/scripts/lang_main_config.toml b/scripts/lang_main_config.toml index 41e4305..7bca8c4 100644 --- a/scripts/lang_main_config.toml +++ b/scripts/lang_main_config.toml @@ -7,14 +7,19 @@ inputs = './inputs/' results = './results/test_20240807/' dataset = '../data/02_202307/Export4.csv' +[logging] +enabled = true +stderr = true +file = true + # only debugging features, production-ready pipelines should always # be fully executed [control] -preprocessing_skip = true +preprocessing_skip = false token_analysis_skip = true -graph_postprocessing_skip = false -graph_rescaling_skip = false -graph_static_rendering_skip = false +graph_postprocessing_skip = true +graph_rescaling_skip = true +graph_static_rendering_skip = true time_analysis_skip = true [preprocess] diff --git a/src/lang_main/__init__.py b/src/lang_main/__init__.py index f10c95c..ea3a891 100644 --- a/src/lang_main/__init__.py +++ b/src/lang_main/__init__.py @@ -1,56 +1,127 @@ import logging -import os -import shutil -import sys from pathlib import Path -from time import gmtime from typing import Any, Final -import py4cytoscape as p4c +_has_py4cyto: bool = True +try: + import py4cytoscape as p4c +except ImportError: + _has_py4cyto = False from lang_main.io import load_toml_config # ** py4cytoscape config -p4c.set_summary_logger(False) -p4c.py4cytoscape_logger.detail_logger.setLevel('ERROR') -p4c.py4cytoscape_logger.detail_logger.removeHandler(p4c.py4cytoscape_logger.detail_handler) -p4c.py4cytoscape_logger.detail_logger.addHandler(logging.NullHandler()) +if _has_py4cyto: + p4c.set_summary_logger(False) + p4c.py4cytoscape_logger.detail_logger.setLevel('ERROR') + p4c.py4cytoscape_logger.detail_logger.removeHandler( + p4c.py4cytoscape_logger.detail_handler + ) + p4c.py4cytoscape_logger.detail_logger.addHandler(logging.NullHandler()) # ** lang-main config -logging.Formatter.converter = gmtime -LOG_FMT: Final[str] = '%(asctime)s | lang_main:%(module)s:%(levelname)s | %(message)s' -LOG_DATE_FMT: Final[str] = '%Y-%m-%d %H:%M:%S +0000' -logging.basicConfig( - stream=sys.stdout, - format=LOG_FMT, - datefmt=LOG_DATE_FMT, -) - CONFIG_FILENAME: Final[str] = 'lang_main_config.toml' CYTO_STYLESHEET_FILENAME: Final[str] = r'cytoscape_config/lang_main.xml' -USE_INTERNAL_CONFIG: Final[bool] = False +PREFER_INTERNAL_CONFIG: Final[bool] = False pkg_dir = Path(__file__).parent cfg_path_internal = (pkg_dir / CONFIG_FILENAME).resolve() cyto_stylesheet_path = (pkg_dir / CYTO_STYLESHEET_FILENAME).resolve() -# ** load config data: internal/external -if USE_INTERNAL_CONFIG: - loaded_cfg = load_toml_config(path_to_toml=cfg_path_internal) -else: - cfg_path_external = (Path.cwd() / CONFIG_FILENAME).resolve() - if not cfg_path_external.exists(): - shutil.copy(cfg_path_internal, cfg_path_external) - sys.exit( - ( - 'No config file was found. A new one with default values was created ' - 'in the execution path. Please fill in the necessary values and ' - 'restart the programm.' - ) - ) - # raise NotImplementedError("External config data not implemented yet.") - loaded_cfg = load_toml_config(path_to_toml=cfg_path_external) -CONFIG: Final[dict[str, Any]] = loaded_cfg.copy() +# ** load config data: internal/external +# look for external config first, if not found use internal one +def search_cwd( + glob_pattern: str = CONFIG_FILENAME, +) -> Path | None: + """Searches the current working directory and looks for files + matching the glob pattern. + Returns the first match encountered. + + Parameters + ---------- + glob_pattern : str, optional + pattern to look for, first match will be returned, + by default CONFIG_FILENAME + + Returns + ------- + Path | None + Path if corresponding object was found, None otherwise + """ + cfg_path: Path | None = None + res = tuple(Path.cwd().glob(glob_pattern)) + if res: + cfg_path = res[0] + + return cfg_path + + +def search_iterative( + starting_path: Path, + glob_pattern: str = CONFIG_FILENAME, + stop_folder_name: str | None = None, +) -> Path | None: + """Iteratively searches the parent directories of the starting path + and look for files matching the glob pattern. The starting path is not + searched, only its parents. Therefore the starting path can also point + to a file. The folder in which it is placed in will be searched. + Returns the first match encountered. + + Parameters + ---------- + starting_path : Path + non-inclusive starting path + glob_pattern : str, optional + pattern to look for, first match will be returned, + by default CONFIG_FILENAME + stop_folder_name : str, optional + name of the last folder in the directory tree to search, by default 'python' + + Returns + ------- + Path | None + Path if corresponding object was found, None otherwise + """ + cfg_path: Path | None = None + for it in range(len(starting_path.parents)): + search_path = starting_path.parents[it] # do not look in library folder + res = tuple(search_path.glob(glob_pattern)) + if res: + cfg_path = res[0] + break + + if stop_folder_name is not None and search_path.name == stop_folder_name: + # library is placed inside a whole python installation for deployment + # only look up to this folder + break + + return cfg_path + + +def load_cfg() -> dict[str, Any]: + cfg_path: Path | None + if PREFER_INTERNAL_CONFIG: + cfg_path = cfg_path_internal + else: + cfg_path = search_cwd(glob_pattern=CONFIG_FILENAME) + + if cfg_path is None: + cfg_path = search_iterative( + starting_path=pkg_dir, + glob_pattern=CONFIG_FILENAME, + stop_folder_name='python', + ) + # backup: use internal config + if cfg_path is None: + cfg_path = cfg_path_internal + + config = load_toml_config(path_to_toml=cfg_path) + + return config.copy() + + +CONFIG: Final[dict[str, Any]] = load_cfg() + # ** Cytoscape configuration # stylesheet @@ -64,7 +135,7 @@ CYTO_PATH_STYLESHEET: Final[Path] = cyto_stylesheet_path # TODO check removal # append Graphviz binary folder to system path if not already contained -if sys.platform == 'win32': - path = Path(r'C:\Program Files\Graphviz\bin') - if path.is_dir() and str(path).lower() not in os.environ['PATH'].lower(): - os.environ['PATH'] += f';{path}' +# if sys.platform == 'win32': +# path = Path(r'C:\Program Files\Graphviz\bin') +# if path.is_dir() and str(path).lower() not in os.environ['PATH'].lower(): +# os.environ['PATH'] += f';{path}' diff --git a/src/lang_main/analysis/graphs.py b/src/lang_main/analysis/graphs.py index 35ff65a..b5c690a 100644 --- a/src/lang_main/analysis/graphs.py +++ b/src/lang_main/analysis/graphs.py @@ -386,7 +386,7 @@ def pipe_rescale_graph_edge_weights( def normalise_array_linear( - array: npt.NDArray[np.float_], + array: npt.NDArray[np.float32], ) -> npt.NDArray[np.float32]: """apply standard linear normalisation @@ -445,7 +445,7 @@ def verify_property( graph: Graph | DiGraph, property: str, ) -> None: - for idx, (node_1, node_2) in enumerate(graph.edges): + for node_1, node_2 in graph.edges: if property not in graph[node_1][node_2]: raise EdgePropertyNotContainedError( ( diff --git a/src/lang_main/analysis/preprocessing.py b/src/lang_main/analysis/preprocessing.py index b5a3eea..81387f2 100644 --- a/src/lang_main/analysis/preprocessing.py +++ b/src/lang_main/analysis/preprocessing.py @@ -1,8 +1,10 @@ +from __future__ import annotations + from collections.abc import Collection from itertools import combinations from math import factorial from pathlib import Path -from typing import cast +from typing import TYPE_CHECKING, cast import numpy as np import pandas as pd @@ -21,15 +23,10 @@ from lang_main.analysis.shared import ( similar_index_groups, ) from lang_main.loggers import logger_preprocess as logger -from lang_main.pipelines.base import Pipeline from lang_main.types import Embedding, PandasIndex -# TODO removal -# pattern_escape_seq = re.compile(r'[\t\n\r\f\v]+') -# pattern_escape_seq_sentences = re.compile(r' *[\t\n\r\f\v]+') -# pattern_repeated_chars = re.compile(r'([,;.:!?-_\+]){2,}') -# pattern_dates = re.compile(r'(\d{1,2}\.)?(\d{1,2}\.)([\d]{2,4})?') -# pattern_whitespace = re.compile(r'[ ]{2,}') +if TYPE_CHECKING: + from lang_main.pipelines.base import Pipeline # ** (1) dataset preparation: loading and simple preprocessing diff --git a/src/lang_main/analysis/shared.py b/src/lang_main/analysis/shared.py index dd66c95..ecfbff0 100644 --- a/src/lang_main/analysis/shared.py +++ b/src/lang_main/analysis/shared.py @@ -5,8 +5,9 @@ from typing import cast import networkx as nx import numpy as np import numpy.typing as npt -import sentence_transformers -import sentence_transformers.util + +# import sentence_transformers # TODO check removal +# import sentence_transformers.util # TODO check removal from networkx import Graph from pandas import DataFrame, Series from sentence_transformers import SentenceTransformer @@ -76,7 +77,6 @@ def candidates_by_index( data_model_input: Series, model: SentenceTransformer, cos_sim_threshold: float = 0.5, - # ) -> Iterator[tuple[PandasIndex, PandasIndex]]: ) -> Iterator[tuple[PandasIndex, PandasIndex]]: """function to filter candidate indices based on cosine similarity using SentenceTransformer model in batch mode, @@ -111,7 +111,9 @@ def candidates_by_index( ), ) # cosine similarity - cos_sim = cast(npt.NDArray, sentence_transformers.util.cos_sim(embds, embds).numpy()) + cos_sim = cast(npt.NDArray, model.similarity(embds, embds).numpy()) + # TODO check removal + # cos_sim = cast(npt.NDArray, sentence_transformers.util.cos_sim(embds, embds).numpy()) np.fill_diagonal(cos_sim, 0.0) cos_sim = np.triu(cos_sim) cos_sim_idx = np.argwhere(cos_sim >= cos_sim_threshold) diff --git a/src/lang_main/analysis/tokens.py b/src/lang_main/analysis/tokens.py index 7e6dedf..6b35b45 100644 --- a/src/lang_main/analysis/tokens.py +++ b/src/lang_main/analysis/tokens.py @@ -11,6 +11,11 @@ from lang_main.analysis.graphs import ( TokenGraph, update_graph, ) +from lang_main.constants import ( + POS_INDIRECT, + POS_OF_INTEREST, + TAG_OF_INTEREST, +) from lang_main.loggers import logger_token_analysis as logger from lang_main.types import ( PandasIndex, @@ -19,24 +24,8 @@ from lang_main.types import ( SpacyToken, ) -# ** POS -# POS_OF_INTEREST: frozenset[str] = frozenset(['NOUN', 'PROPN', 'ADJ', 'VERB', 'AUX']) -# POS_OF_INTEREST: frozenset[str] = frozenset(['NOUN', 'ADJ', 'VERB', 'AUX']) -# POS_OF_INTEREST: frozenset[str] = frozenset(['NOUN', 'PROPN']) -# POS_OF_INTEREST: frozenset[str] = frozenset(['NOUN', 'PROPN', 'VERB', 'AUX']) -POS_OF_INTEREST: frozenset[str] = frozenset(['NOUN', 'PROPN', 'VERB', 'AUX', 'ADV']) - -# POS_INDIRECT: frozenset[str] = frozenset(['AUX', 'VERB']) -POS_INDIRECT: frozenset[str] = frozenset(['AUX']) - -# ** TAG -# TAG_OF_INTEREST: frozenset[str] = frozenset(['ADJD']) -TAG_OF_INTEREST: frozenset[str] = frozenset() - # ** obtaining connection in texts - - def pre_clean_word(string: str) -> str: pattern = r'[^A-Za-zäöüÄÖÜ]+' string = re.sub(pattern, '', string) @@ -49,7 +38,6 @@ def is_str_date( string: str, fuzzy: bool = False, ) -> bool: - # print(string) try: # check if string is a number # if length is greater than 8, it is not a date diff --git a/src/lang_main/constants.py b/src/lang_main/constants.py index e656b1b..d9c8361 100644 --- a/src/lang_main/constants.py +++ b/src/lang_main/constants.py @@ -1,6 +1,10 @@ +from enum import Enum # noqa: I001 +from importlib.util import find_spec from pathlib import Path from typing import Final +from sentence_transformers import SimilarityFunction + from lang_main import CONFIG, CYTO_PATH_STYLESHEET from lang_main import model_loader as m_load from lang_main.types import ( @@ -8,7 +12,12 @@ from lang_main.types import ( CytoLayouts, LanguageModels, ModelLoaderMap, + ONNXExecutionProvider, # noqa: F401 + STFRBackends, STFRDeviceTypes, + STFRModelArgs, + STFRModels, + STFRQuantFilenames, # noqa: F401 ) __all__ = [ @@ -16,8 +25,23 @@ __all__ = [ 'CYTO_PATH_STYLESHEET', ] +# ** dependencies +_has_py4cyto: bool = True if find_spec('py4cytoscape') else False +_has_dash: bool = True if (find_spec('dash') and find_spec('kaleido')) else False +_has_plotly: bool = True if (find_spec('plotly') and find_spec('kaleido')) else False + + +class Dependencies(Enum): + PY4C = _has_py4cyto + DASH = _has_dash + PLOT = _has_plotly + + # ** logging # graphs +ENABLE_LOGGING: Final[bool] = CONFIG['logging']['enabled'] +LOGGING_TO_FILE: Final[bool] = CONFIG['logging']['file'] +LOGGING_TO_STDERR: Final[bool] = CONFIG['logging']['stderr'] LOGGING_DEFAULT_GRAPHS: Final[bool] = False # ** paths @@ -44,14 +68,25 @@ SKIP_TIME_ANALYSIS: Final[bool] = CONFIG['control']['time_analysis_skip'] # ** models # ** loading SPACY_MODEL_NAME: Final[str] = 'de_dep_news_trf' -STFR_MODEL_NAME: Final[str] = 'sentence-transformers/all-mpnet-base-v2' +STFR_MODEL_NAME: Final[STFRModels] = STFRModels.ALL_MPNET_BASE_V2 STFR_DEVICE: Final[STFRDeviceTypes] = STFRDeviceTypes.CPU +STFR_SIMILARITY: Final[SimilarityFunction] = SimilarityFunction.COSINE +STFR_BACKEND: Final[STFRBackends] = STFRBackends.TORCH +STFR_MODEL_ARGS: Final[STFRModelArgs] = {} +# STFR_MODEL_ARGS: Final[STFRModelArgs] = { +# 'file_name': STFRQuantFilenames.ONNX_Q_UINT8, +# 'provider': ONNXExecutionProvider.CPU, +# 'export': False, +# } MODEL_LOADER_MAP: Final[ModelLoaderMap] = { LanguageModels.SENTENCE_TRANSFORMER: { 'func': m_load.load_sentence_transformer, 'kwargs': { 'model_name': STFR_MODEL_NAME, + 'similarity_func': STFR_SIMILARITY, + 'backend': STFR_BACKEND, 'device': STFR_DEVICE, + 'model_kwargs': STFR_MODEL_ARGS, }, }, LanguageModels.SPACY: { @@ -61,6 +96,19 @@ MODEL_LOADER_MAP: Final[ModelLoaderMap] = { }, }, } +# ** language dependency analysis +# ** POS +# POS_OF_INTEREST: frozenset[str] = frozenset(['NOUN', 'PROPN', 'ADJ', 'VERB', 'AUX']) +# POS_OF_INTEREST: frozenset[str] = frozenset(['NOUN', 'ADJ', 'VERB', 'AUX']) +# POS_OF_INTEREST: frozenset[str] = frozenset(['NOUN', 'PROPN']) +# POS_OF_INTEREST: frozenset[str] = frozenset(['NOUN', 'PROPN', 'VERB', 'AUX']) +POS_OF_INTEREST: frozenset[str] = frozenset(['NOUN', 'PROPN', 'VERB', 'AUX', 'ADV']) +# POS_INDIRECT: frozenset[str] = frozenset(['AUX', 'VERB']) +POS_INDIRECT: frozenset[str] = frozenset(['AUX']) +# ** TAG +# TAG_OF_INTEREST: frozenset[str] = frozenset(['ADJD']) +TAG_OF_INTEREST: frozenset[str] = frozenset() + # ** export # ** preprocessing @@ -74,7 +122,6 @@ THRESHOLD_SIMILARITY: Final[float] = CONFIG['preprocess']['threshold_similarity' # ** graph postprocessing EDGE_WEIGHT_DECIMALS: Final[int] = 4 THRESHOLD_EDGE_NUMBER: Final[int] = CONFIG['graph_postprocessing']['threshold_edge_number'] -# THRESHOLD_EDGE_WEIGHT: Final[int] = CONFIG['graph_postprocessing']['threshold_edge_weight'] PROPERTY_NAME_DEGREE_WEIGHTED: Final[str] = 'degree_weighted' # ** graph exports (Cytoscape) diff --git a/src/lang_main/errors.py b/src/lang_main/errors.py index f999e67..88cfbbd 100644 --- a/src/lang_main/errors.py +++ b/src/lang_main/errors.py @@ -14,3 +14,25 @@ class EmptyEdgesError(EmptyGraphError): class GraphRenderError(Exception): """Error raised if a graph object can not be rendered""" + + +class DependencyMissingError(Exception): + """Error raised if needed dependency could not be found""" + + +# ** pipelines to perform given actions on dataset in a customisable manner + + +class NoPerformableActionError(Exception): + """Error describing that no action is available in the current pipeline""" + + +class WrongActionTypeError(Exception): + """Error raised if added action type is not supported by corresponding pipeline""" + + +class OutputInPipelineContainerError(Exception): + """Error raised if an output was detected by one of the performed + actions in a PipelineContainer. Each action in a PipelineContainer is itself a + procedure which does not have any parameters or return values and should therefore not + return any values.""" diff --git a/src/lang_main/lang_main_config.toml b/src/lang_main/lang_main_config.toml index 3a7a171..b83bb12 100644 --- a/src/lang_main/lang_main_config.toml +++ b/src/lang_main/lang_main_config.toml @@ -7,6 +7,11 @@ inputs = './inputs/' results = './results/test_20240807/' dataset = '../data/02_202307/Export4.csv' +[logging] +enabled = true +stderr = true +file = true + # only debugging features, production-ready pipelines should always # be fully executed [control] diff --git a/src/lang_main/loggers.py b/src/lang_main/loggers.py index bc4a992..9fbd553 100644 --- a/src/lang_main/loggers.py +++ b/src/lang_main/loggers.py @@ -1,16 +1,65 @@ import logging +import logging.handlers +from pathlib import Path +from time import gmtime from typing import Final +from lang_main.constants import ( + ENABLE_LOGGING, + LOGGING_TO_FILE, + LOGGING_TO_STDERR, +) from lang_main.types import LoggingLevels -# ** logging -LOGGING_LEVEL_PREPROCESS: Final[LoggingLevels] = LoggingLevels.INFO -LOGGING_LEVEL_PIPELINES: Final[LoggingLevels] = LoggingLevels.INFO -LOGGING_LEVEL_GRAPHS: Final[LoggingLevels] = LoggingLevels.INFO +# ** config +logging.Formatter.converter = gmtime +LOG_FMT: Final[str] = '%(asctime)s | lang_main:%(module)s:%(levelname)s | %(message)s' +LOG_DATE_FMT: Final[str] = '%Y-%m-%d %H:%M:%S +0000' +LOG_FILE_PATH: Final[Path] = Path.cwd() / 'lang-main.log' +# logging.basicConfig( +# format=LOG_FMT, +# datefmt=LOG_DATE_FMT, +# ) + +# ** formatters +logger_all_formater = logging.Formatter(fmt=LOG_FMT, datefmt=LOG_DATE_FMT) + +# ** handlers +null_handler = logging.NullHandler() +if ENABLE_LOGGING and LOGGING_TO_STDERR: + logger_all_handler_stderr = logging.StreamHandler() + logger_all_handler_stderr.setLevel(LoggingLevels.WARNING) + logger_all_handler_stderr.setFormatter(logger_all_formater) +else: + logger_all_handler_stderr = null_handler + +if ENABLE_LOGGING and LOGGING_TO_FILE: + logger_all_handler_file = logging.handlers.RotatingFileHandler( + LOG_FILE_PATH, + encoding='utf-8', + maxBytes=5_242_880, + backupCount=1, + ) + logger_all_handler_file.setLevel(LoggingLevels.DEBUG) + logger_all_handler_file.setFormatter(logger_all_formater) +else: + logger_all_handler_file = null_handler + + +# ** logging levels +LOGGING_LEVEL_ALL: Final[LoggingLevels] = LoggingLevels.DEBUG +LOGGING_LEVEL_PREPROCESS: Final[LoggingLevels] = LoggingLevels.DEBUG +LOGGING_LEVEL_PIPELINES: Final[LoggingLevels] = LoggingLevels.DEBUG +LOGGING_LEVEL_GRAPHS: Final[LoggingLevels] = LoggingLevels.DEBUG LOGGING_LEVEL_TIMELINE: Final[LoggingLevels] = LoggingLevels.DEBUG -LOGGING_LEVEL_TOKEN_ANALYSIS: Final[LoggingLevels] = LoggingLevels.INFO -LOGGING_LEVEL_SHARED_HELPERS: Final[LoggingLevels] = LoggingLevels.INFO -LOGGING_LEVEL_RENDERING: Final[LoggingLevels] = LoggingLevels.INFO +LOGGING_LEVEL_TOKEN_ANALYSIS: Final[LoggingLevels] = LoggingLevels.DEBUG +LOGGING_LEVEL_SHARED_HELPERS: Final[LoggingLevels] = LoggingLevels.DEBUG +LOGGING_LEVEL_RENDERING: Final[LoggingLevels] = LoggingLevels.DEBUG + +# ** loggers and configuration +logger_all = logging.getLogger('lang_main') +logger_all.addHandler(logger_all_handler_stderr) +logger_all.addHandler(logger_all_handler_file) logger_shared_helpers = logging.getLogger('lang_main.shared') logger_shared_helpers.setLevel(LOGGING_LEVEL_SHARED_HELPERS) diff --git a/src/lang_main/model_loader.py b/src/lang_main/model_loader.py index fcac638..072f531 100644 --- a/src/lang_main/model_loader.py +++ b/src/lang_main/model_loader.py @@ -1,18 +1,28 @@ from __future__ import annotations -from typing import Literal, overload +from typing import ( + TYPE_CHECKING, + Any, + Literal, + overload, +) import spacy from sentence_transformers import SentenceTransformer +from lang_main.constants import STFR_SIMILARITY from lang_main.types import ( LanguageModels, Model, ModelLoaderMap, SpacyModel, + STFRBackends, STFRDeviceTypes, ) +if TYPE_CHECKING: + from sentence_transformers import SimilarityFunction + @overload def instantiate_model( @@ -48,6 +58,15 @@ def load_spacy( def load_sentence_transformer( model_name: str, - device: STFRDeviceTypes, + similarity_func: SimilarityFunction = STFR_SIMILARITY, + backend: STFRBackends = STFRBackends.TORCH, + device: STFRDeviceTypes = STFRDeviceTypes.CPU, + model_kwargs: dict[str, Any] | None = None, ) -> SentenceTransformer: - return SentenceTransformer(model_name_or_path=model_name, device=device) + return SentenceTransformer( + model_name_or_path=model_name, + similarity_fn_name=similarity_func, + backend=backend, # type: ignore Literal matches Enum + device=device, + model_kwargs=model_kwargs, + ) diff --git a/src/lang_main/pipelines/base.py b/src/lang_main/pipelines/base.py index d05fc6b..590e7ed 100644 --- a/src/lang_main/pipelines/base.py +++ b/src/lang_main/pipelines/base.py @@ -6,27 +6,15 @@ from pathlib import Path from typing import Any, Never, cast from typing_extensions import override +from lang_main.errors import ( + NoPerformableActionError, + OutputInPipelineContainerError, + WrongActionTypeError, +) from lang_main.io import load_pickle, save_pickle from lang_main.loggers import logger_pipelines as logger from lang_main.types import ResultHandling -# ** pipelines to perform given actions on dataset in a customisable manner - - -class NoPerformableActionError(Exception): - """Error describing that no action is available in the current pipeline""" - - -class WrongActionTypeError(Exception): - """Error raised if added action type is not supported by corresponding pipeline""" - - -class OutputInPipelineContainerError(Exception): - """Error raised if an output was detected by one of the performed - actions in a PipelineContainer. Each action in a PipelineContainer is itself a - procedure which does not have any parameters or return values and should therefore not - return any values.""" - class BasePipeline(ABC): def __init__( diff --git a/src/lang_main/pipelines/predefined.py b/src/lang_main/pipelines/predefined.py index c1cf2e7..a813131 100644 --- a/src/lang_main/pipelines/predefined.py +++ b/src/lang_main/pipelines/predefined.py @@ -42,7 +42,6 @@ from lang_main.constants import ( UNIQUE_CRITERION_FEATURE, ) from lang_main.pipelines.base import Pipeline -from lang_main.render import cytoscape as cyto from lang_main.types import EntryPoints, LanguageModels # ** Models @@ -137,13 +136,6 @@ def build_tk_graph_post_pipe() -> Pipeline: pipe_graph_postprocessing = Pipeline( name='Graph_Postprocessing', working_dir=SAVE_PATH_FOLDER ) - # pipe_graph_postprocessing.add( - # graphs.filter_graph_by_edge_weight, - # { - # 'bound_lower': THRESHOLD_EDGE_WEIGHT, - # 'bound_upper': None, - # }, - # ) pipe_graph_postprocessing.add( graphs.filter_graph_by_number_edges, { @@ -190,6 +182,10 @@ def build_tk_graph_render_pipe( export_folder: Path = SAVE_PATH_FOLDER, base_network_name: str = CYTO_BASE_NETWORK_NAME, ) -> Pipeline: + # optional dependency: late import + # raises exception if necessary modules are not found + from lang_main.render import cytoscape as cyto + pipe_graph_rendering = Pipeline( name='Graph_Static-Rendering', working_dir=SAVE_PATH_FOLDER, diff --git a/src/lang_main/render/__init__.py b/src/lang_main/render/__init__.py index e69de29..2107057 100644 --- a/src/lang_main/render/__init__.py +++ b/src/lang_main/render/__init__.py @@ -0,0 +1,7 @@ +from lang_main.constants import Dependencies +from lang_main.errors import DependencyMissingError + +if not Dependencies.PY4C.value: + raise DependencyMissingError( + 'The module >>render<< needs the package >>Py4Cytoscape<<. Package not found.' + ) diff --git a/src/lang_main/types.py b/src/lang_main/types.py index ebd5c60..6428341 100644 --- a/src/lang_main/types.py +++ b/src/lang_main/types.py @@ -3,6 +3,7 @@ from collections.abc import Callable, Hashable from typing import ( Any, Literal, + NotRequired, Required, TypeAlias, TypedDict, @@ -40,6 +41,27 @@ class LanguageModels(enum.StrEnum): SPACY = enum.auto() +class ONNXExecutionProvider(enum.StrEnum): + CPU = 'CPUExecutionProvider' + + +class STFRModels(enum.StrEnum): + ALL_MPNET_BASE_V2 = 'all-mpnet-base-v2' + ALL_DISTILROBERTA_V1 = 'all-distilroberta-v1' + ALL_MINI_LM_L12_V2 = 'all-MiniLM-L12-v2' + ALL_MINI_LM_L6_V2 = 'all-MiniLM-L6-v2' + + +class STFRQuantFilenames(enum.StrEnum): + ONNX_Q_UINT8 = 'onnx/model_quint8_avx2.onnx' + + +class STFRModelArgs(TypedDict): + provider: NotRequired[ONNXExecutionProvider] + file_name: NotRequired[STFRQuantFilenames] + export: NotRequired[bool] + + Model: TypeAlias = SentenceTransformer | SpacyModel ModelLoaderFunc: TypeAlias = Callable[..., Model] @@ -52,7 +74,12 @@ class ModelLoaderInfo(TypedDict): ModelLoaderMap: TypeAlias = dict[LanguageModels, ModelLoaderInfo] -# ** devices +class STFRBackends(enum.StrEnum): + TORCH = enum.auto() + ONNX = enum.auto() + OPENVINO = enum.auto() + + class STFRDeviceTypes(enum.StrEnum): CPU = enum.auto() GPU = enum.auto()