Source code for asreview.project

# Copyright 2019-2022 The ASReview Authors. All Rights Reserved.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# See the License for the specific language governing permissions and
# limitations under the License.

__all__ = [

import json
import logging
import os
import pickle
import shutil
import tempfile
import time
import zipfile
from datetime import datetime
from functools import wraps
from pathlib import Path
from uuid import uuid4

import jsonschema
import numpy as np
import pandas as pd
from filelock import FileLock
from scipy.sparse import csr_matrix
from scipy.sparse import load_npz
from scipy.sparse import save_npz

from asreview import load_dataset
from asreview._version import get_versions
from asreview.config import LABEL_NA
from asreview.config import PROJECT_MODE_EXPLORE
from asreview.config import PROJECT_MODE_ORACLE
from asreview.config import PROJECT_MODE_SIMULATE
from asreview.config import PROJECT_MODES
from asreview.config import SCHEMA
from asreview.exceptions import CacheDataError
from asreview.state.sqlstate import SQLiteState
from asreview.utils import asreview_path

PATH_PROJECT_CONFIG = "project.json"
PATH_PROJECT_CONFIG_LOCK = "project.json.lock"
PATH_FEATURE_MATRICES = "feature_matrices"

class ProjectError(Exception):

class ProjectExistsError(Exception):

class ProjectNotFoundError(Exception):

[docs] def get_project_path(folder_id): """Get the project directory. Arguments --------- folder_id: str The id of the folder containing a project. If there is no authentication, the folder_id is equal to the project_id. Otherwise, this is equal to {project_owner_id}_{project_id}. """ return Path(asreview_path(), folder_id)
[docs] def project_from_id(f): """Decorator function that takes a user account as parameter, the user account is used to get the correct sub folder in which the projects is """ @wraps(f) def decorated_function(project_id, *args, **kwargs): project_path = get_project_path(project_id) if not is_project(project_path): raise ProjectNotFoundError(f"Project '{project_id}' not found") project = Project(project_path, project_id=project_id) return f(project, *args, **kwargs) return decorated_function
[docs] def get_projects(project_paths=None): """Get the ASReview projects at the given paths. Arguments --------- project_paths : list[Path], optional List of paths to projects. By default all the projects in the asreview folder are used, by default None Returns ------- list[Project] Projects at the given project paths. """ if project_paths is None: project_paths = [path for path in asreview_path().iterdir() if path.is_dir()] return [Project(project_path) for project_path in project_paths]
[docs] def is_project(project_path): project_path = Path(project_path) / PATH_PROJECT_CONFIG return project_path.exists()
[docs] def is_v0_project(project_path): """Check if a project file is of a ASReview version 0 project.""" return not Path(project_path, "reviews").exists()
[docs] class Project: """Project class for ASReview project files.""" def __init__(self, project_path, project_id=None): self.project_path = Path(project_path) self.project_id = project_id
[docs] @classmethod def create( cls, project_path, project_id=None, project_mode="oracle", project_name=None, project_description=None, project_authors=None, project_tags=None, ): """Initialize the necessary files specific to the web app.""" project_path = Path(project_path) if is_project(project_path): raise ProjectExistsError("Project already exists.") if project_mode not in PROJECT_MODES: raise ValueError( f"Project mode '{project_mode}' is not in " f"{PROJECT_MODES}." ) if project_id is None: project_id = project_path.stem if project_name is None: project_name = project_path.stem if project_path.is_dir(): raise IsADirectoryError(f"Project folder {project_path} already exists.") try: project_path.mkdir(parents=True, exist_ok=True) Path(project_path, "data").mkdir(exist_ok=True) Path(project_path, PATH_FEATURE_MATRICES).mkdir(exist_ok=True) Path(project_path, "reviews").mkdir(exist_ok=True) config = { "version": get_versions()["version"], "id": project_id, "mode": project_mode, "name": project_name, "description": project_description, "authors": project_authors, "created_at_unix": int(time.time()), "datetimeCreated": str(, "reviews": [], "feature_matrices": [], "tags": project_tags, } # validate new config before storing jsonschema.validate(instance=config, schema=SCHEMA) project_fp = Path(project_path, PATH_PROJECT_CONFIG) project_fp_lock = Path(project_path, PATH_PROJECT_CONFIG_LOCK) lock = FileLock(project_fp_lock, timeout=3) # create a file with project info with lock: with open(project_fp, "w") as f: json.dump(config, f) except Exception as err: # remove all generated folders and raise error shutil.rmtree(project_path) raise err return cls(project_path, project_id=project_id)
@property def config(self): try: return self._config except AttributeError: project_fp = Path(self.project_path, PATH_PROJECT_CONFIG) project_fp_lock = Path(self.project_path, PATH_PROJECT_CONFIG_LOCK) lock = FileLock(project_fp_lock, timeout=3) if not project_fp.exists(): raise ProjectNotFoundError(f"Project '{self.project_path}' not found") with lock: # read the file with project info with open(project_fp) as fp: config = json.load(fp) self._config = config return config @config.setter def config(self, config): project_fp = Path(self.project_path, PATH_PROJECT_CONFIG) project_fp_lock = Path(self.project_path, PATH_PROJECT_CONFIG_LOCK) lock = FileLock(project_fp_lock, timeout=3) with lock: with open(project_fp, "w") as f: json.dump(config, f) self._config = config
[docs] def update_config(self, **kwargs): """Update project info""" kwargs_copy = kwargs.copy() # validate schema if "mode" in kwargs_copy and kwargs_copy["mode"] not in PROJECT_MODES: raise ValueError("Project mode '{}' not found.".format(kwargs_copy["mode"])) # update project file config = self.config config.update(kwargs_copy) # validate new config before storing jsonschema.validate(instance=config, schema=SCHEMA) self.config = config return config
[docs] def add_dataset(self, file_name): """Add file path to the project file. Add file to data subfolder and fill the pool of iteration 0. """ # fill the pool of the first iteration fp_data = Path(self.project_path, "data", file_name) as_data = load_dataset(fp_data) if self.config["mode"] == PROJECT_MODE_SIMULATE and ( as_data.labels is None or (as_data.labels == LABEL_NA).any() ): raise ValueError("Import fully labeled dataset") if self.config["mode"] == PROJECT_MODE_EXPLORE and as_data.labels is None: raise ValueError("Import partially or fully labeled dataset") self.update_config(dataset_path=file_name, name=file_name.rsplit(".", 1)[0]) state = SQLiteState(read_only=False) try: review_id = uuid4().hex state._create_new_state_file(self.project_path, review_id) self.add_review(review_id) # save the record ids in the state file state.add_record_table(as_data.record_ids) # if the data contains labels and oracle mode, add them to the state file if ( self.config["mode"] == PROJECT_MODE_ORACLE and as_data.labels is not None ): labeled_indices = np.where(as_data.labels != LABEL_NA)[0] labels = as_data.labels[labeled_indices].tolist() labeled_record_ids = as_data.record_ids[labeled_indices].tolist() # add the labels as prior data state.add_labeling_data( record_ids=labeled_record_ids, labels=labels, notes=[None for _ in labeled_record_ids], prior=True, ) finally: try: state.close() except AttributeError: pass
[docs] def remove_dataset(self): """Remove dataset from project.""" # reset dataset_path self.update_config(dataset_path=None) # remove datasets from project shutil.rmtree(Path(self.project_path, "data")) self.clean_tmp_files() # remove state file if present if Path(self.project_path, "reviews").is_dir() and any( Path(self.project_path, "reviews").iterdir() ): self.delete_review()
def _read_data_from_cache(self, version_check=True): fp_data_pickle = Path(self.project_path, "tmp", "data.pickle") try: with open(fp_data_pickle, "rb") as f_pickle_read: data_obj, data_obj_version = pickle.load(f_pickle_read) if not isinstance(data_obj.df, pd.DataFrame): raise ValueError() if (not version_check) or (get_versions()["version"] == data_obj_version): return data_obj except FileNotFoundError: pass except Exception as err: logging.error(f"Error reading cache file: {err}") try: os.remove(fp_data_pickle) except FileNotFoundError: pass raise CacheDataError()
[docs] def read_data(self, use_cache=True, save_cache=True): """Get Dataset object from file. Parameters ---------- use_cache: bool Use the pickle file if available. save_cache: bool Save the file to a pickle file if not available. Returns ------- Dataset: The data object for internal use in ASReview. """ if use_cache: try: return self._read_data_from_cache() except CacheDataError: pass try: as_data = load_dataset( Path(self.project_path, "data", self.config["dataset_path"]) ) except Exception: raise FileNotFoundError("Dataset not found") if save_cache: Path(self.project_path, "tmp").mkdir(exist_ok=True) fp_data_pickle = Path(self.project_path, "tmp", "data.pickle") with open(fp_data_pickle, "wb") as f_pickle: pickle.dump((as_data, get_versions()["version"]), f_pickle) return as_data
[docs] def clean_tmp_files(self): """Clean temporary files in a project. Arguments --------- project_id: str The id of the current project. """ try: os.remove(Path(self.project_path, "tmp")) except OSError as e: print(f"Error: {e.strerror}")
@property def feature_matrices(self): try: return self.config["feature_matrices"] except Exception: return []
[docs] def add_feature_matrix(self, feature_matrix, feature_extraction_method): """Add feature matrix to project file. Arguments --------- feature_matrix: numpy.ndarray, scipy.sparse.csr.csr_matrix The feature matrix to add to the project file. feature_extraction_method: str Name of the feature extraction method. """ # Make sure the feature matrix is in csr format. if isinstance(feature_matrix, np.ndarray): feature_matrix = csr_matrix(feature_matrix) if not isinstance(feature_matrix, csr_matrix): raise ValueError( "The feature matrix should be convertible to type " "scipy.sparse.csr.csr_matrix." ) matrix_filename = f"{feature_extraction_method}_feature_matrix.npz" save_npz( Path(self.project_path, PATH_FEATURE_MATRICES, matrix_filename), feature_matrix, ) # Add the feature matrix to the project config. config = self.config feature_matrix_config = { "id": feature_extraction_method, "filename": matrix_filename, } # Add container for feature matrices. if "feature_matrices" not in config: config["feature_matrices"] = [] config["feature_matrices"].append(feature_matrix_config) self.config = config
[docs] def get_feature_matrix(self, feature_extraction_method): """Get the feature matrix from the project file. Arguments --------- feature_extraction_method: str Name of the feature extraction method for which to get the matrix. Returns ------- scipy.sparse.csr_matrix: Feature matrix in sparse format. """ matrix_filename = f"{feature_extraction_method}_feature_matrix.npz" return load_npz(Path(self.project_path, PATH_FEATURE_MATRICES, matrix_filename))
@property def reviews(self): try: return self.config["reviews"] except Exception: return []
[docs] def add_review(self, review_id, start_time=None, status="setup"): """Add new review metadata. Arguments --------- review_id: str The review_id uuid4. status: str The status of the review. One of 'setup', 'running', 'finished'. start_time: Start of the review. """ if start_time is None: start_time = # Add the review to the project. config = self.config review_config = { "id": review_id, "start_time": str(start_time), "status": status, # "end_time": } # add container for reviews if "reviews" not in config: config["reviews"] = [] config["reviews"].append(review_config) self.config = config
[docs] def update_review(self, review_id=None, **kwargs): """Update review metadata. Arguments --------- review_id: str The review_id uuid4. Default None, which is the first added review. status: str The status of the review. One of 'setup', 'running', 'finished'. start_time: Start of the review. end_time: End time of the review. """ # read the file with project info config = self.config if review_id is None: review_index = 0 else: review_index = [x["id"] for x in self.config["reviews"]].index(review_id) review_config = config["reviews"][review_index] review_config.update(kwargs) config["reviews"][review_index] = review_config # update the file with project info self.config = config
[docs] def delete_review(self, remove_folders=False): try: # remove the folder tree shutil.rmtree(Path(self.project_path, PATH_FEATURE_MATRICES)) # recreate folder structure if True if not remove_folders: Path(self.project_path, PATH_FEATURE_MATRICES).mkdir(exist_ok=True) except Exception: print("Failed to remove feature matrices.") try: path_review = Path(self.project_path, "reviews") shutil.rmtree(path_review) if not remove_folders: Path(self.project_path, "reviews").mkdir(exist_ok=True) except Exception: print("Failed to remove sql database.") # update the config self.update_config(**{"reviews": [], "feature_matrices": []})
[docs] def mark_review_finished(self, review_id=None): """Mark a review in the project as finished. If no review_id is given, mark the first review as finished. Arguments --------- review_id: str Identifier of the review to mark as finished. """ self.update_review( review_id=review_id, status="finished", end_time=str( )
[docs] def export(self, export_fp): if Path(export_fp).suffix != ".asreview": raise ValueError("Export file should have .asreview extension.") if Path(export_fp) == Path(self.project_path): raise ValueError("export_fp should not be identical to project path.") export_fp_tmp = Path(export_fp).with_suffix("") # copy the source tree, but ignore pickle files shutil.copytree( self.project_path, export_fp_tmp, ignore=shutil.ignore_patterns("tmp", "*.lock"), ) # create the archive shutil.make_archive(export_fp_tmp, "zip", root_dir=export_fp_tmp) # remove the unzipped folder and move zip shutil.rmtree(export_fp_tmp) shutil.move(f"{export_fp_tmp}.zip", export_fp)
[docs] @classmethod def load(cls, asreview_file, project_path, safe_import=False): tmpdir = tempfile.TemporaryDirectory().name try: # Unzip the project file with zipfile.ZipFile(asreview_file, "r") as zip_obj: zip_filenames = zip_obj.namelist() # raise error if no ASReview project file if PATH_PROJECT_CONFIG not in zip_filenames: raise ValueError("Project file is not valid project.") # extract all files to folder for f in zip_filenames: if not f.endswith(".pickle"): zip_obj.extract(f, path=tmpdir) except zipfile.BadZipFile: raise ValueError("File is not an ASReview file.") with open(Path(tmpdir, PATH_PROJECT_CONFIG)) as f: project_config = json.load(f) if safe_import: # assign a new id to the project. project_config["id"] = uuid4().hex with open(Path(tmpdir, PATH_PROJECT_CONFIG), "r+") as f: # write to file json.dump(project_config, f) f.truncate() # location to copy file to # Move the project from the temp folder to the projects folder. os.replace(tmpdir, Path(project_path, project_config["id"])) return cls(Path(project_path, project_config["id"]))
[docs] def set_error(self, err, save_error_message=True): err_type = type(err).__name__ self.update_review(status="error") # write error to file if label method is prior (first iteration) if save_error_message: message = { "message": f"{err_type}: {err}", "type": f"{err_type}", "datetime": str(, } with open(Path(self.project_path, "error.json"), "w") as f: json.dump(message, f)
[docs] def remove_error(self, status): error_path = self.project_path / "error.json" if error_path.exists(): try: os.remove(error_path) except Exception as err: raise ValueError(f"Failed to clear the error. {err}") self.update_review(status=status)