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import collections |
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import os |
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import sys |
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import click |
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import click_log |
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from flask import current_app |
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from flask.cli import ScriptInfo |
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import annif |
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from annif.exception import ConfigurationException |
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from annif.project import Access |
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from annif.suggestion import SuggestionFilter |
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logger = annif.logger |
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def _set_project_config_file_path(ctx, param, value): |
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"""Override the default path or the path given in env by CLI option""" |
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with ctx.ensure_object(ScriptInfo).load_app().app_context(): |
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if value: |
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current_app.config["PROJECTS_CONFIG_PATH"] = value |
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def common_options(f): |
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"""Decorator to add common options for all CLI commands""" |
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f = click.option( |
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"-p", |
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"--projects", |
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help="Set path to project configuration file or directory", |
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type=click.Path(dir_okay=True, exists=True), |
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callback=_set_project_config_file_path, |
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expose_value=False, |
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is_eager=True, |
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)(f) |
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return click_log.simple_verbosity_option(logger)(f) |
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def backend_param_option(f): |
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"""Decorator to add an option for CLI commands to override BE parameters""" |
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return click.option( |
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"--backend-param", |
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"-b", |
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multiple=True, |
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help="Override backend parameter of the config file. " |
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+ "Syntax: `-b <backend>.<parameter>=<value>`.", |
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)(f) |
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def docs_limit_option(f): |
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"""Decorator to add an option for CLI commands to limit the number of documents to |
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use""" |
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return click.option( |
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"--docs-limit", |
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"-d", |
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default=None, |
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type=click.IntRange(0, None), |
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help="Maximum number of documents to use", |
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)(f) |
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def get_project(project_id): |
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""" |
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Helper function to get a project by ID and bail out if it doesn't exist""" |
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try: |
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return annif.registry.get_project(project_id, min_access=Access.private) |
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except ValueError: |
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click.echo("No projects found with id '{0}'.".format(project_id), err=True) |
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sys.exit(1) |
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def get_vocab(vocab_id): |
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""" |
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Helper function to get a vocabulary by ID and bail out if it doesn't |
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exist""" |
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try: |
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return annif.registry.get_vocab(vocab_id, min_access=Access.private) |
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except ValueError: |
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click.echo(f"No vocabularies found with the id '{vocab_id}'.", err=True) |
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sys.exit(1) |
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def open_documents(paths, subject_index, vocab_lang, docs_limit): |
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"""Helper function to open a document corpus from a list of pathnames, |
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each of which is either a TSV file or a directory of TXT files. For |
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directories with subjects in TSV files, the given vocabulary language |
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will be used to convert subject labels into URIs. The corpus will be |
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returned as an instance of DocumentCorpus or LimitingDocumentCorpus.""" |
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def open_doc_path(path, subject_index): |
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"""open a single path and return it as a DocumentCorpus""" |
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if os.path.isdir(path): |
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return annif.corpus.DocumentDirectory( |
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path, subject_index, vocab_lang, require_subjects=True |
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) |
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return annif.corpus.DocumentFile(path, subject_index) |
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if len(paths) == 0: |
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logger.warning("Reading empty file") |
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docs = open_doc_path(os.path.devnull, subject_index) |
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elif len(paths) == 1: |
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docs = open_doc_path(paths[0], subject_index) |
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else: |
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corpora = [open_doc_path(path, subject_index) for path in paths] |
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docs = annif.corpus.CombinedCorpus(corpora) |
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if docs_limit is not None: |
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docs = annif.corpus.LimitingDocumentCorpus(docs, docs_limit) |
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return docs |
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def open_text_documents(paths, docs_limit): |
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""" |
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Helper function to read text documents from the given file paths. Returns a |
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DocumentList object with Documents having no subjects. If a path is "-", the |
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document text is read from standard input. The maximum number of documents to read |
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is set by docs_limit parameter. |
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""" |
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def _docs(paths): |
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for path in paths: |
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if path == "-": |
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doc = annif.corpus.Document(text=sys.stdin.read(), subject_set=None) |
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else: |
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with open(path, errors="replace", encoding="utf-8-sig") as docfile: |
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doc = annif.corpus.Document(text=docfile.read(), subject_set=None) |
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yield doc |
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return annif.corpus.DocumentList(_docs(paths[:docs_limit])) |
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def show_hits(hits, project, lang, file=None): |
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""" |
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Print subject suggestions to the console or a file. The suggestions are displayed as |
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a table, with one row per hit. Each row contains the URI, label, possible notation, |
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and score of the suggestion. The label is given in the specified language. |
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""" |
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for hit in hits.as_list(): |
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subj = project.subjects[hit.subject_id] |
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line = "<{}>\t{}\t{}".format( |
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subj.uri, |
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"\t".join(filter(None, (subj.labels[lang], subj.notation))), |
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hit.score, |
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) |
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click.echo(line, file=file) |
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def parse_backend_params(backend_param, project): |
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"""Parse a list of backend parameters given with the --backend-param |
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option into a nested dict structure""" |
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backend_params = collections.defaultdict(dict) |
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for beparam in backend_param: |
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backend, param = beparam.split(".", 1) |
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key, val = param.split("=", 1) |
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_validate_backend_params(backend, beparam, project) |
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backend_params[backend][key] = val |
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return backend_params |
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def _validate_backend_params(backend, beparam, project): |
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if backend != project.config["backend"]: |
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raise ConfigurationException( |
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'The backend {} in CLI option "-b {}" not matching the project' |
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" backend {}.".format(backend, beparam, project.config["backend"]) |
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) |
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def generate_filter_batches(subjects, filter_batch_max_limit): |
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import annif.eval |
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filter_batches = {} |
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for limit in range(1, filter_batch_max_limit + 1): |
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for threshold in [i * 0.05 for i in range(20)]: |
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hit_filter = SuggestionFilter(subjects, limit, threshold) |
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batch = annif.eval.EvaluationBatch(subjects) |
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filter_batches[(limit, threshold)] = (hit_filter, batch) |
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return filter_batches |
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NatLibFi /
Annif
