annif.cli

Complexity

Total Complexity

64

Size/Duplication

Total Lines	656
Duplicated Lines	70.73 %

Importance

Changes

0

22 Functions

Rating	Name	Duplication	Size	Complexity
A	validate_backend_params()	0	6	2
A	backend_param_option()	0	6	1
A	open_documents()	26	26	5
A	set_project_config_file_path()	0	5	3
A	generate_filter_batches()	0	9	3
A	parse_backend_params()	10	10	2
A	get_vocab()	0	12	2
A	common_options()	0	9	1
A	get_project()	0	11	2
A	run_hyperopt()	39	41	2
A	run_loadvoc()	22	35	3
A	run_train()	29	36	3
B	run_optimize()	72	74	7
A	run_load_vocab()	27	27	4
A	run_suggest()	24	27	2
A	run_learn()	17	21	1
A	run_list_vocabs()	25	25	3
A	run_list_projects()	17	23	2
B	run_index()	45	46	7
A	run_clear_project()	0	9	1
C	run_eval()	94	100	7
A	run_show_project()	17	17	1

"""Definitions for command-line (Click) commands for invoking Annif
operations and printing the results to console."""


import collections
import os.path
import re
import sys
import json
import click
import click_log
from flask import current_app
from flask.cli import FlaskGroup, ScriptInfo
import annif
import annif.corpus
import annif.parallel
import annif.project
import annif.registry
from annif.project import Access
from annif.suggestion import SuggestionFilter, ListSuggestionResult
from annif.exception import ConfigurationException, NotSupportedException
from annif.exception import NotInitializedException
from annif.util import metric_code

logger = annif.logger
click_log.basic_config(logger)

cli = FlaskGroup(create_app=annif.create_app, add_version_option=False)
cli = click.version_option(message='%(version)s')(cli)


def get_project(project_id):
    """
    Helper function to get a project by ID and bail out if it doesn't exist"""
    try:
        return annif.registry.get_project(project_id,
                                          min_access=Access.private)
    except ValueError:
        click.echo(
            "No projects found with id \'{0}\'.".format(project_id),
            err=True)
        sys.exit(1)


def get_vocab(vocab_id):
    """
    Helper function to get a vocabulary by ID and bail out if it doesn't
    exist"""
    try:
        return annif.registry.get_vocab(vocab_id,
                                        min_access=Access.private)
    except ValueError:
        click.echo(
            f"No vocabularies found with the id '{vocab_id}'.",
            err=True)
        sys.exit(1)


def open_documents(paths, subject_index, vocab_lang, docs_limit):

This code seems to be duplicated in your project.

    """Helper function to open a document corpus from a list of pathnames,
    each of which is either a TSV file or a directory of TXT files. For
    directories with subjects in TSV files, the given vocabulary language
    will be used to convert subject labels into URIs. The corpus will be
    returned as an instance of DocumentCorpus or LimitingDocumentCorpus."""

    def open_doc_path(path, subject_index):
        """open a single path and return it as a DocumentCorpus"""
        if os.path.isdir(path):
            return annif.corpus.DocumentDirectory(path, subject_index,
                                                  vocab_lang,
                                                  require_subjects=True)
        return annif.corpus.DocumentFile(path, subject_index)

    if len(paths) == 0:
        logger.warning('Reading empty file')
        docs = open_doc_path(os.path.devnull, subject_index)
    elif len(paths) == 1:
        docs = open_doc_path(paths[0], subject_index)
    else:
        corpora = [open_doc_path(path, subject_index) for path in paths]
        docs = annif.corpus.CombinedCorpus(corpora)
    if docs_limit is not None:
        docs = annif.corpus.LimitingDocumentCorpus(docs, docs_limit)
    return docs


def parse_backend_params(backend_param, project):

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    """Parse a list of backend parameters given with the --backend-param
    option into a nested dict structure"""
    backend_params = collections.defaultdict(dict)
    for beparam in backend_param:
        backend, param = beparam.split('.', 1)
        key, val = param.split('=', 1)
        validate_backend_params(backend, beparam, project)
        backend_params[backend][key] = val
    return backend_params


def validate_backend_params(backend, beparam, project):
    if backend != project.config['backend']:
        raise ConfigurationException(
            'The backend {} in CLI option "-b {}" not matching the project'
            ' backend {}.'
            .format(backend, beparam, project.config['backend']))


BATCH_MAX_LIMIT = 15


def generate_filter_batches(subjects):
    import annif.eval
    filter_batches = collections.OrderedDict()
    for limit in range(1, BATCH_MAX_LIMIT + 1):
        for threshold in [i * 0.05 for i in range(20)]:
            hit_filter = SuggestionFilter(subjects, limit, threshold)
            batch = annif.eval.EvaluationBatch(subjects)
            filter_batches[(limit, threshold)] = (hit_filter, batch)
    return filter_batches


def set_project_config_file_path(ctx, param, value):
    """Override the default path or the path given in env by CLI option"""
    with ctx.ensure_object(ScriptInfo).load_app().app_context():
        if value:
            current_app.config['PROJECTS_CONFIG_PATH'] = value


def common_options(f):
    """Decorator to add common options for all CLI commands"""
    f = click.option(
        '-p', '--projects',
        help='Set path to project configuration file or directory',
        type=click.Path(dir_okay=True, exists=True),
        callback=set_project_config_file_path, expose_value=False,
        is_eager=True)(f)
    return click_log.simple_verbosity_option(logger)(f)


def backend_param_option(f):
    """Decorator to add an option for CLI commands to override BE parameters"""
    return click.option(
        '--backend-param', '-b', multiple=True,
        help='Override backend parameter of the config file. ' +
        'Syntax: `-b <backend>.<parameter>=<value>`.')(f)


@cli.command('list-projects')

This code seems to be duplicated in your project.

@common_options
@click_log.simple_verbosity_option(logger, default='ERROR')
def run_list_projects():
    """
    List available projects.
    \f
    Show a list of currently defined projects. Projects are defined in a
    configuration file, normally called ``projects.cfg``. See `Project
    configuration
    <https://github.com/NatLibFi/Annif/wiki/Project-configuration>`_
    for details.
    """

    template = "{0: <25}{1: <45}{2: <10}{3: <7}"
    header = template.format(
        "Project ID", "Project Name", "Language", "Trained")
    click.echo(header)
    click.echo("-" * len(header))
    for proj in annif.registry.get_projects(
            min_access=Access.private).values():
        click.echo(template.format(
            proj.project_id, proj.name, proj.language, str(proj.is_trained)))


@cli.command('show-project')

This code seems to be duplicated in your project.

@click.argument('project_id')
@common_options
def run_show_project(project_id):
    """
    Show information about a project.
    """

    proj = get_project(project_id)
    click.echo(f'Project ID:        {proj.project_id}')
    click.echo(f'Project Name:      {proj.name}')
    click.echo(f'Language:          {proj.language}')
    click.echo(f'Vocabulary:        {proj.vocab.vocab_id}')
    click.echo(f'Vocab language:    {proj.vocab_lang}')
    click.echo(f'Access:            {proj.access.name}')
    click.echo(f'Trained:           {proj.is_trained}')
    click.echo(f'Modification time: {proj.modification_time}')


@cli.command('clear')
@click.argument('project_id')
@common_options
def run_clear_project(project_id):
    """
    Initialize the project to its original, untrained state.
    """
    proj = get_project(project_id)
    proj.remove_model_data()


@cli.command('list-vocabs')

This code seems to be duplicated in your project.

@common_options
@click_log.simple_verbosity_option(logger, default='ERROR')
def run_list_vocabs():
    """
    List available vocabularies.
    """

    template = "{0: <20}{1: <20}{2: >10}  {3: <6}"
    header = template.format(
        "Vocabulary ID", "Languages", "Size", "Loaded")
    click.echo(header)
    click.echo("-" * len(header))
    for vocab in annif.registry.get_vocabs(
            min_access=Access.private).values():
        try:
            languages = ','.join(sorted(vocab.languages))
            size = len(vocab)
            loaded = True
        except NotInitializedException:
            languages = '-'
            size = '-'
            loaded = False
        click.echo(template.format(
            vocab.vocab_id, languages, size, str(loaded)))


@cli.command('loadvoc', deprecated=True)

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@click.argument('project_id')
@click.argument('subjectfile', type=click.Path(exists=True, dir_okay=False))
@click.option('--force', '-f', default=False, is_flag=True,
              help='Replace existing vocabulary completely ' +
                   'instead of updating it')
@common_options
def run_loadvoc(project_id, force, subjectfile):
    """
    Load a vocabulary for a project.
    \f
    This will load the vocabulary to be used in subject indexing. Note that
    although ``PROJECT_ID`` is a parameter of the command, the vocabulary is
    shared by all the projects with the same vocab identifier in the project
    configuration, and the vocabulary only needs to be loaded for one of those
    projects.

    If a vocabulary has already been loaded, reinvoking loadvoc with a new
    subject file will update the Annif’s internal vocabulary: label names are
    updated and any subject not appearing in the new subject file is removed.
    Note that new subjects will not be suggested before the project is
    retrained with the updated vocabulary. The update behavior can be
    overridden with the ``--force`` option.
    """
    proj = get_project(project_id)
    if annif.corpus.SubjectFileSKOS.is_rdf_file(subjectfile):
        # SKOS/RDF file supported by rdflib
        subjects = annif.corpus.SubjectFileSKOS(subjectfile)
    elif annif.corpus.SubjectFileCSV.is_csv_file(subjectfile):
        # CSV file
        subjects = annif.corpus.SubjectFileCSV(subjectfile)
    else:
        # probably a TSV file
        subjects = annif.corpus.SubjectFileTSV(subjectfile, proj.vocab_lang)
    proj.vocab.load_vocabulary(subjects, force=force)


@cli.command('load-vocab')

This code seems to be duplicated in your project.

@click.argument('vocab_id')
@click.argument('subjectfile', type=click.Path(exists=True, dir_okay=False))
@click.option('--language', '-L', help='Language of subject file')
@click.option('--force', '-f', default=False, is_flag=True,
              help='Replace existing vocabulary completely ' +
                   'instead of updating it')
@common_options
def run_load_vocab(vocab_id, language, force, subjectfile):
    """
    Load a vocabulary from a subject file.
    """
    vocab = get_vocab(vocab_id)
    if annif.corpus.SubjectFileSKOS.is_rdf_file(subjectfile):
        # SKOS/RDF file supported by rdflib
        subjects = annif.corpus.SubjectFileSKOS(subjectfile)
    elif annif.corpus.SubjectFileCSV.is_csv_file(subjectfile):
        # CSV file
        subjects = annif.corpus.SubjectFileCSV(subjectfile)
    else:
        # probably a TSV file - we need to know its language
        if not language:
            click.echo("Please use --language option to set the language of " +
                       "a TSV vocabulary.", err=True)
            sys.exit(1)
        subjects = annif.corpus.SubjectFileTSV(subjectfile, language)
    vocab.load_vocabulary(subjects, force=force)


@cli.command('train')

This code seems to be duplicated in your project.

@click.argument('project_id')
@click.argument('paths', type=click.Path(exists=True), nargs=-1)
@click.option('--cached/--no-cached', '-c/-C', default=False,
              help='Reuse preprocessed training data from previous run')
@click.option('--docs-limit', '-d', default=None,
              type=click.IntRange(0, None),
              help='Maximum number of documents to use')
@click.option('--jobs',
              '-j',
              default=0,
              help='Number of parallel jobs (0 means choose automatically)')
@backend_param_option
@common_options
def run_train(project_id, paths, cached, docs_limit, jobs, backend_param):
    """
    Train a project on a collection of documents.
    \f
    This will train the project using the documents from ``PATHS`` (directories
    or possibly gzipped TSV files) in a single batch operation. If ``--cached``
    is set, preprocessed training data from the previous run is reused instead
    of documents input; see `Reusing preprocessed training data
    <https://github.com/NatLibFi/Annif/wiki/
    Reusing-preprocessed-training-data>`_.
    """
    proj = get_project(project_id)
    backend_params = parse_backend_params(backend_param, proj)
    if cached:
        if len(paths) > 0:
            raise click.UsageError(
                "Corpus paths cannot be given when using --cached option.")
        documents = 'cached'
    else:
        documents = open_documents(paths, proj.subjects,
                                   proj.vocab_lang, docs_limit)
    proj.train(documents, backend_params, jobs)


@cli.command('learn')

This code seems to be duplicated in your project.

@click.argument('project_id')
@click.argument('paths', type=click.Path(exists=True), nargs=-1)
@click.option('--docs-limit', '-d', default=None,
              type=click.IntRange(0, None),
              help='Maximum number of documents to use')
@backend_param_option
@common_options
def run_learn(project_id, paths, docs_limit, backend_param):
    """
    Further train an existing project on a collection of documents.
    \f
    Similar to the ``train`` command. This will continue training an already
    trained project using the documents given by ``PATHS`` in a single batch
    operation. Not supported by all backends.
    """
    proj = get_project(project_id)
    backend_params = parse_backend_params(backend_param, proj)
    documents = open_documents(paths, proj.subjects,
                               proj.vocab_lang, docs_limit)
    proj.learn(documents, backend_params)


@cli.command('suggest')

This code seems to be duplicated in your project.

@click.argument('project_id')
@click.option('--limit', '-l', default=10, help='Maximum number of subjects')
@click.option('--threshold', '-t', default=0.0, help='Minimum score threshold')
@backend_param_option
@common_options
def run_suggest(project_id, limit, threshold, backend_param):
    """
    Suggest subjects for a single document from standard input.
    \f
    This will read a text document from standard input and suggest subjects for
    it.
    """
    project = get_project(project_id)
    text = sys.stdin.read()
    backend_params = parse_backend_params(backend_param, project)
    hit_filter = SuggestionFilter(project.subjects, limit, threshold)
    hits = hit_filter(project.suggest(text, backend_params))
    for hit in hits.as_list():
        subj = project.subjects[hit.subject_id]
        click.echo(
            "<{}>\t{}\t{}".format(
                subj.uri,
                '\t'.join(filter(None,
                                 (subj.labels[project.vocab_lang],
                                  subj.notation))),
                hit.score))


@cli.command('index')

This code seems to be duplicated in your project.

@click.argument('project_id')
@click.argument('directory', type=click.Path(exists=True, file_okay=False))
@click.option(
    '--suffix',
    '-s',
    default='.annif',
    help='File name suffix for result files')
@click.option('--force/--no-force', '-f/-F', default=False,
              help='Force overwriting of existing result files')
@click.option('--limit', '-l', default=10, help='Maximum number of subjects')
@click.option('--threshold', '-t', default=0.0, help='Minimum score threshold')
@backend_param_option
@common_options
def run_index(project_id, directory, suffix, force,
              limit, threshold, backend_param):
    """
    Index a directory with documents, suggesting subjects for each document.
    Write the results in TSV files with the given suffix (``.annif`` by
    default).
    """
    project = get_project(project_id)
    backend_params = parse_backend_params(backend_param, project)
    hit_filter = SuggestionFilter(project.subjects, limit, threshold)

    for docfilename, dummy_subjectfn in annif.corpus.DocumentDirectory(
            directory, project.subjects, project.vocab_lang,
            require_subjects=False):
        with open(docfilename, encoding='utf-8-sig') as docfile:
            text = docfile.read()
        subjectfilename = re.sub(r'\.txt$', suffix, docfilename)
        if os.path.exists(subjectfilename) and not force:
            click.echo(
                "Not overwriting {} (use --force to override)".format(
                    subjectfilename))
            continue
        with open(subjectfilename, 'w', encoding='utf-8') as subjfile:
            results = project.suggest(text, backend_params)
            for hit in hit_filter(results).as_list():
                subj = project.subjects[hit.subject_id]
                line = "<{}>\t{}\t{}".format(
                    subj.uri,
                    '\t'.join(filter(None, (subj.labels[project.vocab_lang],
                                            subj.notation))),
                    hit.score)
                click.echo(line, file=subjfile)


@cli.command('eval')

This code seems to be duplicated in your project.

@click.argument('project_id')
@click.argument('paths', type=click.Path(exists=True), nargs=-1)
@click.option('--limit', '-l', default=10, help='Maximum number of subjects')
@click.option('--threshold', '-t', default=0.0, help='Minimum score threshold')
@click.option('--docs-limit', '-d', default=None,
              type=click.IntRange(0, None),
              help='Maximum number of documents to use')
@click.option('--metric', '-m', default=[], multiple=True,
              help='Metric to calculate (default: all)')
@click.option(
    '--metrics-file',
    '-M',
    type=click.File(
        'w',
        encoding='utf-8',
        errors='ignore',
        lazy=True),
    help="""Specify file in order to write evaluation metrics in JSON format.
    File directory must exist, existing file will be overwritten.""")
@click.option(
    '--results-file',
    '-r',
    type=click.File(
        'w',
        encoding='utf-8',
        errors='ignore',
        lazy=True),
    help="""Specify file in order to write non-aggregated results per subject.
    File directory must exist, existing file will be overwritten.""")
@click.option('--jobs',
              '-j',
              default=1,
              help='Number of parallel jobs (0 means all CPUs)')
@backend_param_option
@common_options
def run_eval(
        project_id,
        paths,
        limit,
        threshold,
        docs_limit,
        metric,
        metrics_file,
        results_file,
        jobs,
        backend_param):
    """
    Suggest subjects for documents and evaluate the results by comparing
    against a gold standard.
    \f
    With this command the documents from ``PATHS`` (directories or possibly
    gzipped TSV files) will be assigned subject suggestions and then
    statistical measures are calculated that quantify how well the suggested
    subjects match the gold-standard subjects in the documents.

    Normally the output is the list of the metrics calculated across documents.
    If ``--results-file <FILENAME>`` option is given, the metrics are
    calculated separately for each subject, and written to the given file.
    """

    project = get_project(project_id)
    backend_params = parse_backend_params(backend_param, project)

    import annif.eval
    eval_batch = annif.eval.EvaluationBatch(project.subjects)

    if results_file:
        try:
            print('', end='', file=results_file)
            click.echo('Writing per subject evaluation results to {!s}'.format(
                results_file.name))
        except Exception as e:
            raise NotSupportedException(
                "cannot open results-file for writing: " + str(e))
    docs = open_documents(paths, project.subjects,
                          project.vocab_lang, docs_limit)

    jobs, pool_class = annif.parallel.get_pool(jobs)

    project.initialize(parallel=True)
    psmap = annif.parallel.ProjectSuggestMap(
        project.registry, [project_id], backend_params, limit, threshold)

    with pool_class(jobs) as pool:
        for hits, subject_set in pool.imap_unordered(
                psmap.suggest, docs.documents):
            eval_batch.evaluate(hits[project_id],
                                subject_set)

    template = "{0:<30}\t{1}"
    metrics = eval_batch.results(metrics=metric,
                                 results_file=results_file,
                                 language=project.vocab_lang)
    for metric, score in metrics.items():
        click.echo(template.format(metric + ":", score))
    if metrics_file:
        json.dump(
            {metric_code(mname): val for mname, val in metrics.items()},
            metrics_file, indent=2)


@cli.command('optimize')

This code seems to be duplicated in your project.

@click.argument('project_id')
@click.argument('paths', type=click.Path(exists=True), nargs=-1)
@click.option('--docs-limit', '-d', default=None,
              type=click.IntRange(0, None),
              help='Maximum number of documents to use')
@backend_param_option
@common_options
def run_optimize(project_id, paths, docs_limit, backend_param):
    """
    Suggest subjects for documents, testing multiple limits and thresholds.
    \f
    This command will use different limit (maximum number of subjects) and
    score threshold values when assigning subjects to each document given by
    ``PATHS`` and compare the results against the gold standard subjects in the
    documents. The output is a list of parameter combinations and their scores.
    From the output, you can determine the optimum limit and threshold
    parameters depending on which measure you want to target.
    """
    project = get_project(project_id)
    backend_params = parse_backend_params(backend_param, project)

    filter_batches = generate_filter_batches(project.subjects)

    ndocs = 0
    docs = open_documents(paths, project.subjects,
                          project.vocab_lang, docs_limit)
    for doc in docs.documents:
        raw_hits = project.suggest(doc.text, backend_params)
        hits = raw_hits.filter(project.subjects, limit=BATCH_MAX_LIMIT)
        assert isinstance(hits, ListSuggestionResult), \
            "Optimize should only be done with ListSuggestionResult " + \
            "as it would be very slow with VectorSuggestionResult."
        for hit_filter, batch in filter_batches.values():
            batch.evaluate(hit_filter(hits), doc.subject_set)
        ndocs += 1

    click.echo("\t".join(('Limit', 'Thresh.', 'Prec.', 'Rec.', 'F1')))

    best_scores = collections.defaultdict(float)
    best_params = {}

    template = "{:d}\t{:.02f}\t{:.04f}\t{:.04f}\t{:.04f}"
    # Store the batches in a list that gets consumed along the way
    # This way GC will have a chance to reclaim the memory
    filter_batches = list(filter_batches.items())
    while filter_batches:
        params, filter_batch = filter_batches.pop(0)
        metrics = ['Precision (doc avg)',
                   'Recall (doc avg)',
                   'F1 score (doc avg)']
        results = filter_batch[1].results(metrics=metrics)
        for metric, score in results.items():
            if score >= best_scores[metric]:
                best_scores[metric] = score
                best_params[metric] = params
        click.echo(
            template.format(
                params[0],
                params[1],
                results['Precision (doc avg)'],
                results['Recall (doc avg)'],
                results['F1 score (doc avg)']))

    click.echo()
    template2 = "Best {:>19}: {:.04f}\tLimit: {:d}\tThreshold: {:.02f}"
    for metric in metrics:
        click.echo(
            template2.format(
                metric,
                best_scores[metric],
                best_params[metric][0],
                best_params[metric][1]))
    click.echo("Documents evaluated:\t{}".format(ndocs))


@cli.command('hyperopt')

This code seems to be duplicated in your project.

@click.argument('project_id')
@click.argument('paths', type=click.Path(exists=True), nargs=-1)
@click.option('--docs-limit', '-d', default=None,
              type=click.IntRange(0, None),
              help='Maximum number of documents to use')
@click.option('--trials', '-T', default=10, help='Number of trials')
@click.option('--jobs',
              '-j',
              default=1,
              help='Number of parallel runs (0 means all CPUs)')
@click.option('--metric', '-m', default='NDCG',
              help='Metric to optimize (default: NDCG)')
@click.option(
    '--results-file',
    '-r',
    type=click.File(
        'w',
        encoding='utf-8',
        errors='ignore',
        lazy=True),
    help="""Specify file path to write trial results as CSV.
    File directory must exist, existing file will be overwritten.""")
@common_options
def run_hyperopt(project_id, paths, docs_limit, trials, jobs, metric,
                 results_file):
    """
    Optimize the hyperparameters of a project using validation documents from
    ``PATHS``. Not supported by all backends. Output is a list of trial results
    and a report of the best performing parameters.
    """
    proj = get_project(project_id)
    documents = open_documents(paths, proj.subjects,
                               proj.vocab_lang, docs_limit)
    click.echo(f"Looking for optimal hyperparameters using {trials} trials")
    rec = proj.hyperopt(documents, trials, jobs, metric, results_file)
    click.echo(f"Got best {metric} score {rec.score:.4f} with:")
    click.echo("---")
    for line in rec.lines:
        click.echo(line)
    click.echo("---")


if __name__ == '__main__':
    cli()