annif.corpus.subject.SubjectSet.as_vector() - Code Metrics - Inspection of "Refactor SubjectSet to store subject IDs instead o..." - NatLibFi/Annif - Measure and Improve Code Quality continuously with Scrutinizer

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Pull Request — master (#606)

by Osma

created 2022-08-12 08:32 UTC

annif.corpus.subject.SubjectSet.as_vector() A

↳ Parent: annif.corpus.subject

Complexity

Conditions

Size

Total Lines	11
Code Lines	5

Duplication

Lines	11
Ratio	100 %

Importance

Changes

Metric	Value
cc	2
eloc	5
nop	3
dl	11
loc	11
rs	10
c	0
b	0
f	0

"""Classes for supporting subject corpora expressed as directories or files"""

import annif.util
import numpy as np
from annif import logger
from .types import Subject
from .skos import serialize_subjects_to_skos


class SubjectFileTSV:

    """A subject vocabulary stored in a TSV file."""

    def __init__(self, path):
        self.path = path

    def _parse_line(self, line):
        vals = line.strip().split('\t', 2)
        clean_uri = annif.util.cleanup_uri(vals[0])
        label = vals[1] if len(vals) >= 2 else None
        notation = vals[2] if len(vals) >= 3 else None
        yield Subject(uri=clean_uri, label=label, notation=notation)

    @property
    def languages(self):
        # we don't have information about the language(s) of labels
        return None

    def subjects(self, language):
        with open(self.path, encoding='utf-8-sig') as subjfile:
            for line in subjfile:
                yield from self._parse_line(line)

    def save_skos(self, path, language):
        """Save the contents of the subject vocabulary into a SKOS/Turtle
        file with the given path name."""
        serialize_subjects_to_skos(self.subjects(language), language, path)


class SubjectIndex:

    """An index that remembers the associations between integers subject IDs
    and their URIs and labels."""

    def __init__(self):
        self._uris = []
        self._labels = []
        self._notations = []
        self._uri_idx = {}
        self._label_idx = {}

    def load_subjects(self, corpus, language):
        """Initialize the subject index from a subject corpus using labels
        in the given language."""

        for subject_id, subject in enumerate(corpus.subjects(language)):
            self._append(subject_id, subject)

    def __len__(self):
        return len(self._uris)

    def __getitem__(self, subject_id):
        return Subject(uri=self._uris[subject_id],
                       label=self._labels[subject_id],
                       notation=self._notations[subject_id])

    def _append(self, subject_id, subject):
        self._uris.append(subject.uri)
        self._labels.append(subject.label)
        self._notations.append(subject.notation)
        self._uri_idx[subject.uri] = subject_id
        self._label_idx[subject.label] = subject_id

    def append(self, subject):
        subject_id = len(self._uris)
        self._append(subject_id, subject)

    def contains_uri(self, uri):
        return uri in self._uri_idx

    def by_uri(self, uri, warnings=True):
        """return the subject index of a subject by its URI, or None if not found.
        If warnings=True, log a warning message if the URI cannot be found."""
        try:
            return self._uri_idx[uri]
        except KeyError:
            if warnings:
                logger.warning('Unknown subject URI <%s>', uri)
            return None

    def by_label(self, label):
        """return the subject index of a subject by its label"""
        try:
            return self._label_idx[label]
        except KeyError:
            logger.warning('Unknown subject label "%s"', label)
            return None

    def deprecated_ids(self):
        """return indices of deprecated subjects"""

        return [subject_id for subject_id, label in enumerate(self._labels)
                if label is None]

    @property
    def active(self):
        """return a list of (subject_id, uri, label, notation) tuples of all
        subjects that are not deprecated"""

        return [(subj_id, uri, label, notation)
                for subj_id, (uri, label, notation)
                in enumerate(zip(self._uris, self._labels, self._notations))
                if label is not None]

    def save(self, path):
        """Save this subject index into a file."""

        with open(path, 'w', encoding='utf-8') as subjfile:
            for uri, label, notation in self:
                line = "<{}>".format(uri)
                if label is not None:
                    line += ('\t' + label)
                    if notation is not None:
                        line += ('\t' + notation)
                print(line, file=subjfile)

    @classmethod
    def load(cls, path):
        """Load a subject index from a TSV file and return it."""

        corpus = SubjectFileTSV(path)
        subject_index = cls()
        subject_index.load_subjects(corpus, None)
        return subject_index


class SubjectSet:

    """Represents a set of subjects for a document."""

    def __init__(self, subject_ids=None):
        """Create a SubjectSet and optionally initialize it from an iterable
        of subject IDs"""

        if subject_ids:
            # use set comprehension to eliminate possible duplicates
            self._subject_ids = list({subject_id
                                      for subject_id in subject_ids
                                      if subject_id is not None})
        else:
            self._subject_ids = []

    def __len__(self):
        return len(self._subject_ids)

    def __getitem__(self, idx):
        return self._subject_ids[idx]

    def __bool__(self):
        return bool(self._subject_ids)

    def __eq__(self, other):
        if isinstance(other, SubjectSet):
            return self._subject_ids == other._subject_ids

        return False

    @classmethod
    def from_string(cls, subj_data, subject_index):
        subject_ids = set()
        for line in subj_data.splitlines():
            uri, label = cls._parse_line(line)
            if uri is not None:
                subject_ids.add(subject_index.by_uri(uri))
            else:
                subject_ids.add(subject_index.by_label(label))
        return cls(subject_ids)

    @staticmethod
    def _parse_line(line):
        uri = label = None
        vals = line.split("\t")
        for val in vals:
            val = val.strip()
            if val == '':
                continue
            if val.startswith('<') and val.endswith('>'):  # URI
                uri = val[1:-1]
                continue
            label = val
            break
        return uri, label

    def as_vector(self, size=None, destination=None):
        """Return the hits as a one-dimensional NumPy array in sklearn
           multilabel indicator format. Use destination array if given (not
           None), otherwise create and return a new one of the given size."""

        if destination is None:
            destination = np.zeros(size, dtype=bool)

        destination[list(self._subject_ids)] = True

        return destination


1		"""Classes for supporting subject corpora expressed as directories or files"""
2
3		import annif.util
4		import numpy as np
5		from annif import logger
6		from .types import Subject
7		from .skos import serialize_subjects_to_skos
8
9
10	View Code Duplication	class SubjectFileTSV:
		0 ignored issues – show Duplication introduced 2022-01-18 08:57 UTC by Report Bug Copy Issue Report This code seems to be duplicated in your project. Loading history...
11		"""A subject vocabulary stored in a TSV file."""
12
13		def __init__(self, path):
14		self.path = path
15
16		def _parse_line(self, line):
17		vals = line.strip().split('\t', 2)
18		clean_uri = annif.util.cleanup_uri(vals[0])
19		label = vals[1] if len(vals) >= 2 else None
20		notation = vals[2] if len(vals) >= 3 else None
21		yield Subject(uri=clean_uri, label=label, notation=notation)
22
23		@property
24		def languages(self):
25		# we don't have information about the language(s) of labels
26		return None
27
28		def subjects(self, language):
29		with open(self.path, encoding='utf-8-sig') as subjfile:
30		for line in subjfile:
31		yield from self._parse_line(line)
32
33		def save_skos(self, path, language):
34		"""Save the contents of the subject vocabulary into a SKOS/Turtle
35		file with the given path name."""
36		serialize_subjects_to_skos(self.subjects(language), language, path)
37
38
39	View Code Duplication	class SubjectIndex:
		0 ignored issues – show Duplication introduced 2022-01-18 08:57 UTC by Report Bug Copy Issue Report This code seems to be duplicated in your project. Loading history...
40		"""An index that remembers the associations between integers subject IDs
41		and their URIs and labels."""
42
43		def __init__(self):
44		self._uris = []
45		self._labels = []
46		self._notations = []
47		self._uri_idx = {}
48		self._label_idx = {}
49
50		def load_subjects(self, corpus, language):
51		"""Initialize the subject index from a subject corpus using labels
52		in the given language."""
53
54		for subject_id, subject in enumerate(corpus.subjects(language)):
55		self._append(subject_id, subject)
56
57		def __len__(self):
58		return len(self._uris)
59
60		def __getitem__(self, subject_id):
61		return Subject(uri=self._uris[subject_id],
62		label=self._labels[subject_id],
63		notation=self._notations[subject_id])
64
65		def _append(self, subject_id, subject):
66		self._uris.append(subject.uri)
67		self._labels.append(subject.label)
68		self._notations.append(subject.notation)
69		self._uri_idx[subject.uri] = subject_id
70		self._label_idx[subject.label] = subject_id
71
72		def append(self, subject):
73		subject_id = len(self._uris)
74		self._append(subject_id, subject)
75
76		def contains_uri(self, uri):
77		return uri in self._uri_idx
78
79		def by_uri(self, uri, warnings=True):
80		"""return the subject index of a subject by its URI, or None if not found.
81		If warnings=True, log a warning message if the URI cannot be found."""
82		try:
83		return self._uri_idx[uri]
84		except KeyError:
85		if warnings:
86		logger.warning('Unknown subject URI <%s>', uri)
87		return None
88
89		def by_label(self, label):
90		"""return the subject index of a subject by its label"""
91		try:
92		return self._label_idx[label]
93		except KeyError:
94		logger.warning('Unknown subject label "%s"', label)
95		return None
96
97		def deprecated_ids(self):
98		"""return indices of deprecated subjects"""
99
100		return [subject_id for subject_id, label in enumerate(self._labels)
101		if label is None]
102
103		@property
104		def active(self):
105		"""return a list of (subject_id, uri, label, notation) tuples of all
106		subjects that are not deprecated"""
107
108		return [(subj_id, uri, label, notation)
109		for subj_id, (uri, label, notation)
110		in enumerate(zip(self._uris, self._labels, self._notations))
111		if label is not None]
112
113		def save(self, path):
114		"""Save this subject index into a file."""
115
116		with open(path, 'w', encoding='utf-8') as subjfile:
117		for uri, label, notation in self:
118		line = "<{}>".format(uri)
119		if label is not None:
120		line += ('\t' + label)
121		if notation is not None:
122		line += ('\t' + notation)
123		print(line, file=subjfile)
124
125		@classmethod
126		def load(cls, path):
127		"""Load a subject index from a TSV file and return it."""
128
129		corpus = SubjectFileTSV(path)
130		subject_index = cls()
131		subject_index.load_subjects(corpus, None)
132		return subject_index
133
134
135	View Code Duplication	class SubjectSet:
		0 ignored issues – show Duplication introduced 2022-01-18 08:57 UTC by Report Bug Copy Issue Report This code seems to be duplicated in your project. Loading history...
136		"""Represents a set of subjects for a document."""
137
138		def __init__(self, subject_ids=None):
139		"""Create a SubjectSet and optionally initialize it from an iterable
140		of subject IDs"""
141
142		if subject_ids:
143		# use set comprehension to eliminate possible duplicates
144		self._subject_ids = list({subject_id
145		for subject_id in subject_ids
146		if subject_id is not None})
147		else:
148		self._subject_ids = []
149
150		def __len__(self):
151		return len(self._subject_ids)
152
153		def __getitem__(self, idx):
154		return self._subject_ids[idx]
155
156		def __bool__(self):
157		return bool(self._subject_ids)
158
159		def __eq__(self, other):
160		if isinstance(other, SubjectSet):
161		return self._subject_ids == other._subject_ids
162
163		return False
164
165		@classmethod
166		def from_string(cls, subj_data, subject_index):
167		subject_ids = set()
168		for line in subj_data.splitlines():
169		uri, label = cls._parse_line(line)
170		if uri is not None:
171		subject_ids.add(subject_index.by_uri(uri))
172		else:
173		subject_ids.add(subject_index.by_label(label))
174		return cls(subject_ids)
175
176		@staticmethod
177		def _parse_line(line):
178		uri = label = None
179		vals = line.split("\t")
180		for val in vals:
181		val = val.strip()
182		if val == '':
183		continue
184		if val.startswith('<') and val.endswith('>'): # URI
185		uri = val[1:-1]
186		continue
187		label = val
188		break
189		return uri, label
190
191		def as_vector(self, size=None, destination=None):
192		"""Return the hits as a one-dimensional NumPy array in sklearn
193		multilabel indicator format. Use destination array if given (not
194		None), otherwise create and return a new one of the given size."""
195
196		if destination is None:
197		destination = np.zeros(size, dtype=bool)
198
199		destination[list(self._subject_ids)] = True
200
201		return destination
202

NatLibFi / Annif

Pull Request — master (#606)

annif.corpus.subject.SubjectSet.as_vector() A

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