annif.corpus.document.DocumentFileCSV._check_fields() - Code Metrics - Inspection of "WIP: Add JSON fulltext corpus format" - NatLibFi/Annif - Measure and Improve Code Quality continuously with Scrutinizer

Passed

Pull Request — main (#872)

by Osma

created 2025-08-13 13:24 UTC

DocumentFileCSV._check_fields() A

↳ Parent: annif.corpus.document

Complexity

Conditions

Size

Total Lines	3
Code Lines	3

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
cc	1
eloc	3
nop	2
dl	0
loc	3
rs	10
c	0
b	0
f	0

"""Clases for supporting document corpora"""

from __future__ import annotations

import csv
import glob
import gzip
import json
import os.path
import re
from itertools import islice
from typing import TYPE_CHECKING

import annif.util
from annif.exception import OperationFailedException

from .types import Document, DocumentCorpus, SubjectSet

if TYPE_CHECKING:
    from collections.abc import Iterator

    from annif.corpus.subject import SubjectIndex

logger = annif.logger


class DocumentDirectory(DocumentCorpus):
    """A directory of files as a full text document corpus"""

    def __init__(
        self,
        path: str,
        subject_index: SubjectIndex | None = None,
        language: str | None = None,
        require_subjects: bool = False,
    ) -> None:
        self.path = path
        self.subject_index = subject_index
        self.language = language
        self.require_subjects = require_subjects

    def __iter__(self) -> Iterator[str]:
        """Iterate through the directory, yielding file paths with corpus documents."""

        # txt files
        for filename in sorted(glob.glob(os.path.join(self.path, "*.txt"))):
            yield filename

        # json files
        for filename in sorted(glob.glob(os.path.join(self.path, "*.json"))):
            yield filename

    @staticmethod
    def _get_subject_filename(filename: str) -> str | None:
        tsvfilename = re.sub(r"\.txt$", ".tsv", filename)
        if os.path.exists(tsvfilename):
            return tsvfilename

        keyfilename = re.sub(r"\.txt$", ".key", filename)
        if os.path.exists(keyfilename):
            return keyfilename

        return None

    def _read_txt_file(self, filename: str) -> Document | None:
        with open(filename, errors="replace", encoding="utf-8-sig") as docfile:
            text = docfile.read()
        if not self.require_subjects:
            return Document(text=text, subject_set=None)

        subjfilename = self._get_subject_filename(filename)
        if subjfilename is None:
            # subjects required but not found, skipping this docfile
            return None

        with open(subjfilename, encoding="utf-8-sig") as subjfile:
            subjects = SubjectSet.from_string(
                subjfile.read(), self.subject_index, self.language
            )
        return Document(text=text, subject_set=subjects)

    def _read_json_file(self, filename: str) -> Document | None:
        with open(filename) as jsonfile:
            data = json.load(jsonfile)

        subjects = SubjectSet(
            [
                self.subject_index.by_uri(subj["uri"])
                for subj in data.get("subjects", [])
            ]
        )
        if self.require_subjects and not subjects:
            return None

        return Document(
            text=data.get("text", ""),
            metadata=data.get("metadata", {}),
            subject_set=subjects,
        )

    @property
    def documents(self) -> Iterator[Document]:
        for docfilename in self:
            if docfilename.endswith(".txt"):
                doc = self._read_txt_file(docfilename)
            else:
                doc = self._read_json_file(docfilename)

            if doc is not None:
                yield doc


class DocumentFileTSV(DocumentCorpus):
    """A TSV file as a corpus of documents with subjects"""

    def __init__(self, path: str, subject_index: SubjectIndex) -> None:
        self.path = path
        self.subject_index = subject_index

    @property
    def documents(self) -> Iterator[Document]:
        if self.path.endswith(".gz"):
            opener = gzip.open
        else:
            opener = open
        with opener(self.path, mode="rt", encoding="utf-8-sig") as tsvfile:
            for line in tsvfile:
                yield from self._parse_tsv_line(line)

    def _parse_tsv_line(self, line: str) -> Iterator[Document]:
        if "\t" in line:
            text, uris = line.split("\t", maxsplit=1)
            subject_ids = {
                self.subject_index.by_uri(annif.util.cleanup_uri(uri))
                for uri in uris.split()
            }
            yield Document(text=text, subject_set=SubjectSet(subject_ids))
        else:
            logger.warning('Skipping invalid line (missing tab): "%s"', line.rstrip())


class DocumentFileCSV(DocumentCorpus):
    """A CSV file as a corpus of documents with subjects"""

    def __init__(self, path: str, subject_index: SubjectIndex) -> None:
        self.path = path
        self.subject_index = subject_index

    @property
    def documents(self) -> Iterator[Document]:
        if self.path.endswith(".gz"):
            opener = gzip.open
        else:
            opener = open
        with opener(self.path, mode="rt", encoding="utf-8-sig") as csvfile:
            reader = csv.DictReader(csvfile)
            if not self._check_fields(reader):
                raise OperationFailedException(
                    f"Cannot parse CSV file {self.path}. "
                    + "The file must have a header row that defines at least "
                    + "the columns 'text' and 'subject_uris'."
                )
            for row in reader:
                yield from self._parse_row(row)

    def _parse_row(self, row: dict[str, str]) -> Iterator[Document]:
        subject_ids = {
            self.subject_index.by_uri(annif.util.cleanup_uri(uri))
            for uri in (row["subject_uris"] or "").strip().split()
        }
        metadata = {
            key: val for key, val in row.items() if key not in ("text", "subject_uris")
        }
        yield Document(
            text=(row["text"] or ""),
            subject_set=SubjectSet(subject_ids),
            metadata=metadata,
        )

    def _check_fields(self, reader: csv.DictReader) -> bool:
        fns = reader.fieldnames
        return fns is not None and "text" in fns and "subject_uris" in fns

    @staticmethod
    def is_csv_file(path: str) -> bool:
        """return True if the path looks like a CSV file"""

        path_lc = path.lower()
        return path_lc.endswith(".csv") or path_lc.endswith(".csv.gz")


class DocumentList(DocumentCorpus):
    """A document corpus based on a list of other iterable of Document
    objects"""

    def __init__(self, documents):
        self._documents = documents

    @property
    def documents(self):
        yield from self._documents


class TransformingDocumentCorpus(DocumentCorpus):
    """A document corpus that wraps another document corpus but transforms the
    documents using a given transform function"""

    def __init__(self, corpus, transform_fn):
        self._orig_corpus = corpus
        self._transform_fn = transform_fn

    @property
    def documents(self):
        for doc in self._orig_corpus.documents:
            yield self._transform_fn(doc)


class LimitingDocumentCorpus(DocumentCorpus):
    """A document corpus that wraps another document corpus but limits the
    number of documents to a given limit"""

    def __init__(self, corpus, docs_limit):
        self._orig_corpus = corpus
        self.docs_limit = docs_limit

    @property
    def documents(self):
        for doc in islice(self._orig_corpus.documents, self.docs_limit):
            yield doc


1			"""Clases for supporting document corpora"""
2
3			from __future__ import annotations
4
5			import csv
6			import glob
7			import gzip
8			import json
9			import os.path
10			import re
11			from itertools import islice
12			from typing import TYPE_CHECKING
13
14			import annif.util
15			from annif.exception import OperationFailedException
16
17			from .types import Document, DocumentCorpus, SubjectSet
18
19			if TYPE_CHECKING:
20			from collections.abc import Iterator
21
22			from annif.corpus.subject import SubjectIndex
23
24			logger = annif.logger
25
26
27			class DocumentDirectory(DocumentCorpus):
28			"""A directory of files as a full text document corpus"""
29
30			def __init__(
31			self,
32			path: str,
33			subject_index: SubjectIndex \| None = None,
34			language: str \| None = None,
35			require_subjects: bool = False,
36			) -> None:
37			self.path = path
38			self.subject_index = subject_index
39			self.language = language
40			self.require_subjects = require_subjects
41
42			def __iter__(self) -> Iterator[str]:
43			"""Iterate through the directory, yielding file paths with corpus documents."""
44
45			# txt files
46			for filename in sorted(glob.glob(os.path.join(self.path, "*.txt"))):
47			yield filename
48
49			# json files
50			for filename in sorted(glob.glob(os.path.join(self.path, "*.json"))):
51			yield filename
52
53			@staticmethod
54			def _get_subject_filename(filename: str) -> str \| None:
55			tsvfilename = re.sub(r"\.txt$", ".tsv", filename)
56			if os.path.exists(tsvfilename):
57			return tsvfilename
58
59			keyfilename = re.sub(r"\.txt$", ".key", filename)
60			if os.path.exists(keyfilename):
61			return keyfilename
62
63			return None
64
65			def _read_txt_file(self, filename: str) -> Document \| None:
66			with open(filename, errors="replace", encoding="utf-8-sig") as docfile:
67			text = docfile.read()
68			if not self.require_subjects:
69			return Document(text=text, subject_set=None)
70
71			subjfilename = self._get_subject_filename(filename)
72			if subjfilename is None:
73			# subjects required but not found, skipping this docfile
74			return None
75
76			with open(subjfilename, encoding="utf-8-sig") as subjfile:
77			subjects = SubjectSet.from_string(
78			subjfile.read(), self.subject_index, self.language
79			)
80			return Document(text=text, subject_set=subjects)
81
82			def _read_json_file(self, filename: str) -> Document \| None:
83			with open(filename) as jsonfile:
84			data = json.load(jsonfile)
85
86			subjects = SubjectSet(
87			[
88			self.subject_index.by_uri(subj["uri"])
89			for subj in data.get("subjects", [])
90			]
91			)
92			if self.require_subjects and not subjects:
93			return None
94
95			return Document(
96			text=data.get("text", ""),
97			metadata=data.get("metadata", {}),
98			subject_set=subjects,
99			)
100
101			@property
102			def documents(self) -> Iterator[Document]:
103			for docfilename in self:
104			if docfilename.endswith(".txt"):
105			doc = self._read_txt_file(docfilename)
106			else:
107			doc = self._read_json_file(docfilename)
108
109			if doc is not None:
110			yield doc
111
112
113			class DocumentFileTSV(DocumentCorpus):
114			"""A TSV file as a corpus of documents with subjects"""
115
116			def __init__(self, path: str, subject_index: SubjectIndex) -> None:
117			self.path = path
118			self.subject_index = subject_index
119
120			@property
121			def documents(self) -> Iterator[Document]:
122			if self.path.endswith(".gz"):
123			opener = gzip.open
124			else:
125			opener = open
126			with opener(self.path, mode="rt", encoding="utf-8-sig") as tsvfile:
127			for line in tsvfile:
128			yield from self._parse_tsv_line(line)
129
130			def _parse_tsv_line(self, line: str) -> Iterator[Document]:
131			if "\t" in line:
132			text, uris = line.split("\t", maxsplit=1)
133			subject_ids = {
134			self.subject_index.by_uri(annif.util.cleanup_uri(uri))
135			for uri in uris.split()
136			}
137			yield Document(text=text, subject_set=SubjectSet(subject_ids))
138			else:
139			logger.warning('Skipping invalid line (missing tab): "%s"', line.rstrip())
140
141
142			class DocumentFileCSV(DocumentCorpus):
143			"""A CSV file as a corpus of documents with subjects"""
144
145			def __init__(self, path: str, subject_index: SubjectIndex) -> None:
146			self.path = path
147			self.subject_index = subject_index
148
149			@property
150			def documents(self) -> Iterator[Document]:
151			if self.path.endswith(".gz"):
152			opener = gzip.open
153			else:
154			opener = open
155			with opener(self.path, mode="rt", encoding="utf-8-sig") as csvfile:
156			reader = csv.DictReader(csvfile)
157			if not self._check_fields(reader):
158			raise OperationFailedException(
159			f"Cannot parse CSV file {self.path}. "
160			+ "The file must have a header row that defines at least "
161			+ "the columns 'text' and 'subject_uris'."
162			)
163			for row in reader:
164			yield from self._parse_row(row)
165
166			def _parse_row(self, row: dict[str, str]) -> Iterator[Document]:
167			subject_ids = {
168			self.subject_index.by_uri(annif.util.cleanup_uri(uri))
169			for uri in (row["subject_uris"] or "").strip().split()
170			}
171			metadata = {
172			key: val for key, val in row.items() if key not in ("text", "subject_uris")
173			}
174			yield Document(
175			text=(row["text"] or ""),
176			subject_set=SubjectSet(subject_ids),
177			metadata=metadata,
178			)
179
180			def _check_fields(self, reader: csv.DictReader) -> bool:
181			fns = reader.fieldnames
182			return fns is not None and "text" in fns and "subject_uris" in fns
183
184			@staticmethod
185			def is_csv_file(path: str) -> bool:
186			"""return True if the path looks like a CSV file"""
187
188			path_lc = path.lower()
189			return path_lc.endswith(".csv") or path_lc.endswith(".csv.gz")
190
191
192			class DocumentList(DocumentCorpus):
193			"""A document corpus based on a list of other iterable of Document
194			objects"""
195
196			def __init__(self, documents):
197			self._documents = documents
198
199			@property
200			def documents(self):
201			yield from self._documents
202
203
204			class TransformingDocumentCorpus(DocumentCorpus):
205			"""A document corpus that wraps another document corpus but transforms the
206			documents using a given transform function"""
207
208			def __init__(self, corpus, transform_fn):
209			self._orig_corpus = corpus
210			self._transform_fn = transform_fn
211
212			@property
213			def documents(self):
214			for doc in self._orig_corpus.documents:
215			yield self._transform_fn(doc)
216
217
218			class LimitingDocumentCorpus(DocumentCorpus):
219			"""A document corpus that wraps another document corpus but limits the
220			number of documents to a given limit"""
221
222			def __init__(self, corpus, docs_limit):
223			self._orig_corpus = corpus
224			self.docs_limit = docs_limit
225
226			@property
227			def documents(self):
228			for doc in islice(self._orig_corpus.documents, self.docs_limit):
229			yield doc
230

NatLibFi / Annif

Pull Request — main (#872)

DocumentFileCSV._check_fields() A

Complexity

Size

Duplication

Importance

Duplication Side-by-Side

Filter issues like