def test_entry_set_month(
month: Tuple[int, str], expected: str, caplog: pytest.LogCaptureFixture
) -> None:
"""Test month setting.
Args:
month: a pair containing the month index and full name.
expected: the expected three-letter code of the month.
caplog: the built-in pytest fixture.
"""
entry = Entry("Cao_2019", EXAMPLE_ENTRY_DICT)
assert entry.data["month"] == "aug"
entry.month = month[0] # type: ignore
assert entry.data["month"] == expected
assert (
"cobib.database.entry",
20,
f"Converting field 'month' of entry 'Cao_2019' from '{month[0]}' to '{expected}'.",
) in caplog.record_tuples
entry.month = month[1]
assert entry.data["month"] == expected
assert (
"cobib.database.entry",
20,
f"Converting field 'month' of entry 'Cao_2019' from '{month[1]}' to '{expected}'.",
) in caplog.record_tuples
def assert_default_test_entry(entry: Entry) -> None:
"""Asserts that the passed entry is the default testing entry.
Args:
entry: the entry to assert.
"""
entry.escape_special_chars()
assert entry.label == "Grimsley_2019"
assert entry.data["doi"] == "10.1038/s41467-019-10988-2"
assert entry.data["url"] == [
"https://doi.org/10.1038%2Fs41467-019-10988-2"
]
assert entry.data["year"] == 2019
assert entry.data["month"] == "jul"
assert entry.data[
"publisher"] == "Springer Science and Business Media {LLC}"
assert entry.data["volume"] == 10
assert entry.data["number"] == 1
assert (
entry.data["author"] ==
"Harper R. Grimsley and Sophia E. Economou and Edwin Barnes and Nicholas J. Mayhall"
)
assert (
entry.data["title"] ==
"An adaptive variational algorithm for exact molecular simulations on a quantum computer"
)
assert entry.data["journal"] == "Nature Communications"
def test_save() -> None:
"""Test the `cobib.database.Entry.save` method."""
entry = Entry("Cao_2019", EXAMPLE_ENTRY_DICT)
entry_str = entry.save()
with open(EXAMPLE_YAML_FILE, "r", encoding="utf-8") as expected:
for line, truth in zip(entry_str.split("\n"), expected):
assert line == truth.strip("\n")
def test_search(query: str, context: int, ignore_case: bool, expected: List[List[str]]) -> None:
"""Test search method.
Args:
query: the string to search for.
context: the number of lines to provide as context for the search results.
ignore_case: whether to perform a case-insensitive search.
expected: the expected lines.
"""
entry = Entry(
"search_dummy",
{
"ENTRYTYPE": "article",
"abstract": "\n".join(
[
"search_query",
"something else",
"Search_Query",
"something else",
]
* 2
),
},
)
results = entry.search(query, context=context, ignore_case=ignore_case)
assert results == expected
def test_equality() -> None:
"""Test entry equality."""
entry_1 = Entry("Cao_2019", EXAMPLE_ENTRY_DICT)
entry_2 = Entry("Cao_2019", EXAMPLE_ENTRY_DICT)
# assert mutability of Entry
assert entry_1 is not entry_2
# assert equality of entries
assert entry_1 == entry_2
def test_match_with_wrong_key() -> None:
"""Asserts issue #1 is fixed.
When `cobib.database.Entry.matches` is called with a key in the filter which does not exist in
the entry, the key should be ignored and the function should return normally.
"""
entry = Entry("Cao_2019", EXAMPLE_ENTRY_DICT)
filter_ = {("tags", False): ["test"]}
assert entry.matches(filter_, or_=False)
def test_entry_matches(filter_: Dict[Tuple[str, bool], Any], or_: bool) -> None:
"""Test match filter.
Args:
filter_: a filter as explained be `cobib.database.Entry.matches`.
or_: whether to use logical `OR` rather than `AND` for filter combination.
"""
entry = Entry("Cao_2019", EXAMPLE_ENTRY_DICT)
# author must match
assert entry.matches(filter_, or_=or_)
def test_search_with_file() -> None:
"""Test the `cobib.database.Entry.search` method with associated file."""
entry = Entry("Cao_2019", EXAMPLE_ENTRY_DICT)
entry.file = EXAMPLE_YAML_FILE # type: ignore
results = entry.search("Chemical", context=0)
expected = [
[" journal = {Chemical Reviews},"],
[" publisher = {American Chemical Society ({ACS})},"],
["journal: Chemical Reviews"],
["publisher: American Chemical Society ({ACS})"],
]
for res, exp in zip(results, expected):
assert res == exp
def test_entry_set_url(caplog: pytest.LogCaptureFixture) -> None:
"""Test url setting.
Args:
caplog: the built-in pytest fixture.
"""
entry = Entry("Cao_2019", EXAMPLE_ENTRY_DICT)
entry.url = "https://dummy.org/, https://dummy.com/" # type: ignore
assert entry.url == ["https://dummy.org/", "https://dummy.com/"]
assert (
"cobib.database.entry",
20,
"Converted the field 'url' of entry 'Cao_2019' to a list. You can consider storing it as "
"such directly.",
) in caplog.record_tuples
def dump(self, entry: Entry) -> str:
# pdoc will inherit the docstring from the base class
# noqa: D102
Event.PreBibtexDump.fire(entry)
database = bibtexparser.bibdatabase.BibDatabase()
stringified_entry = entry.stringify()
stringified_entry["ID"] = stringified_entry.pop("label")
if "month" in stringified_entry.keys():
# convert month to bibtexexpression
stringified_entry[
"month"] = bibtexparser.bibtexexpression.BibDataStringExpression(
[
bibtexparser.bibdatabase.BibDataString(
database, stringified_entry["month"])
])
database.entries = [stringified_entry]
LOGGER.debug("Converting entry %s to BibTex format.", entry.label)
writer = bibtexparser.bwriter.BibTexWriter()
writer.common_strings = True
string: str = writer.write(database)
string = Event.PostBibtexDump.fire(string) or string
return string
def parse(self, string: str) -> Dict[str, Entry]:
# pdoc will inherit the docstring from the base class
# noqa: D102
string = Event.PreBibtexParse.fire(string) or string
bparser = bibtexparser.bparser.BibTexParser()
bparser.ignore_nonstandard_types = config.parsers.bibtex.ignore_non_standard_types
bparser.common_strings = True
bparser.interpolate_strings = False
try:
LOGGER.debug("Loading BibTex data from file: %s.", string)
with open(string, "r", encoding="utf-8") as file:
database = bibtexparser.load(file, parser=bparser)
except (OSError, FileNotFoundError):
LOGGER.debug("Loading BibTex string: %s.", string)
database = bibtexparser.loads(string, parser=bparser)
bib = OrderedDict()
for entry in database.entries:
if "month" in entry.keys() and isinstance(
entry["month"],
bibtexparser.bibtexexpression.BibDataStringExpression):
entry["month"] = entry["month"].expr[0].name
label = entry.pop("ID")
bib[label] = Entry(label, entry)
Event.PostBibtexParse.fire(bib)
return bib
def test_stringify() -> None:
"""Test the `cobib.database.Entry.stringify` method."""
entry = Entry(
"dummy",
{
"file": ["/tmp/a.txt", "/tmp/b.txt"],
"month": 8,
"tags": ["tag1", "tag2"],
},
)
expected = {
"label": "dummy",
"file": "/tmp/a.txt, /tmp/b.txt",
"month": "aug",
"tags": "tag1, tag2",
}
assert entry.stringify() == expected
def test_event_post_yaml_dump(self) -> None:
"""Tests the PostYAMLDump event."""
@Event.PostYAMLDump.subscribe
def hook(string: str) -> Optional[str]:
return "Hello world!"
assert Event.PostYAMLDump.validate()
entry = Entry("Cao_2019", self.EXAMPLE_ENTRY_DICT.copy())
entry_str = YAMLParser().dump(entry)
assert entry_str == "Hello world!"
def test_event_pre_yaml_dump(self) -> None:
"""Tests the PreYAMLDump event."""
@Event.PreYAMLDump.subscribe
def hook(entry: Entry) -> None:
entry.label = "Cao2019"
assert Event.PreYAMLDump.validate()
entry = Entry("Cao_2019", self.EXAMPLE_ENTRY_DICT.copy())
entry_str = YAMLParser().dump(entry)
assert cast(str, entry_str).split("\n")[1] == "Cao2019:"
def test_event_pre_bibtex_dump(self) -> None:
"""Tests the PreBibtexDump event."""
@Event.PreBibtexDump.subscribe
def hook(entry: Entry) -> None:
entry.label = "Cao2019"
assert Event.PreBibtexDump.validate()
entry = Entry("Cao_2019", self.EXAMPLE_ENTRY_DICT.copy())
entry_str = BibtexParser().dump(entry)
assert entry_str.split("\n")[0] == "@article{Cao2019,"
def test_entry_set_file(files: List[str], caplog: pytest.LogCaptureFixture) -> None:
"""Test file setting.
Args:
files: a list of paths to files.
caplog: the built-in pytest fixture.
"""
entry = Entry("Cao_2019", EXAMPLE_ENTRY_DICT)
entry.file = files[0] if len(files) == 1 else files # type: ignore
expected = [str(RelPath(file)) for file in files]
assert entry.file == expected
# check lint logging
if len(files) > 1:
entry.file = ", ".join(files) # type: ignore
assert entry.file == expected
assert (
"cobib.database.entry",
20,
"Converted the field 'file' of entry 'Cao_2019' to a list. You can consider storing it "
"as such directly.",
) in caplog.record_tuples
def assert_default_test_entry(entry: Entry) -> None:
"""Asserts that the passed entry is the default testing entry.
Args:
entry: the entry to assert.
"""
entry.escape_special_chars()
assert entry.label == "Cao2018"
assert entry.data["archivePrefix"] == "arXiv"
assert entry.data["arxivid"].startswith("1812.09976")
assert (
entry.data["author"] ==
"Yudong Cao and Jonathan Romero and Jonathan P. Olson and Matthias Degroote and "
+
"Peter D. Johnson and M{\\'a}ria Kieferov{\\'a} and Ian D. Kivlichan and Tim Menke "
+
"and Borja Peropadre and Nicolas P. D. Sawaya and Sukin Sim and Libor Veis and "
+ "Al{\\'a}n Aspuru-Guzik")
assert entry.data["doi"].startswith("10.1021/acs.chemrev.8b00803")
assert entry.data[
"title"] == "Quantum Chemistry in the Age of Quantum Computing"
assert entry.data["year"] == 2018
assert entry.data["_download"] == "http://arxiv.org/pdf/1812.09976v2"
def test_dump(self, caplog: pytest.LogCaptureFixture) -> None:
"""Test dumping.
Args:
caplog: the built-in pytest fixture.
"""
entry = Entry("dummy", {"ENTRYTYPE": "unpublished"})
ISBNParser().dump(entry)
assert (
"cobib.parsers.isbn",
logging.ERROR,
"Cannot dump an entry as an ISBN.",
) in caplog.record_tuples
def test_entry_set_tags(caplog: pytest.LogCaptureFixture) -> None:
"""Test tags setting.
Args:
caplog: the built-in pytest fixture.
"""
entry = Entry("Cao_2019", EXAMPLE_ENTRY_DICT)
assert entry.tags == []
# NB: tags must be a list
entry.tags = ["foo"]
assert entry.tags == ["foo"]
# list works as expected
entry.tags = ["foo", "bar"]
assert entry.tags == ["foo", "bar"]
# check lint logging
entry.tags = "foo, bar" # type: ignore
assert entry.tags == ["foo", "bar"]
assert (
"cobib.database.entry",
20,
"Converted the field 'tags' of entry 'Cao_2019' to a list. You can consider storing it as "
"such directly.",
) in caplog.record_tuples
def test_init_logging(caplog: pytest.LogCaptureFixture) -> None:
"""Test init logging for linting purposes.
Args:
caplog: the built-in pytest fixture.
"""
entry = Entry("dummy", {"ID": "dummy", "number": "1"})
assert entry.data["number"] == 1
assert (
"cobib.database.entry",
20,
"Converting field 'number' of entry 'dummy' to integer: 1.",
) in caplog.record_tuples
assert entry.label == "dummy"
assert "ID" not in entry.data
assert (
"cobib.database.entry",
20,
"The field 'ID' of entry 'dummy' is no longer required. It will be inferred from the entry "
"label.",
) in caplog.record_tuples
def parse(self, string: str) -> Dict[str, Entry]:
# pdoc will inherit the docstring from the base class
# noqa: D102
string = Event.PreArxivParse.fire(string) or string
try:
match = re.search(ARXIV_REGEX, string)
if match is None:
raise AssertionError
except AssertionError:
msg = f"'{string}' is not a valid arXiv ID."
LOGGER.warning(msg)
return OrderedDict()
arxiv_id = match.group(1)
LOGGER.info("Gathering BibTex data for arXiv ID: %s.", arxiv_id)
try:
page = requests.get(ARXIV_URL + arxiv_id, timeout=10)
except requests.exceptions.RequestException as err:
LOGGER.error("An Exception occurred while trying to query the arXiv ID: %s.", arxiv_id)
LOGGER.error(err)
return OrderedDict()
xml = BeautifulSoup(page.text, features="html.parser")
if xml.feed.entry.title.contents[0] == "Error":
msg = (
"The arXiv API returned the following error: " + xml.feed.entry.summary.contents[0]
)
LOGGER.warning(msg)
return OrderedDict()
label = ""
entry: Dict[str, Any] = {}
entry["archivePrefix"] = "arXiv"
for key in xml.feed.entry.findChildren(recursive=False):
if key.name == "arxiv:doi":
entry["doi"] = str(key.contents[0])
elif key.name == "id":
entry["arxivid"] = str(key.contents[0]).replace("http://arxiv.org/abs/", "")
entry["eprint"] = str(key.contents[0])
elif key.name == "arxiv:primary_category":
entry["primaryClass"] = str(key.attrs["term"])
elif key.name == "published":
# The year must also be stored as a string for compatibility reasons with
# bibtexparser. However, we perform a conversion to an integer first, to ensure that
# the year can actually be represented as such.
entry["year"] = int(key.contents[0].split("-")[0])
label += str(entry["year"])
elif key.name == "title":
entry["title"] = re.sub(r"\s+", " ", key.contents[0].strip().replace("\n", " "))
elif key.name == "author":
if "author" not in entry:
first = True
entry["author"] = ""
name = [n.contents[0] for n in key.findChildren()][0]
if first:
label = name.split()[-1] + label
first = False
entry["author"] += f"{name} and "
elif key.name == "summary":
entry["abstract"] = re.sub(r"\s+", " ", key.contents[0].strip().replace("\n", " "))
elif key.name == "link":
if key.attrs.get("title", None) == "doi":
entry["url"] = key.attrs["href"]
elif key.attrs.get("title", None) == "pdf":
entry["_download"] = key.attrs.get("href", "")
else:
LOGGER.warning("The key '%s' of this arXiv entry is not being processed!", key.name)
if "doi" in entry:
entry["ENTRYTYPE"] = "article"
else:
entry["ENTRYTYPE"] = "unpublished"
# strip last 'and' from author field
entry["author"] = entry["author"][:-5]
bib = OrderedDict()
bib[label] = Entry(label, entry)
Event.PostArxivParse.fire(bib)
return bib
def hook(new_entry: Entry) -> None:
new_entry.data["tags"] = "test"
from typing import Any, Callable, Generator, Tuple
import pytest
from cobib.config import LabelSuffix, config
from cobib.database import Database, Entry
from .. import get_resource
TMPDIR = Path(tempfile.gettempdir())
EXAMPLE_LITERATURE = get_resource("example_literature.yaml")
DUMMY_ENTRY = Entry(
"dummy",
{
"ENTRYTYPE": "misc",
"author": "D. Dummy",
"title": "Something dumb",
},
)
DUMMY_ENTRY_YAML = """---
dummy:
ENTRYTYPE: misc
author: D. Dummy
title: Something dumb
...
"""
@pytest.fixture(autouse=True)
def setup() -> Generator[Any, None, None]:
def execute(self, args: List[str], out: IO[Any] = sys.stdout) -> None:
"""Adds a new entry.
Depending on the `args`, if a keyword for one of the available `cobib.parsers` was used
together with a matching input, that parser will be used to create the new entry.
Otherwise, the command is only valid if the `--label` option was used to specify a new entry
label, in which case this command will trigger the `cobib.commands.edit.EditCommand` for a
manual entry addition.
Args:
args: a sequence of additional arguments used for the execution. The following values
are allowed for this command:
* `-l`, `--label`: the label to give to the new entry.
* `-u`, `--update`: updates an existing database entry if it already exists.
* `-f`, `--file`: one or multiple files to associate with this entry. This data
will be stored in the `cobib.database.Entry.file` property.
* `-p`, `--path`: the path to store the downloaded associated file in. This can
be used to overwrite the `config.utils.file_downloader.default_location`.
* `--skip-download`: skips the automatic download of an associated file.
* `--skip-existing`: skips entry if label exists instead of running label
disambiguation.
* in addition to the options above, a *mutually exclusive group* of keyword
arguments for all available `cobib.parsers` are registered at runtime. Please
check the output of `cobib add --help` for the exact list.
* any *positional* arguments (i.e. those, not preceded by a keyword) are
interpreted as tags and will be stored in the `cobib.database.Entry.tags`
property.
out: the output IO stream. This defaults to `sys.stdout`.
"""
LOGGER.debug("Starting Add command.")
parser = ArgumentParser(prog="add", description="Add subcommand parser.")
parser.add_argument("-l", "--label", type=str, help="the label for the new database entry")
parser.add_argument(
"-u",
"--update",
action="store_true",
help="update an entry if the label exists already",
)
file_action = "extend" if sys.version_info[1] >= 8 else "append"
parser.add_argument(
"-f",
"--file",
type=str,
nargs="+",
action=file_action,
help="files associated with this entry",
)
parser.add_argument("-p", "--path", type=str, help="the path for the associated file")
parser.add_argument(
"--skip-download",
action="store_true",
help="skip the automatic download of an associated file",
)
parser.add_argument(
"--skip-existing",
action="store_true",
help="skips entry addition if existent instead of using label disambiguation",
)
group_add = parser.add_mutually_exclusive_group()
avail_parsers = {
cls.name: cls for _, cls in inspect.getmembers(parsers) if inspect.isclass(cls)
}
for name in avail_parsers.keys():
try:
group_add.add_argument(
f"-{name[0]}", f"--{name}", type=str, help=f"{name} object identfier"
)
except argparse.ArgumentError:
try:
group_add.add_argument(f"--{name}", type=str, help=f"{name} object identfier")
except argparse.ArgumentError:
continue
parser.add_argument(
"tags",
nargs=argparse.REMAINDER,
help="A list of space-separated tags to associate with this entry."
"\nYou can use quotes to specify tags with spaces in them.",
)
if not args:
parser.print_usage(sys.stderr)
sys.exit(1)
try:
largs = parser.parse_args(args)
except argparse.ArgumentError as exc:
LOGGER.error(exc.message)
return
Event.PreAddCommand.fire(largs)
new_entries: Dict[str, Entry] = OrderedDict()
edit_entries = False
for name, cls in avail_parsers.items():
string = getattr(largs, name, None)
if string is None:
continue
LOGGER.debug("Adding entries from %s: '%s'.", name, string)
new_entries = cls().parse(string)
break
else:
if largs.label is not None:
LOGGER.warning("No input to parse. Creating new entry '%s' manually.", largs.label)
new_entries = {
largs.label: Entry(
largs.label,
{"ENTRYTYPE": config.commands.edit.default_entry_type},
)
}
edit_entries = True
else:
msg = "Neither an input to parse nor a label for manual creation specified!"
LOGGER.error(msg)
return
if largs.label is not None:
assert len(new_entries.values()) == 1
for value in new_entries.values():
# logging done by cobib/database/entry.py
value.label = largs.label
new_entries = OrderedDict((largs.label, value) for value in new_entries.values())
else:
formatted_entries = OrderedDict()
for label, value in new_entries.items():
formatted_label = evaluate_as_f_string(
config.database.format.label_default, {"label": label, **value.data.copy()}
)
value.label = formatted_label
formatted_entries[formatted_label] = value
new_entries = formatted_entries
if largs.file is not None:
if file_action == "append":
# We need to flatten the potentially nested list.
# pylint: disable=import-outside-toplevel
from itertools import chain
largs.file = list(chain.from_iterable(largs.file))
assert len(new_entries.values()) == 1
for value in new_entries.values():
# logging done by cobib/database/entry.py
value.file = largs.file
if largs.tags != []:
assert len(new_entries.values()) == 1
for value in new_entries.values():
# logging done by cobib/database/entry.py
value.tags = largs.tags
bib = Database()
existing_labels = set(bib.keys())
for lbl, entry in new_entries.copy().items():
# check if label already exists
if lbl in existing_labels:
if not largs.update:
msg = f"You tried to add a new entry '{lbl}' which already exists!"
LOGGER.warning(msg)
if edit_entries or largs.skip_existing:
msg = f"Please use `cobib edit {lbl}` instead!"
LOGGER.warning(msg)
continue
msg = (
"The label will be disambiguated based on the configuration option: "
"config.database.format.label_suffix"
)
LOGGER.warning(msg)
new_label = bib.disambiguate_label(lbl, entry)
entry.label = new_label
new_entries[new_label] = entry
new_entries.pop(lbl)
else:
# label exists but the user asked to update an existing entry
existing_data = bib[lbl].data.copy()
existing_data.update(entry.data)
entry.data = existing_data.copy()
# download associated file (if requested)
if "_download" in entry.data.keys():
if largs.skip_download:
entry.data.pop("_download")
else:
path = FileDownloader().download(
entry.data.pop("_download"), lbl, folder=largs.path, overwrite=largs.update
)
if path is not None:
entry.data["file"] = str(path)
# check journal abbreviation
if "journal" in entry.data.keys():
entry.data["journal"] = JournalAbbreviations.elongate(entry.data["journal"])
Event.PostAddCommand.fire(new_entries)
bib.update(new_entries)
if edit_entries:
EditCommand().execute([largs.label])
bib.save()
self.git(args=vars(largs))
for label in new_entries:
msg = f"'{label}' was added to the database."
LOGGER.info(msg)
def test_entry_set_label() -> None:
"""Test label changing."""
# this test may fail if the input dict is not copied
entry = Entry("Cao_2019", EXAMPLE_ENTRY_DICT)
entry.label = "Cao2019"
assert entry.label == "Cao2019"
def execute(self, args: List[str], out: IO[Any] = sys.stdout) -> None:
"""Opens an entry for manual editing.
This command opens an `cobib.database.Entry` in YAML format for manual editing.
The editor program can be configured via `config.commands.edit.editor`.
By default, this setting will respect your `$EDITOR` environment variable, but fall back to
using `vim` if that variable is not set.
Args:
args: a sequence of additional arguments used for the execution. The following values
are allowed for this command:
* `label`: the label of the entry to edit.
* `-a`, `--add`: if specified, allows adding new entries for non-existent
labels. The default entry type of this new entry can be configured via
`config.commands.edit.default_entry_type`.
out: the output IO stream. This defaults to `sys.stdout`.
"""
LOGGER.debug("Starting Edit command.")
parser = ArgumentParser(prog="edit",
description="Edit subcommand parser.")
parser.add_argument("label", type=str, help="label of the entry")
parser.add_argument(
"-a",
"--add",
action="store_true",
help="if specified, will add a new entry for unknown labels",
)
parser.add_argument("--preserve-files",
action="store_true",
help="do not rename associated files")
if not args:
parser.print_usage(sys.stderr)
sys.exit(1)
try:
largs = parser.parse_args(args)
except argparse.ArgumentError as exc:
LOGGER.error(exc.message)
return
Event.PreEditCommand.fire(largs)
yml = YAMLParser()
bib = Database()
try:
entry = bib[largs.label]
prv = yml.dump(entry)
if largs.add:
LOGGER.warning(
"Entry '%s' already exists! Ignoring the `--add` argument.",
largs.label)
largs.add = False
except KeyError:
# No entry for given label found
if largs.add:
# add a new entry for the unknown label
entry = Entry(
largs.label,
{"ENTRYTYPE": config.commands.edit.default_entry_type},
)
prv = yml.dump(entry)
else:
msg = (
f"No entry with the label '{largs.label}' could be found."
"\nUse `--add` to add a new entry with this label.")
LOGGER.error(msg)
return
if prv is None:
# No entry found to be edited. This should never occur unless the YAMLParser experiences
# an unexpected error.
return
LOGGER.debug("Creating temporary file.")
with tempfile.NamedTemporaryFile(mode="w+",
prefix="cobib-",
suffix=".yaml") as tmp_file:
tmp_file_name = tmp_file.name
tmp_file.write(prv)
tmp_file.flush()
LOGGER.debug('Starting editor "%s".', config.commands.edit.editor)
status = os.system(config.commands.edit.editor + " " +
tmp_file.name)
assert status == 0
LOGGER.debug("Editor finished successfully.")
new_entries = YAMLParser().parse(tmp_file.name)
new_entry = list(new_entries.values())[0]
assert not Path(tmp_file_name).exists()
if entry == new_entry and not largs.add:
LOGGER.info("No changes detected.")
return
bib.update({new_entry.label: new_entry})
if new_entry.label != largs.label:
bib.rename(largs.label, new_entry.label)
if not largs.preserve_files:
new_files = []
for file in new_entry.file:
path = RelPath(file)
if path.path.stem == largs.label:
LOGGER.info("Also renaming associated file '%s'.",
str(path))
target = RelPath(path.path.parent /
f"{new_entry.label}.pdf")
if target.path.exists():
LOGGER.warning(
"Found conflicting file, not renaming '%s'.",
str(path))
else:
path.path.rename(target.path)
new_files.append(str(target))
continue
new_files.append(file)
new_entry.file = new_files
Event.PostEditCommand.fire(new_entry)
bib.save()
self.git(args=vars(largs))
msg = f"'{largs.label}' was successfully edited."
LOGGER.info(msg)
def parse(self, string: str) -> Dict[str, Entry]:
# pdoc will inherit the docstring from the base class
# noqa: D102
string = Event.PreISBNParse.fire(string) or string
try:
match = re.search(ISBN_REGEX, string)
if match is None:
raise AssertionError
except AssertionError:
msg = f"'{string}' is not a valid ISBN."
LOGGER.warning(msg)
return OrderedDict()
isbn = match.group(1)
LOGGER.info("Gathering BibTex data for ISBN: %s.", isbn)
isbn_plain = "".join([i for i in isbn if i.isdigit()])
try:
page = requests.get(ISBN_URL + isbn_plain +
"&jscmd=data&format=json",
timeout=10)
except requests.exceptions.RequestException as err:
LOGGER.error(
"An Exception occurred while trying to query the ISBN: %s.",
isbn)
LOGGER.error(err)
return OrderedDict()
try:
contents = dict(json.loads(page.content))
except json.JSONDecodeError as err:
LOGGER.error(
"An Exception occurred while parsing the query results: %s.",
page.content)
LOGGER.error(err)
return OrderedDict()
if not contents:
msg = (
f'No data was found for ISBN "{isbn}". If you think this is an error and '
+
"the openlibrary API should provide an entry, please file a bug report. "
+
"Otherwise please try adding this entry manually until more APIs are "
+ "available in coBib.")
LOGGER.warning(msg)
return OrderedDict()
label = ""
entry = {}
for key, value in contents[list(contents.keys())[0]].items():
if key in ["title", "url"]:
entry[key] = value
elif key == "number_of_pages":
# we explicitly convert to a string to prevent type errors in the bibtexparser
str_val = str(value)
entry["pages"] = int(
str_val) if str_val.isnumeric() else str_val
elif key == "publish_date":
entry["date"] = value
try:
match = re.search(r"\d{4}", value)
if match is None:
raise AttributeError # pragma: no cover
entry["year"] = int(match.group())
label += str(entry["year"])
except AttributeError: # pragma: no cover
pass # pragma: no cover
elif key == "authors":
label = value[0]["name"].split()[-1] + label
entry["author"] = " and".join([a["name"] for a in value])
elif key == "publishers":
entry["publisher"] = " and".join([a["name"] for a in value])
# set entry-type do 'book'
entry["ENTRYTYPE"] = "book"
bib = OrderedDict()
bib[label] = Entry(label, entry)
Event.PostISBNParse.fire(bib)
return bib
def test_to_yaml(self) -> None:
"""Test to yaml conversion."""
entry = Entry("Cao_2019", self.EXAMPLE_ENTRY_DICT)
yaml_str = YAMLParser().dump(entry)
with open(self.EXAMPLE_YAML_FILE, "r", encoding="utf-8") as file:
assert yaml_str == file.read()
def hook(entry: Entry) -> None:
entry.label = "Cao2019"