Module manubot.cite.tests.test_doi
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import pytest
from manubot.cite.doi import (
expand_short_doi,
get_doi_csl_item,
get_doi_csl_item_datacite,
get_doi_csl_item_default,
get_doi_csl_item_zotero,
)
def test_expand_short_doi():
doi = expand_short_doi("10/b6vnmd")
assert doi == "10.1016/s0933-3657(96)00367-3"
def test_expand_short_doi_invalid():
with pytest.raises(ValueError, match="Handle not found. Double check short_doi"):
expand_short_doi("10/b6vnmdxxxxxx")
def test_expand_short_doi_not_short():
with pytest.raises(ValueError, match="shortDOIs start with `10/`"):
expand_short_doi("10.1016/S0933-3657(96)00367-3")
def test_get_doi_csl_item_default():
doi = "10.1101/142760"
csl_item = get_doi_csl_item_default(doi)
assert isinstance(csl_item, dict)
assert csl_item["publisher"] == "Cold Spring Harbor Laboratory"
def test_get_doi_csl_item_zotero():
"""
As of 2019-10-25, DOI Content Negotiation (i.e. crosscite) encodes the consortium
in author.name rather than author.literal. Zotero translation-server encodes
the consortium in author.family, which is better than nothing since it's a valid
CSL JSON field.
https://github.com/manubot/manubot/issues/158
"""
doi = "10.1038/ng.3834"
csl_item = get_doi_csl_item_zotero(doi)
assert isinstance(csl_item, dict)
# for an unknown reason, GTEx Consortium becomes the first author
# which differs from the publisher HTML and Crossref metadata ordering.
assert csl_item["author"][0]["family"] == "GTEx Consortium"
def test_get_doi_csl_item():
"""
Test URL is set with shortDOI when calling get_doi_csl_item.
"""
doi = "10.1101/142760"
csl_item = get_doi_csl_item(doi)
assert isinstance(csl_item, dict)
assert csl_item["URL"] == "https://doi.org/gbpvh5"
@pytest.mark.xfail(
reason="DataCite Content Negotiation decided to stop supporting Crossref DOIs. https://github.com/crosscite/content-negotiation/issues/104"
)
def test_get_doi_crosscite_with_consortium_author():
"""
Make sure the author "GTEx Consortium" is properly encoded
using the `author.literal` CSL JSON field.
References:
- <https://github.com/manubot/manubot/issues/158>
- <https://github.com/crosscite/content-negotiation/issues/92>
"""
doi = "10.1038/ng.3834"
csl_item = get_doi_csl_item_datacite(doi)
assert isinstance(csl_item, dict)
assert any(
author.get("literal") == "GTEx Consortium" for author in csl_item["author"]
)
Functions
test_expand_short_doi
def test_expand_short_doi(
)
View Source
def test_expand_short_doi():
doi = expand_short_doi("10/b6vnmd")
assert doi == "10.1016/s0933-3657(96)00367-3"
test_expand_short_doi_invalid
def test_expand_short_doi_invalid(
)
View Source
def test_expand_short_doi_invalid():
with pytest.raises(ValueError, match="Handle not found. Double check short_doi"):
expand_short_doi("10/b6vnmdxxxxxx")
test_expand_short_doi_not_short
def test_expand_short_doi_not_short(
)
View Source
def test_expand_short_doi_not_short():
with pytest.raises(ValueError, match="shortDOIs start with `10/`"):
expand_short_doi("10.1016/S0933-3657(96)00367-3")
test_get_doi_crosscite_with_consortium_author
def test_get_doi_crosscite_with_consortium_author(
)
Make sure the author "GTEx Consortium" is properly encoded
using the author.literal CSL JSON field.
References:
- https://github.com/manubot/manubot/issues/158
- https://github.com/crosscite/content-negotiation/issues/92
View Source
@pytest.mark.xfail(
reason="DataCite Content Negotiation decided to stop supporting Crossref DOIs. https://github.com/crosscite/content-negotiation/issues/104"
)
def test_get_doi_crosscite_with_consortium_author():
"""
Make sure the author "GTEx Consortium" is properly encoded
using the `author.literal` CSL JSON field.
References:
- <https://github.com/manubot/manubot/issues/158>
- <https://github.com/crosscite/content-negotiation/issues/92>
"""
doi = "10.1038/ng.3834"
csl_item = get_doi_csl_item_datacite(doi)
assert isinstance(csl_item, dict)
assert any(
author.get("literal") == "GTEx Consortium" for author in csl_item["author"]
)
test_get_doi_csl_item
def test_get_doi_csl_item(
)
Test URL is set with shortDOI when calling get_doi_csl_item.
View Source
def test_get_doi_csl_item():
"""
Test URL is set with shortDOI when calling get_doi_csl_item.
"""
doi = "10.1101/142760"
csl_item = get_doi_csl_item(doi)
assert isinstance(csl_item, dict)
assert csl_item["URL"] == "https://doi.org/gbpvh5"
test_get_doi_csl_item_default
def test_get_doi_csl_item_default(
)
View Source
def test_get_doi_csl_item_default():
doi = "10.1101/142760"
csl_item = get_doi_csl_item_default(doi)
assert isinstance(csl_item, dict)
assert csl_item["publisher"] == "Cold Spring Harbor Laboratory"
test_get_doi_csl_item_zotero
def test_get_doi_csl_item_zotero(
)
As of 2019-10-25, DOI Content Negotiation (i.e. crosscite) encodes the consortium
in author.name rather than author.literal. Zotero translation-server encodes the consortium in author.family, which is better than nothing since it's a valid CSL JSON field. https://github.com/manubot/manubot/issues/158
View Source
def test_get_doi_csl_item_zotero():
"""
As of 2019-10-25, DOI Content Negotiation (i.e. crosscite) encodes the consortium
in author.name rather than author.literal. Zotero translation-server encodes
the consortium in author.family, which is better than nothing since it's a valid
CSL JSON field.
https://github.com/manubot/manubot/issues/158
"""
doi = "10.1038/ng.3834"
csl_item = get_doi_csl_item_zotero(doi)
assert isinstance(csl_item, dict)
# for an unknown reason, GTEx Consortium becomes the first author
# which differs from the publisher HTML and Crossref metadata ordering.
assert csl_item["author"][0]["family"] == "GTEx Consortium"