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Module manubot.cite.tests.test_citations

View Source 
import pathlib

import pytest

from manubot.cite.citations import Citations

def test_citations_filter_pandoc_xnos():

    input_ids = [

        "fig:pandoc-fignos-key",  # should filter

        "eq:pandoc-eqnos-key",  # should filter

        "tbl:pandoc-tablenos-key",  # should filter

        "sec:pandoc-secnos-key",  # should filter

        "not-pandoc-xnos-key",  # should keep

    ]

    citations = Citations(input_ids)

    citations.filter_pandoc_xnos()

    assert len(citations.citekeys) == 1

    assert citations.citekeys[0].input_id == "not-pandoc-xnos-key"

def test_citations_filter_unhandled():

    input_ids = [

        "citekey-with-no-prefix",

        "bad-prefix:citekey",

        ":empty-prefix",

        "doi:handled-prefix",

    ]

    citations = Citations(input_ids)

    citations.filter_unhandled()

    assert len(citations.citekeys) == 1

    assert citations.citekeys[0].input_id == "doi:handled-prefix"

def test_citations_check_collisions(caplog):

    input_ids = [

        "citekey-1",

        "citekey-1",

        "citekey-2",

        "Citekey-2",

    ]

    citations = Citations(input_ids)

    citations.check_collisions()

    assert not caplog.records

def test_citations_check_multiple_input_ids(caplog):

    input_ids = [

        "doi:10/b6vnmd",

        "DOI:10/B6VNMD",

        "doi:10.1016/s0933-3657(96)00367-3",

        "ugly-doi-alias",

        "other-citekey",

    ]

    citekey_aliases = {"ugly-doi-alias": "DOI:10.1016/s0933-3657(96)00367-3"}

    citations = Citations(input_ids, citekey_aliases)

    citations.check_multiple_input_ids()

    expected = "Multiple citekey input_ids refer to the same standard_id doi:10.1016/s0933-3657(96)00367-3:"

    "['doi:10/b6vnmd', 'DOI:10/B6VNMD', 'doi:10.1016/s0933-3657(96)00367-3', 'ugly-doi-alias']"

    assert expected in caplog.text

def test_citations_citekeys_tsv():

    input_ids = [

        "citekey-1",

        "arXiv:1806.05726v1",

        "DOI:10.7717/peerj.338",

        "pmid:29618526",

    ]

    citations = Citations(input_ids)

    citekeys_tsv = citations.citekeys_tsv

    assert isinstance(citekeys_tsv, str)

    assert "arxiv:1806.05726v1" in citekeys_tsv.splitlines()[2].split("\t")

def test_citations_inspect():

    input_ids = [

        "citekey-1",  # passes inspection

        "arXiv:1806.05726v1",  # passes inspection

        "arXiv:bad-id",

        "DOI:bad-id",

        "pmid:bad-id",

        "DOID:not-disease-ontology-id",

    ]

    citations = Citations(input_ids)

    report = citations.inspect(log_level="INFO")

    print(report)

    assert len(report.splitlines()) == 4

    assert "pmid:bad-id -- PubMed Identifiers should be 1-8 digits" in report

@pytest.mark.parametrize("csl_format", ["json", "yaml"])

def test_citations_csl_serialization(csl_format):

    ccr_dir = pathlib.Path(__file__).parent.joinpath("cite-command-rendered")

    citations = Citations(

        ["arxiv:1806.05726v1", "doi:10.7717/peerj.338", "pubmed:29618526"]

    )

    citations.load_manual_references(

        paths=[ccr_dir.joinpath("input-bibliography.json")]

    )

    citations.get_csl_items()

    path_out = ccr_dir.joinpath(f"output-bibliography.{csl_format}")

    # uncomment the following line to regenerate test output

    # citations.write_csl_items(path_out)

    csl_out = getattr(citations, f"csl_{csl_format}")

    assert csl_out == path_out.read_text()

Functions

test_citations_check_collisions

def test_citations_check_collisions(
    caplog
)
View Source 
def test_citations_check_collisions(caplog):

    input_ids = [

        "citekey-1",

        "citekey-1",

        "citekey-2",

        "Citekey-2",

    ]

    citations = Citations(input_ids)

    citations.check_collisions()

    assert not caplog.records

test_citations_check_multiple_input_ids

def test_citations_check_multiple_input_ids(
    caplog
)
View Source 
def test_citations_check_multiple_input_ids(caplog):

    input_ids = [

        "doi:10/b6vnmd",

        "DOI:10/B6VNMD",

        "doi:10.1016/s0933-3657(96)00367-3",

        "ugly-doi-alias",

        "other-citekey",

    ]

    citekey_aliases = {"ugly-doi-alias": "DOI:10.1016/s0933-3657(96)00367-3"}

    citations = Citations(input_ids, citekey_aliases)

    citations.check_multiple_input_ids()

    expected = "Multiple citekey input_ids refer to the same standard_id doi:10.1016/s0933-3657(96)00367-3:"

    "['doi:10/b6vnmd', 'DOI:10/B6VNMD', 'doi:10.1016/s0933-3657(96)00367-3', 'ugly-doi-alias']"

    assert expected in caplog.text

test_citations_citekeys_tsv

def test_citations_citekeys_tsv(

)
View Source 
def test_citations_citekeys_tsv():

    input_ids = [

        "citekey-1",

        "arXiv:1806.05726v1",

        "DOI:10.7717/peerj.338",

        "pmid:29618526",

    ]

    citations = Citations(input_ids)

    citekeys_tsv = citations.citekeys_tsv

    assert isinstance(citekeys_tsv, str)

    assert "arxiv:1806.05726v1" in citekeys_tsv.splitlines()[2].split("\t")

test_citations_csl_serialization

def test_citations_csl_serialization(
    csl_format
)
View Source 
@pytest.mark.parametrize("csl_format", ["json", "yaml"])

def test_citations_csl_serialization(csl_format):

    ccr_dir = pathlib.Path(__file__).parent.joinpath("cite-command-rendered")

    citations = Citations(

        ["arxiv:1806.05726v1", "doi:10.7717/peerj.338", "pubmed:29618526"]

    )

    citations.load_manual_references(

        paths=[ccr_dir.joinpath("input-bibliography.json")]

    )

    citations.get_csl_items()

    path_out = ccr_dir.joinpath(f"output-bibliography.{csl_format}")

    # uncomment the following line to regenerate test output

    # citations.write_csl_items(path_out)

    csl_out = getattr(citations, f"csl_{csl_format}")

    assert csl_out == path_out.read_text()

test_citations_filter_pandoc_xnos

def test_citations_filter_pandoc_xnos(

)
View Source 
def test_citations_filter_pandoc_xnos():

    input_ids = [

        "fig:pandoc-fignos-key",  # should filter

        "eq:pandoc-eqnos-key",  # should filter

        "tbl:pandoc-tablenos-key",  # should filter

        "sec:pandoc-secnos-key",  # should filter

        "not-pandoc-xnos-key",  # should keep

    ]

    citations = Citations(input_ids)

    citations.filter_pandoc_xnos()

    assert len(citations.citekeys) == 1

    assert citations.citekeys[0].input_id == "not-pandoc-xnos-key"

test_citations_filter_unhandled

def test_citations_filter_unhandled(

)
View Source 
def test_citations_filter_unhandled():

    input_ids = [

        "citekey-with-no-prefix",

        "bad-prefix:citekey",

        ":empty-prefix",

        "doi:handled-prefix",

    ]

    citations = Citations(input_ids)

    citations.filter_unhandled()

    assert len(citations.citekeys) == 1

    assert citations.citekeys[0].input_id == "doi:handled-prefix"

test_citations_inspect

def test_citations_inspect(

)
View Source 
def test_citations_inspect():

    input_ids = [

        "citekey-1",  # passes inspection

        "arXiv:1806.05726v1",  # passes inspection

        "arXiv:bad-id",

        "DOI:bad-id",

        "pmid:bad-id",

        "DOID:not-disease-ontology-id",

    ]

    citations = Citations(input_ids)

    report = citations.inspect(log_level="INFO")

    print(report)

    assert len(report.splitlines()) == 4

    assert "pmid:bad-id -- PubMed Identifiers should be 1-8 digits" in report