Module manubot.cite.tests.test_pubmed

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import pytest

from manubot.cite.pubmed import (

    get_pmcid_and_pmid_for_doi,

    get_pmid_for_doi,

    get_pubmed_ids_for_doi,

)

@pytest.mark.parametrize(

    ("doi", "pmid"),

    [

        ("10.1098/rsif.2017.0387", "29618526"),  # in PubMed and PMC

        ("10.1161/CIRCGENETICS.115.001181", "27094199"),  # in PubMed but not PMC

        ("10.7717/peerj-cs.134", None),  # DOI in journal not indexed by PubMed

        ("10.1161/CIRC", None),  # invalid DOI

    ],

)

def test_get_pmid_for_doi(doi, pmid):

    output = get_pmid_for_doi(doi)

    assert pmid == output

@pytest.mark.parametrize(

    ("doi", "id_dict"),

    [

        ("10.1098/rsif.2017.0387", {"PMCID": "PMC5938574", "PMID": "29618526"}),

        ("10.7554/ELIFE.32822", {"PMCID": "PMC5832410", "PMID": "29424689"}),

        ("10.1161/CIRCGENETICS.115.001181", {}),  # only in PubMed, not in PMC

        ("10.7717/peerj.000", {}),  # Non-existent DOI

        ("10.peerj.000", {}),  # malformed DOI

    ],

)

def test_get_pmcid_and_pmid_for_doi(doi, id_dict):

    output = get_pmcid_and_pmid_for_doi(doi)

    assert id_dict == output

@pytest.mark.parametrize(

    ("doi", "id_dict"),

    [

        ("10.1098/rsif.2017.0387", {"PMCID": "PMC5938574", "PMID": "29618526"}),

        ("10.7554/ELIFE.32822", {"PMCID": "PMC5832410", "PMID": "29424689"}),

        (

            "10.1161/CIRCGENETICS.115.001181",

            {"PMID": "27094199"},

        ),  # only in PubMed, not in PMC

        ("10.7717/peerj.000", {}),  # Non-existent DOI

    ],

)

def test_get_pubmed_ids_for_doi(doi, id_dict):

    output = get_pubmed_ids_for_doi(doi)

    assert id_dict == output

Functions

test_get_pmcid_and_pmid_for_doi

def test_get_pmcid_and_pmid_for_doi(
    doi,
    id_dict
)

View Source

@pytest.mark.parametrize(

    ("doi", "id_dict"),

    [

        ("10.1098/rsif.2017.0387", {"PMCID": "PMC5938574", "PMID": "29618526"}),

        ("10.7554/ELIFE.32822", {"PMCID": "PMC5832410", "PMID": "29424689"}),

        ("10.1161/CIRCGENETICS.115.001181", {}),  # only in PubMed, not in PMC

        ("10.7717/peerj.000", {}),  # Non-existent DOI

        ("10.peerj.000", {}),  # malformed DOI

    ],

)

def test_get_pmcid_and_pmid_for_doi(doi, id_dict):

    output = get_pmcid_and_pmid_for_doi(doi)

    assert id_dict == output

test_get_pmid_for_doi

def test_get_pmid_for_doi(
    doi,
    pmid
)

View Source

@pytest.mark.parametrize(

    ("doi", "pmid"),

    [

        ("10.1098/rsif.2017.0387", "29618526"),  # in PubMed and PMC

        ("10.1161/CIRCGENETICS.115.001181", "27094199"),  # in PubMed but not PMC

        ("10.7717/peerj-cs.134", None),  # DOI in journal not indexed by PubMed

        ("10.1161/CIRC", None),  # invalid DOI

    ],

)

def test_get_pmid_for_doi(doi, pmid):

    output = get_pmid_for_doi(doi)

    assert pmid == output

test_get_pubmed_ids_for_doi

def test_get_pubmed_ids_for_doi(
    doi,
    id_dict
)

View Source

@pytest.mark.parametrize(

    ("doi", "id_dict"),

    [

        ("10.1098/rsif.2017.0387", {"PMCID": "PMC5938574", "PMID": "29618526"}),

        ("10.7554/ELIFE.32822", {"PMCID": "PMC5832410", "PMID": "29424689"}),

        (

            "10.1161/CIRCGENETICS.115.001181",

            {"PMID": "27094199"},

        ),  # only in PubMed, not in PMC

        ("10.7717/peerj.000", {}),  # Non-existent DOI

    ],

)

def test_get_pubmed_ids_for_doi(doi, id_dict):

    output = get_pubmed_ids_for_doi(doi)

    assert id_dict == output