def test_number_of_calls(self):
# Test that genetic map citations are converted.
species = stdpopsim.get_species("HomSap")
genetic_map = species.get_genetic_map("HapMapII_GRCh37")
contig = species.get_contig("chr20", genetic_map=genetic_map.id)
model = stdpopsim.PiecewiseConstantSize(species.population_size)
engine = stdpopsim.get_default_engine()
local_cites = stdpopsim.Citation.merge(
[stdpopsim.citations._stdpopsim_citation]
+ genetic_map.citations
+ model.citations
+ engine.citations
+ species.genome.citations
+ species.citations
)
dois = set([ref.doi for ref in local_cites])
ncite = len(dois)
assert ncite == len(local_cites)
cli_cites = cli.get_citations(engine, model, contig, species)
assert len(cli_cites) == len(local_cites)
# Patch out writing to a file, then
# ensure that the method is called
# the correct number of times.
with mock.patch("builtins.open", mock.mock_open()):
with open("tmp.bib", "w") as bib:
with mock.patch.object(
stdpopsim.citations.Citation, "fetch_bibtex", autospec=True
) as mock_bib:
cli.write_bibtex(engine, model, contig, species, bib)
assert mock_bib.call_count == ncite
def test_number_of_calls(self):
# Test that genetic map citations are converted.
species = stdpopsim.get_species("HomSap")
genetic_map = species.get_genetic_map("HapMapII_GRCh37")
contig = species.get_contig("chr22", genetic_map=genetic_map.id)
model = stdpopsim.PiecewiseConstantSize(species.population_size)
engine = stdpopsim.get_default_engine()
cites_and_cites = [
genetic_map.citations,
model.citations,
engine.citations,
species.genome.mutation_rate_citations,
species.genome.recombination_rate_citations,
species.genome.assembly_citations,
]
ncite = len(set([ref.doi for cites in cites_and_cites for ref in cites]))
# Patch out writing to a file, then
# ensure that the method is called
# the correct number of times.
with mock.patch("builtins.open", mock.mock_open()):
with open('tmp.bib', 'w') as bib:
with mock.patch.object(
stdpopsim.citations.Citation,
"fetch_bibtex") as mock_bib:
cli.write_bibtex(engine, model, contig, species, bib)
self.assertEqual(mock_bib.call_count, ncite)
