def test_reset_dir(monkeypatch):
"""Test resetting the data directory"""
monkeypatch.delenv("PPX_DATA_DIR")
ppx.set_data_dir()
assert ppx.get_data_dir() == Path(Path.home(), ".ppx")
ppx.PrideProject(PXID)
assert Path(Path.home(), ".ppx").exists()
def test_init(tmp_path):
"""Test initialization"""
proj = ppx.PrideProject(PXID)
url = "ftp://ftp.pride.ebi.ac.uk/pride-archive/2012/03/PXD000001"
assert proj.id == PXID
assert proj.url == url
assert proj.local == tmp_path / "PXD000001"
assert not proj.fetch
with pytest.raises(ValueError):
ppx.PrideProject("PXD;MaLiCiOuScOdE!")
with pytest.raises(ValueError):
ppx.PrideProject("MSV000001")
with pytest.raises(ValueError):
ppx.PrideProject("PXD1")
proj = ppx.PrideProject(PXID, local=tmp_path / "test")
assert proj.local == tmp_path / "test"
proj = ppx.PrideProject(PXID, fetch=True)
assert proj.fetch
proj = ppx.PrideProject(PXID, timeout=5)
assert proj.timeout == 5
proj.timeout = 10
assert proj.timeout == 10
def test_env(monkeypatch, tmp_path):
"""Test that the environment variable works"""
data_dir = tmp_path / "envpath"
data_dir.mkdir()
monkeypatch.setenv("PPX_DATA_DIR", str(data_dir))
ppx.set_data_dir()
proj = ppx.PrideProject(PXID)
out_path = Path(data_dir, PXID)
assert proj.local == out_path
def test_no_internet(monkeypatch):
"""Test what happens when connection is blocked"""
proj = ppx.PrideProject(PXID, timeout=None)
remote_files = proj.remote_files()
fname = "F063721.dat-mztab.txt"
def retrbinary(*args, **kwargs):
raise OSError("Mock error")
monkeypatch.setattr(FTP, "retrbinary", retrbinary)
with pytest.raises(error_temp):
txt = proj.download(fname)
def test_local_files(local_files, tmp_path):
"""Test that finding local files works"""
proj = ppx.PrideProject(PXID, local=tmp_path)
res = proj.local_files(), proj.local_dirs()
assert res == local_files
res = proj.local_files("**/*.mzML")
assert res == [f for f in local_files[0] if str(f).endswith("mzML")]
res = proj.local_files("*.mzML")
assert res == [tmp_path / "test_file.mzML"]
res = proj.local_dirs("*0")
assert res == [tmp_path / "test_dir0"]
def test_change_dir(monkeypatch, tmp_path):
"""Test changing the data dir"""
test_dir = tmp_path / "test"
with pytest.raises(FileNotFoundError):
ppx.set_data_dir(test_dir)
test_dir.mkdir()
ppx.set_data_dir(test_dir)
assert ppx.get_data_dir() == test_dir
proj = ppx.PrideProject(PXID)
assert proj.local == test_dir / PXID
test_dir = tmp_path / "test2"
monkeypatch.setenv("PPX_DATA_DIR", str(test_dir))
with pytest.raises(FileNotFoundError):
ppx.set_data_dir()
test_dir.mkdir()
ppx.set_data_dir(test_dir)
assert ppx.get_data_dir() == test_dir
proj = ppx.PrideProject(PXID)
assert proj.local == test_dir / PXID
def test_cached_remote_dirs(tmp_path, mock_pride_project_response):
"""Test that caching remote directories works"""
cached = tmp_path / ".remote_dirs"
test_dirs = ["test1", "test2"]
with cached.open("w+") as ref:
ref.write("\n".join(test_dirs))
proj = ppx.PrideProject(PXID, local=tmp_path)
files = proj.remote_dirs()
assert files == test_dirs
proj.fetch = True
files = proj.remote_dirs()
assert files != test_dirs
def test_remote_files(mock_pride_project_response):
"""Test that listing remote files works"""
proj = ppx.PrideProject(PXID)
files = proj.remote_files()
true_files = [
"F063721.dat",
"F063721.dat-mztab.txt",
"PRIDE_Exp_Complete_Ac_22134.xml.gz",
"PRIDE_Exp_mzData_Ac_22134.xml.gz",
"PXD000001_mztab.txt",
"README.txt",
"TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzML",
"TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzXML",
"TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzXML",
"TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.raw",
"erwinia_carotovora.fasta",
"generated/PRIDE_Exp_Complete_Ac_22134.pride.mgf.gz",
"generated/PRIDE_Exp_Complete_Ac_22134.pride.mztab.gz",
]
assert files == true_files
gzipped = proj.remote_files("*.gz")
print(gzipped)
true_gzipped = [
"PRIDE_Exp_Complete_Ac_22134.xml.gz",
"PRIDE_Exp_mzData_Ac_22134.xml.gz",
"generated/PRIDE_Exp_Complete_Ac_22134.pride.mgf.gz",
"generated/PRIDE_Exp_Complete_Ac_22134.pride.mztab.gz",
]
assert gzipped == true_gzipped
ms_files = proj.remote_files("*60min_01*")
true_ms_files = [
"TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzML",
"TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzXML",
"TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzXML",
"TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.raw",
]
assert ms_files == true_ms_files
assert proj.remote_files("blah") == []
def test_metadata(mock_pride_project_response):
"""Test that getting the metadata works"""
proj = ppx.PrideProject(PXID)
assert not (proj.local / ".pride-metadata").exists()
meta = proj.metadata
assert (proj.local / ".pride-metadata").exists()
with Path("tests/data/pride_project_response.json").open() as ref:
true_meta = json.load(ref)
assert meta == true_meta
title = (
"TMT spikes - Using R and Bioconductor for proteomics data analysis")
assert proj.title == title
desc = (
"Expected reporter ion ratios: Erwinia peptides: 1:1:1:1:1:1 "
"Enolase spike (sp|P00924|ENO1_YEAST): 10:5:2.5:1:2.5:10 BSA spike "
"(sp|P02769|ALBU_BOVIN): 1:2.5:5:10:5:1 PhosB spike "
"(sp|P00489|PYGM_RABIT): 2:2:2:2:1:1 Cytochrome C spike "
"(sp|P62894|CYC_BOVIN): 1:1:1:1:1:2")
assert proj.description == desc
assert proj.sample_processing_protocol == "Not available"
data_prot = (
"Two extra files have been added post-publication:<br>"
'<a href="ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2012/03/'
"PXD000001/TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-"
'20141210.mzML" target="_top">TMT_Erwinia_1uLSike_Top10HCD_isol2_'
'45stepped_60min_01-20141210.mzML</a><br><a href="ftp://ftp.pride.'
"ebi.ac.uk/pride/data/archive/2012/03/PXD000001/TMT_Erwinia_1uLSike_"
'Top10HCD_isol2_45stepped_60min_01-20141210.mzXML" target="_top">'
"TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzXML"
"</a>")
assert proj.data_processing_protocol == data_prot
assert proj.doi == "10.6019/PXD000001"
def test_pride_download(tmp_path):
"""Test downloading data from PRIDE"""
proj = ppx.PrideProject(PXID)
files = proj.local_files()
assert files == []
fname = "F063721.dat-mztab.txt"
txt = proj.download(fname)
files = proj.local_files()
local_txt = tmp_path / PXID / fname
orig_sig = sig(local_txt)
assert txt == [local_txt]
assert files[0] == local_txt
txt = proj.download(fname) # should do nothing
assert orig_sig == sig(local_txt)
txt = proj.download(fname, force_=True)
new_size, new_mtime = sig(local_txt)
assert orig_sig[0] == new_size
assert orig_sig[1] != new_mtime
proj.timeout = 10
assert proj._parser_state is None
def test_remote_files(mock_pride_project_response):
"""Test that listing remote directories works"""
proj = ppx.PrideProject(PXID)
dirs = proj.remote_dirs()
assert dirs == ["generated"]
