def test_set_format_file():
"""Test set format with file path"""
i = Index()
assert i is not None
assert i.format == indexfile.default_format
i.set_format('test/data/format.json')
assert i.format
assert i.format != indexfile.default_format
def test_set_format_none():
"""Test set format with no argument"""
i = Index()
assert i is not None
assert i.format == indexfile.default_format
i.set_format()
assert i.format
assert i.format == indexfile.default_format
def test_lookup_simple_dataset():
i = Index()
i.insert(id='1', age=65, path='test.txt', type='txt')
selected = i.lookup(id='1')
assert selected.datasets == i.datasets
dataset = selected.datasets.get('1')
assert dataset is not None
assert dataset.id == '1'
assert dataset.age == 65
assert len(dataset) == 1
def test_open_empty():
"""Open empty index"""
i = Index()
assert i is not None
# Disable warning about:
# - missing pytest.raises
# - statement with no effect
# pylint: disable=E1101,W0104
with pytest.raises(AttributeError):
i.open()
def test_export_no_format_no_map():
"""Test export"""
i = Index()
#assert i is not None
i.insert(id="myId",
path="test/data/index.txt",
type="text",
view="TxtFile")
exp = i.export(map=None, export_type='tab', tags=['id'])
assert len(exp) == 1
assert exp[0] == 'myId'
def test_remove_fileinfo():
i = Index()
i.insert(id='1', age=65, path='test.txt', type='txt')
i.insert(id='1', path='test1.txt', type='txt')
i.insert(id='1', path='test1.jpg', type='jpeg')
assert len(i.datasets) == 1
dataset = i.datasets.get('1')
assert len(dataset) == 3
i.remove(type='jpeg')
print i.datasets.get('1')._files
assert len(i.datasets) == 1
assert len(i.datasets.get('1')) == 2
def test_add_file_external():
index = '''.\tage=-; cell=Neutrophils; dataType=RNA-Seq; dateSubmittedFirst=2012-10-17T09:49:23+0200; donorId=C000XW; ethnicity=NA; lab=MPIMG; labExpId=ERR180946; labProtocolId=C000XWB1; libProtocol=I_bc_pelib_858; localization="Primary Cell"; quality=phred; readStrand=MATE2_SENSE; readType=2x76D; rnaExtract=total; seqPlatform=ILLUMINA; seqRun=1; sex=Male; sraSampleAccession=ERS150362; sraStudyAccession=ERP001664; tissue="Cord blood";'''
i = Index()
i.set_format('test/data/tsv_format.json')
i.insert(**Index.parse_line(index, **i.format))
i.insert(
id="ERR180946",
path=
"/users/rg/epalumbo/projects/BluePrint/reads/20130805/data/ERR180946_1.fastq.gz",
view="FastqRd1",
type="fastq")
assert i.export(
map=None
)[0] == '''/users/rg/epalumbo/projects/BluePrint/reads/20130805/data/ERR180946_1.fastq.gz\tage=-; cell=Neutrophils; dataType=RNA-Seq; dateSubmittedFirst=2012-10-17T09:49:23+0200; donorId=C000XW; ethnicity=NA; lab=MPIMG; labExpId=ERR180946; labProtocolId=C000XWB1; libProtocol=I_bc_pelib_858; localization="Primary Cell"; quality=phred; readStrand=MATE2_SENSE; readType=2x76D; rnaExtract=total; seqPlatform=ILLUMINA; seqRun=1; sex=Male; sraSampleAccession=ERS150362; sraStudyAccession=ERP001664; tissue="Cord blood"; type=fastq; view=FastqRd1;'''
def test_insert():
"""Test insertion into the index"""
i = Index()
i.insert(id='1', age=65, path='test.txt', type='txt')
assert len(i.datasets) == 1
dataset = i.datasets.get('1')
assert dataset is not None
assert len(dataset) == 1
assert hasattr(dataset, 'id')
assert hasattr(dataset, 'age')
assert dataset.id == '1'
assert dataset.age == 65
assert dataset.dice('test.txt') is not None
assert len(dataset['test.txt']) == 1
assert hasattr(dataset['test.txt'], 'type')
assert dataset['test.txt'].type == 'txt'
def test_remove_file():
i = Index()
i.insert(id='1', age=65, path='test.txt', type='txt')
i.insert(id='1', path='test1.txt', type='txt')
assert len(i.datasets) == 1
dataset = i.datasets.get('1')
assert len(dataset) == 2
i.remove(path='test.txt')
assert len(i.datasets) == 1
assert len(i.datasets.get('1')) == 1
def test_lookup_full_index():
"""Test export"""
i = Index('test/data/index.txt')
assert i is not None
i.set_format('test/data/format.json')
i.open()
result = i.lookup(type='gtf')
assert result.export()[0][0] != '.'
def test_export_ol_no_map_tab_path():
"""Test export"""
i = Index('test/data/index_oneline.txt')
assert i is not None
i.set_format('test/data/format.json')
i.open()
exp = i.export(map=None, export_type='tab', tags=['path'])
assert exp[0] == 'aWL3.2/aWL3.2_4204_ACTGAT_transcript.gtf'
def test_lookup_more_types_index_id():
"""Test export"""
i = Index('test/data/index_gfs.txt')
assert i is not None
i.set_format('test/data/format.json')
i.open()
result = i.lookup(id='WWP.1')
assert result.export()[0][0] != '.'
def test_export_oneline():
"""Test export one known line"""
i = Index('test/data/index_oneline.txt')
assert i is not None
i.set_format('test/data/format.json')
i.open()
exp = i.export()
assert exp[
0] == '''aWL3.2/aWL3.2_4204_ACTGAT_transcript.gtf\tLIBRARY_ID=aWL3.2; RNA_quantity=100; barcode=AR025; cell=anterior; dataType=rnaSeq; developmental_point=L3; library_Bioanalyser="5.8 ng/uL (30 nM) 08/04/2013"; localization=cell; max_peak=297; n_sequences=37478754; organism=dmel; pool_ID=2; readStrand=MATE1_SENSE; readType=2x75D; replicate=2; rnaExtract=longPolyA; sequence=ACTGAT(A); tissue=wing; type=gtf; view=TranscriptFB554;'''
def test_lookup_multiple_or():
i = Index()
i.insert(id='1', age=65, path='test1.txt', type='txt')
i.insert(id='2', age=63, path='test2.txt', type='txt')
i.insert(id='3', age=70, path='test3.jpg', type='jpg')
i.insert(id='4', age=45, path='test4.pdf', type='pdf')
selected = i.lookup(type='txt', path='test3.jpg', or_query=True)
assert selected.datasets != i.datasets
assert len(selected.datasets) == 3
def test_export_oneline_no_map():
"""Test export one known line"""
i = Index('test/data/index_oneline.txt')
assert i is not None
i.set_format('test/data/format.json')
i.open()
exp = i.export(map=None)
assert exp[
0] == '''aWL3.2/aWL3.2_4204_ACTGAT_transcript.gtf\tadaptor=ACTGAT(A); age=L3; barcode=AR025; cell=anterior; dataType=rnaSeq; labExpId=aWL3.2; libBio="5.8 ng/uL (30 nM) 08/04/2013"; localization=cell; maxPeak=297; nReads=37478754; organism=dmel; poolId=2; readStrand=MATE1_SENSE; readType=2x75D; replicate=2; rnaExtract=longPolyA; rnaQuantity=100; tissue=wing; type=gtf; view=TranscriptFB554;'''
def test_export_ol_no_map_tab_all():
"""Test export"""
i = Index('test/data/index_oneline.txt')
assert i is not None
i.set_format('test/data/format.json')
i.open()
exp = i.export(map=None, export_type='tab')
assert exp[
0] == '''ACTGAT(A)\tL3\tAR025\tanterior\trnaSeq\taWL3.2\t"5.8 ng/uL (30 nM) 08/04/2013"\tcell\t297\t37478754\tdmel\taWL3.2/aWL3.2_4204_ACTGAT_transcript.gtf\t2\tMATE1_SENSE\t2x75D\t2\tlongPolyA\t100\twing\tgtf\tTranscriptFB554'''
def test_set_format_string():
"""Test set format with JSON string"""
form = '''{
"id": "labExpId",
"colsep": "\\t",
"fileinfo": [
"path",
"size",
"md5"
],
"kw_sep": " ",
"sep": "=",
"trail": ";"
}'''
i = Index()
assert i is not None
assert i.format == indexfile.default_format
i.set_format(form)
assert i.format
assert i.format != indexfile.default_format
def test_export_no_map():
"""Test export"""
i = Index('test/data/index.txt')
assert i is not None
i.set_format('test/data/format.json')
i.open()
exp = i.export(map=None)
assert len(exp) == 216
assert 'labExpId' in exp[0]
assert 'fileinfo' not in exp[0]
def test_lookup_more_types_index():
"""Test export"""
i = Index('test/data/index_one_gfs.txt')
assert i is not None
i.set_format('test/data/format.json')
i.open()
result = i.lookup(type='gtf')
assert result != None
assert result.datasets != {}
assert result.export()[0][0] != '.'
def test_export():
"""Test export"""
i = Index('test/data/index.txt')
assert i is not None
i.set_format('test/data/format.json')
i.open()
exp = i.export()
assert type(exp) == list
assert len(exp) == 216
assert 'LIBRARY_ID' in exp[0]
def test_load_existing():
"""Load existing index"""
i = Index('test/data/index.txt')
assert i is not None
i.set_format('test/data/format.json')
i.open()
assert len(i) == 36
def test_open_string():
"""Test open with string parameter"""
i = Index()
assert i is not None
i.set_format('test/data/format.json')
i.open('test/data/index.txt')
assert len(i) == 36
def test_export_ol_no_map_tab_all_header():
"""Test export"""
i = Index('test/data/index_oneline.txt')
assert i is not None
i.set_format('test/data/format.json')
i.open()
exp = i.export(map=None, export_type='tab', header=True)
assert exp[
0] == 'adaptor\tage\tbarcode\tcell\tdataType\tlabExpId\tlibBio\tlocalization\tmaxPeak\tnReads\torganism\tpath\tpoolId\treadStrand\treadType\treplicate\trnaExtract\trnaQuantity\ttissue\ttype\tview'
assert exp[
1] == '''ACTGAT(A)\tL3\tAR025\tanterior\trnaSeq\taWL3.2\t"5.8 ng/uL (30 nM) 08/04/2013"\tcell\t297\t37478754\tdmel\taWL3.2/aWL3.2_4204_ACTGAT_transcript.gtf\t2\tMATE1_SENSE\t2x75D\t2\tlongPolyA\t100\twing\tgtf\tTranscriptFB554'''
def test_lookup_no_path():
i = Index('test/data/index.txt')
i.set_format('test/data/format.json')
i.open()
assert i.datasets.get('WLP.2') is not None
selected = i.lookup(id='WLP.2')
assert selected.datasets != i.datasets
assert len(selected.datasets) == 1
dataset = selected.datasets.get('WLP.2')
assert dataset is not None
dataset.id = 'WLP.2'
def test_export_ol_no_map_tab_repeated_tags_header():
"""Test export"""
i = Index('test/data/index_oneline.txt')
assert i is not None
i.set_format('test/data/format.json')
i.open()
exp = i.export(map=None,
export_type='tab',
tags=['id', 'id', 'path'],
header=True)
assert exp[0] == 'labExpId\tlabExpId\tpath'
assert exp[1] == 'aWL3.2\taWL3.2\taWL3.2/aWL3.2_4204_ACTGAT_transcript.gtf'
def test_lookup_path():
i = Index()
i.insert(id='1', age=65, path='test1.txt', type='txt')
i.insert(id='2', age=63, path='test2.txt', type='txt')
i.insert(id='3', age=70, path='test3.jpg', type='jpg')
selected = i.lookup(path='test3.jpg')
assert selected.datasets != i.datasets
dataset = selected.datasets.get('3')
assert dataset is not None
assert dataset.id == '3'
assert dataset.age == 70
assert len(dataset) == 1
def test_create_empty_w_format():
"""Create empty index with custom format"""
form = {
"id": "labExpId",
"colsep": "\t",
"fileinfo": ["path", "size", "md5"],
"kw_sep": " ",
"sep": "=",
"trail": ";"
}
i = Index(format=form)
assert i is not None
assert i.format != indexfile.default_format
assert len(i) == 0
def test_open_file():
"""Test open with file parameter"""
i = Index()
assert i is not None
i.set_format('test/data/format.json')
f = open('test/data/index.txt', 'r')
i.open(f)
f.close()
assert len(i) == 36
def test_export_no_map_tab_repeated_tags():
"""Test export tab output with repeated tags"""
i = Index('test/data/index.txt')
assert i is not None
i.set_format('test/data/format.json')
i.open()
exp = i.export(map=None,
export_type='tab',
tags=['id', 'id', 'path'],
hide_missing=True)
assert len(exp) == 200
assert exp[
0] == 'EL3.1\tEL3.1\t/users/rg/epalumbo/projects/ERC/fly/bp.pipeline/EL3.1/EL3.1_5355_ATCACG.minusRaw.bigwig'
def test_export_no_map_tab_path_template():
"""Test export tab output with path template"""
i = Index('test/data/index.txt')
assert i is not None
i.set_format('test/data/format.json')
i.open()
exp = i.export(map=None,
export_type='tab',
tags=['path', '{dirname}/{id}.{view}.{ext}'],
hide_missing=True)
assert len(exp) == 200
assert exp[
0] == '/users/rg/epalumbo/projects/ERC/fly/bp.pipeline/EL3.1/EL3.1_5355_ATCACG.minusRaw.bigwig\t/users/rg/epalumbo/projects/ERC/fly/bp.pipeline/EL3.1/EL3.1.MinusRawSignal.bigwig'
def open_index(config):
"""Open index file from config dictionary"""
i = Index()
index = config.get('index')
idx_format = config.get('format')
try:
i.set_format(idx_format)
i.open(index)
except csv.Error:
index = config.get('index')
i.open(index)
except AttributeError:
pass
return i