def test_dbci002_inner_outer_radii(dash_duo):
app = dash.Dash(__name__)
app.layout = html.Div(simple_app_layout(
dash_bio.Circos(
id=_COMPONENT_ID,
layout=_data['GRCh37']
)
))
change_radii_config = {'innerRadius': 20, 'outerRadius': 100}
simple_app_callback(
app,
dash_duo,
component_id=_COMPONENT_ID,
test_prop_name='config',
test_prop_value=json.dumps(change_radii_config),
prop_value_type='dict',
validation_fn=lambda x:
x['innerRadius'] == change_radii_config['innerRadius']
and x['outerRadius'] == change_radii_config['outerRadius']
)
chr_one_div = dash_duo.find_element('path#chr1')
assert int(chr_one_div.size['width']) == 41
assert int(chr_one_div.size['height']) == 81
def test_dbsp006_custom_view(dash_duo):
app = dash.Dash(__name__)
app.layout = html.Div(
simple_app_layout(dash_bio.Speck(id=_COMPONENT_ID, data=_data)))
new_view = {
'ao': 0.1,
'outline': 1,
'dofStrength': 0.4,
'resolution': 600,
'atomScale': 0.15,
'relativeAtomScale': 0.51,
'bonds': True,
'bondScale': 0.75
}
simple_app_callback(
app,
dash_duo,
component_id=_COMPONENT_ID,
test_prop_name='view',
test_prop_value=json.dumps(new_view),
prop_value_type='dict',
validation_fn=lambda x: json.dumps(x) == json.dumps(new_view),
take_snapshot=True)
def test_dbci001_graph_type(dash_duo):
app = dash.Dash(__name__)
app.layout = html.Div(simple_app_layout(
dash_bio.Circos(
id=_COMPONENT_ID,
layout=_data['GRCh37'],
)
))
histogram_layout = [
{'type': 'HISTOGRAM', 'data': _data['histogram'][:5]}
]
simple_app_callback(
app,
dash_duo,
component_id=_COMPONENT_ID,
test_prop_name='tracks',
test_prop_value=json.dumps(histogram_layout),
prop_value_type='dict',
validation_fn=lambda x: json.dumps(x) == json.dumps(histogram_layout)
)
# there should be five bins in the histogram
assert len(dash_duo.find_elements('path.bin')) == 5
def test_dbm2003_select_atoms_via_callback(dash_duo):
app = dash.Dash(__name__)
app.layout = html.Div(
simple_app_layout(
dash_bio.Molecule2dViewer(id=_COMPONENT_ID, modelData=_data)))
simple_app_callback(
app,
dash_duo,
component_id=_COMPONENT_ID,
test_prop_name='selectedAtomIds',
test_prop_value=json.dumps([1, 4]),
prop_value_type='list',
validation_fn=lambda x: json.dumps(x) == json.dumps([1, 4]))
assert len(
dash_duo.find_elements(
'g.nodes-container > g.node.selected[index="1"]')) == 1
assert len(
dash_duo.find_elements(
'g.nodes-container > g.node.selected[index="2"]')) == 0
assert len(
dash_duo.find_elements(
'g.nodes-container > g.node.selected[index="3"]')) == 0
assert len(
dash_duo.find_elements(
'g.nodes-container > g.node.selected[index="4"]')) == 1
def test_dbav003_change_conservation_colorscale(dash_duo):
app = dash.Dash(__name__)
app.layout = html.Div(
simple_app_layout(dash_bio.AlignmentChart(id=_COMPONENT_ID,
data=_data)))
simple_app_callback(app,
dash_duo,
component_id=_COMPONENT_ID,
test_prop_name='conservationcolorscale',
test_prop_value='Blackbody',
prop_value_type='string')
bars = dash_duo.find_elements('g.cartesianlayer g.subplot.xy2 g.plot path')
# first bar should be black
match = re.search(r'.*fill: ([\w\s,\(\)]+);.*',
bars[0].get_attribute('style'))
assert match.group(1) == 'rgb(0, 0, 0)'
# second bar should be orange
match = re.search(r'.*fill: ([\w\s,\(\)]+);.*',
bars[1].get_attribute('style'))
assert match.group(1) == 'rgb(230, 103, 0)'
def test_dbid001_displayed_chromosomes(dash_duo):
app = dash.Dash(__name__)
app.layout = html.Div(simple_app_layout(
dash_bio.Ideogram(
id=_COMPONENT_ID
)
))
chromosome_set_new = [str(i+1) for i in range(5)]
simple_app_callback(
app,
dash_duo,
component_id=_COMPONENT_ID,
test_prop_name='chromosomes',
test_prop_value=json.dumps(chromosome_set_new),
prop_value_type='dict',
validation_fn=lambda x: json.dumps(x) == json.dumps(chromosome_set_new)
)
WebDriverWait(dash_duo.driver, 1).until(
lambda _:
len(dash_duo.find_elements('g.chromosome-set-container')) == 5
)
def test_dbsv002_selection(dash_duo):
app = dash.Dash(__name__)
app.layout = html.Div(simple_app_layout(
dash_bio.SequenceViewer(
id=_COMPONENT_ID,
sequence=_data
)
))
new_selection = [50, 75, 'rgb(120, 0, 200)']
simple_app_callback(
app,
dash_duo,
component_id=_COMPONENT_ID,
test_prop_name='selection',
test_prop_value=json.dumps(new_selection),
prop_value_type='list',
validation_fn=lambda x: json.dumps(x) == json.dumps(new_selection),
take_snapshot=True
)
selection = dash_duo.find_element('.fastaSeq span.stringSelected')
match = re.search(
r'.*background:\s*([\w\s,\(\)]+);.*',
selection.get_attribute('style')
)
assert match.group(1) == new_selection[2]
assert selection.get_attribute('innerHTML').replace(
' ', ''.replace('<br>', '')) == \
_data[new_selection[0]:new_selection[1]]
def test_dbm3001_selection_type(dash_duo):
app = dash.Dash(__name__)
app.layout = html.Div(
simple_app_layout(
dash_bio.Molecule3dViewer(id=_COMPONENT_ID,
modelData=_model_data,
styles=_styles_data)))
simple_app_callback(app,
dash_duo,
component_id=_COMPONENT_ID,
test_prop_name='selectionType',
test_prop_value='chain',
prop_value_type='string')
# find and click on one of the DNA strands
mol3d = dash_duo.find_element('#test-mol3d canvas')
ac = ActionChains(dash_duo.driver)
ac.move_to_element(mol3d).move_by_offset(0, -50).click().perform()
dash_duo.wait_for_element_by_css_selector('.molecule-3d')
dash_duo.percy_snapshot('test-mol3d_selectionType_chain' +
generate_identifier(),
convert_canvases=True)
def test_dbpu004_no_tracks(dash_duo):
app = dash.Dash(__name__)
TWOBIT_URL = os.path.join(app.get_asset_url(''), "pileup",
"chr17_little.2bit")
app.layout = html.Div(
simple_app_layout(
dash_bio.Pileup(id=_COMPONENT_ID,
range={
"contig": 'chr17',
"start": 7512284,
"stop": 7512644
},
reference={
"label": _GENOME,
"url": TWOBIT_URL
}), ))
dash_duo.start_server(app)
# Check that the genome loaded
dash_duo.wait_for_text_to_equal('.reference>.track-label', _GENOME)
# Check that reference track loaded
tracks = dash_duo.find_elements('.reference')
assert len(tracks) == 1 # track-label and track-content
assert tracks[0].text == _GENOME
def test_dbid002_click_rotation(dash_duo):
app = dash.Dash(__name__)
app.layout = html.Div(simple_app_layout(
dash_bio.Ideogram(
id=_COMPONENT_ID
)
))
simple_app_callback(
app,
dash_duo,
component_id=_COMPONENT_ID,
test_prop_name='rotatable',
test_prop_value=str(True),
prop_value_type='bool',
validation_fn=lambda x: x is True
)
# ensure that it loads un-rotated
WebDriverWait(dash_duo.driver, 1).until(
lambda _: 'rotate(90)' in dash_duo.find_element(
'#chr1-9606-chromosome-set').get_attribute('transform'))
# click to rotate and ensure that the correct chromosome is rotated
dash_duo.find_element('#chr1-9606-chromosome-set').click()
# rotation shouldn't take more than 1-2 seconds
WebDriverWait(dash_duo.driver, 1).until(
lambda _: 'rotate(0)' in dash_duo.find_element(
'#chr1-9606-chromosome-set').get_attribute('transform'))
def test_dbid003_click_rotation_disabled(dash_duo):
app = dash.Dash(__name__)
app.layout = html.Div(simple_app_layout(
dash_bio.Ideogram(
id=_COMPONENT_ID
)
))
simple_app_callback(
app,
dash_duo,
component_id=_COMPONENT_ID,
test_prop_name='rotatable',
test_prop_value=str(False),
prop_value_type='bool',
validation_fn=lambda x: x is False
)
WebDriverWait(dash_duo.driver, 1).until(
lambda _: 'rotate(90)' in dash_duo.find_element(
'#chr1-9606-chromosome-set').get_attribute('transform'))
# click to rotate and ensure that the correct chromosome is rotated
dash_duo.find_element('#chr1-9606-chromosome-set').click()
WebDriverWait(dash_duo.driver, 1)
assert 'rotate(90)' in dash_duo.find_element(
'#chr1-9606-chromosome-set').get_attribute('transform')
def test_dbigv002_ASM985889v3_tracks(dash_duo):
app = dash.Dash(__name__)
try:
requests.get('https://www.google.com/').status_code
data_path = 'https://s3.amazonaws.com/igv.org.genomes/'
except requests.exceptions.ConnectionError:
print("Running test with local datasets")
data_path = app.get_asset_url('')
app.layout = html.Div(
simple_app_layout(
dash_bio.Igv(
id=_COMPONENT_ID,
reference={
"id":
"ASM985889v3",
"name":
"Sars-CoV-2 (ASM985889v3)",
"fastaURL":
data_path +
"covid_ASM985889v3/GCF_009858895.2_ASM985889v3_genomic.fna",
"indexURL":
data_path +
"covid_ASM985889v3/GCF_009858895.2_ASM985889v3_genomic.fna.fai",
"order":
1000000,
"tracks": [{
"name": "Annotations",
"url": data_path +
"covid_ASM985889v3/GCF_009858895.2_ASM985889v3_genomic.gff.gz",
"displayMode": "EXPANDED",
"nameField": "gene",
"height": 150
}]
},
tracks=
[{ # normally, tracks listed here would not duplicate those already present above
"name": "Genes",
"type": "annotation",
"url": data_path +
"covid_ASM985889v3/GCF_009858895.2_ASM985889v3_genomic.gff.gz",
"displayMode": "EXPANDED"
}],
minimumBases=100,
style=igvStyle), ))
dash_duo.start_server(app)
# Check that the genome loaded
dash_duo.wait_for_text_to_equal('.igv-current-genome', 'ASM985889v3')
# Check that track(s) loaded
tracks = dash_duo.find_elements('.igv-track-label')
assert tracks[0].text == 'Annotations'
assert tracks[1].text == 'Genes'
def test_dbdn001_viewer_loaded(dash_duo):
app = dash.Dash(__name__)
app.layout = html.Div(simple_app_layout(viewer, ))
dash_duo.start_server(app)
dash_duo.wait_for_element("#" + _COMPONENT_ID + " canvas")
assert dash_duo.find_element("#" + _COMPONENT_ID + " canvas")
def test_dbpu002_json(dash_duo):
app = dash.Dash(__name__)
TWOBIT_URL = os.path.join(app.get_asset_url(''), "pileup",
"chr17_little.2bit")
# read in JSON as string: local file
dir_path = os.path.dirname(os.path.realpath(__file__))
file = os.path.join(dir_path, "assets", "pileup",
"alignments.ga4gh.chr17.1-250.json")
with open(file, "r") as f:
json = re.sub(r'\s+', '', f.read())
pileup_label = 'bam file in GA4GH json'
tracks = [{
'viz': 'pileup',
'label': pileup_label,
'source': 'alignmentJson',
'sourceOptions': json
}]
app.layout = html.Div(
simple_app_layout(
dash_bio.Pileup(id=_COMPONENT_ID,
range={
"contig": 'chr17',
"start": 7512284,
"stop": 7512644
},
reference={
"label": _GENOME,
"url": TWOBIT_URL
},
tracks=tracks), ))
dash_duo.start_server(app)
# Check that the genome loaded
dash_duo.wait_for_text_to_equal('.reference>.track-label', _GENOME)
# Check that reference track loaded
tracks = dash_duo.find_elements('.reference')
assert len(tracks) == 1 # track-label and track-content
assert tracks[0].text == _GENOME
# Check that pileup track loaded
tracks = dash_duo.find_elements('.pileup')
assert len(tracks) == 1 # track-label and track-content
# gear and track name should be printed
assert pileup_label in tracks[0].text
assert _GEAR_ICON in tracks[0].text
def test_dbsp005_preset_view_stickball(dash_duo):
app = dash.Dash(__name__)
app.layout = html.Div(
simple_app_layout(dash_bio.Speck(id=_COMPONENT_ID, data=_data)))
simple_app_callback(app,
dash_duo,
component_id=_COMPONENT_ID,
test_prop_name='presetView',
test_prop_value='stickball',
prop_value_type='string',
take_snapshot=True)
def test_dbav002_change_colorscale(dash_duo):
app = dash.Dash(__name__)
app.layout = html.Div(
simple_app_layout(dash_bio.AlignmentChart(id=_COMPONENT_ID,
data=_data)))
simple_app_callback(app,
dash_duo,
component_id=_COMPONENT_ID,
test_prop_name='colorscale',
test_prop_value='hydro',
prop_value_type='string',
take_snapshot=True)
def test_dbav001_hide_conservation(dash_duo):
app = dash.Dash(__name__)
app.layout = html.Div(
simple_app_layout(dash_bio.AlignmentChart(id=_COMPONENT_ID,
data=_data)))
simple_app_callback(app,
dash_duo,
component_id=_COMPONENT_ID,
test_prop_name='showconservation',
test_prop_value=str(False),
prop_value_type='bool',
validation_fn=lambda x: x is False)
assert len(dash_duo.find_elements('g.cartesianlayer.xy3')) == 0
def test_ASM985889v3_tracks(dash_duo):
app = dash.Dash(__name__)
app.layout = html.Div(simple_app_layout(
dash_bio.Igv(
id=_COMPONENT_ID,
reference={
"id": "ASM985889v3",
"name": "Sars-CoV-2 (ASM985889v3)",
"fastaURL": "https://s3.amazonaws.com/igv.org.genomes/covid_ASM985889v3/GCF_009858895.2_ASM985889v3_genomic.fna",
"indexURL": "https://s3.amazonaws.com/igv.org.genomes/covid_ASM985889v3/GCF_009858895.2_ASM985889v3_genomic.fna.fai",
"order": 1000000,
"tracks": [
{
"name": "Annotations",
"url": "https://s3.amazonaws.com/igv.org.genomes/covid_ASM985889v3/GCF_009858895.2_ASM985889v3_genomic.gff.gz",
"displayMode": "EXPANDED",
"nameField": "gene",
"height": 150
}
]
},
tracks=[{ # normally, tracks listed here would not duplicate those already present above
"name": "Genes",
"type": "annotation",
"url": "https://s3.amazonaws.com/igv.org.genomes/covid_ASM985889v3/GCF_009858895.2_ASM985889v3_genomic.gff.gz",
"displayMode": "EXPANDED"
}],
minimumBases=100,
style=igvStyle
),
))
dash_duo.start_server(app)
# Check that the genome loaded
dash_duo.wait_for_text_to_equal('#igv-current_genome', 'ASM985889v3')
# Check that track(s) loaded
tracks = dash_duo.find_elements('.igv-track-label')
assert tracks[0].text == 'Annotations'
assert tracks[1].text == 'Genes'
def test_dbigv003_sacCer3(dash_duo):
app = dash.Dash(__name__)
try:
requests.get('https://www.google.com/').status_code
data_path = 'https://s3.dualstack.us-east-1.amazonaws.com/igv.org.genomes/'
except requests.exceptions.ConnectionError:
print("Running test with local datasets")
data_path = app.get_asset_url('')
app.layout = html.Div(
simple_app_layout(
dash_bio.Igv(id=_COMPONENT_ID,
reference={
"id":
"sacCer3",
"name":
"S. cerevisiae (sacCer3)",
"fastaURL":
data_path + "sacCer3/sacCer3.fa",
"indexURL":
data_path + "sacCer3/sacCer3.fa.fai",
"tracks": [{
"name": "Ensembl Genes",
"type": "annotation",
"format": "ensgene",
"displayMode": "EXPANDED",
"url": data_path + "sacCer3/ensGene.txt.gz",
"indexed": False,
"supportsWholeGenome": False
}]
},
minimumBases=100,
style=igvStyle), ))
dash_duo.start_server(app)
# Check that the genome loaded
dash_duo.wait_for_text_to_equal('.igv-current-genome', 'sacCer3')
# Check that track(s) loaded
tracks = dash_duo.find_elements('.igv-track-label')
assert len(tracks) == 1
assert tracks[0].text == 'Ensembl Genes'
def test_dbm2002_preselected_atoms(dash_duo):
app = dash.Dash(__name__)
app.layout = html.Div(
simple_app_layout(
dash_bio.Molecule2dViewer(id=_COMPONENT_ID,
modelData=_data,
selectedAtomIds=[1, 3])))
dash_duo.start_server(app)
dash_duo.wait_for_element('#test-mol2d')
assert len(
dash_duo.find_elements(
'g.nodes-container > g.node.selected[index="1"]')) == 1
assert len(
dash_duo.find_elements(
'g.nodes-container > g.node.selected[index="3"]')) == 1
def test_dbop002_colorscale(dash_duo):
app = dash.Dash(__name__)
new_colorscale = {
'AMP': 'rgb(10, 200, 100)',
'FUSION': 'rgb(100, 10, 20)',
'HOMDEL': 'rgb(200, 50, 60)'
}
# fusion deep del amp
app.layout = html.Div(
simple_app_layout(dash_bio.OncoPrint(id=_COMPONENT_ID, data=_data)))
simple_app_callback(
app,
dash_duo,
component_id=_COMPONENT_ID,
test_prop_name='colorscale',
test_prop_value=json.dumps(new_colorscale),
prop_value_type='dict',
validation_fn=lambda x: json.dumps(x) == json.dumps(new_colorscale),
take_snapshot=True)
fus = dash_duo.find_elements(
'g.cartesianlayer g.plot g.trace.bars:nth-child(2) g.point > path')
for point in fus:
match = re.search(r'.*fill: ([\w\s,\(\)]+);.*',
point.get_attribute('style'))
assert match.group(1) == 'rgb(100, 10, 20)'
deep_del = dash_duo.find_elements(
'g.cartesianlayer g.plot g.trace.bars:nth-child(3) g.point > path')
for point in deep_del:
match = re.search(r'.*fill: ([\w\s,\(\)]+);.*',
point.get_attribute('style'))
assert match.group(1) == 'rgb(200, 50, 60)'
amp = dash_duo.find_elements(
'g.cartesianlayer g.plot g.trace.bars:nth-child(4) g.point > path')
for point in amp:
match = re.search(r'.*fill: ([\w\s,\(\)]+);.*',
point.get_attribute('style'))
assert match.group(1) == 'rgb(10, 200, 100)'
def test_dbm3003_selected_atom_ids(dash_duo):
app = dash.Dash(__name__)
app.layout = html.Div(
simple_app_layout(
dash_bio.Molecule3dViewer(id=_COMPONENT_ID,
modelData=_model_data,
styles=_styles_data)))
simple_app_callback(app,
dash_duo,
component_id=_COMPONENT_ID,
test_prop_name='selectedAtomIds',
test_prop_value=json.dumps([1306, 1371, 1339, 1404]),
prop_value_type='list',
validation_fn=lambda x: json.dumps(x) == json.dumps(
[1306, 1371, 1339, 1404]),
take_snapshot=True)
def test_dbnp002_domainStyle(dash_duo):
app = dash.Dash(__name__)
app.layout = html.Div(simple_app_layout(
dash_bio.NeedlePlot(
id=_COMPONENT_ID,
mutationData=_data
)
))
new_domain_style = {
'domainColor': ['rgb(200, 100, 0)',
'rgb(120, 246, 100)',
'rgb(150, 245, 170)',
'rgb(0, 200, 150)',
'rgb(100, 70, 25)'],
'displayMinorDomains': False
}
simple_app_callback(
app,
dash_duo,
component_id=_COMPONENT_ID,
test_prop_name='domainStyle',
test_prop_value=json.dumps(new_domain_style),
prop_value_type='dict',
validation_fn=lambda x: json.dumps(x) == json.dumps(new_domain_style),
take_snapshot=True
)
domains = dash_duo.find_elements('g.overplot g.scatterlayer.mlayer path.js-fill')
for domain in domains:
match = re.search(
r'.*fill: ([\w\s,\(\)]+);.*',
domain.get_attribute('style')
)
assert match.group(1) in new_domain_style['domainColor']
def test_dbdn002_change_background(dash_duo):
stage_config = {
"backgroundColor": "black",
"quality": "medium",
"cameraType": "perspective",
}
app = dash.Dash(__name__)
app.layout = html.Div(simple_app_layout(viewer, ))
simple_app_callback(
app,
dash_duo,
component_id=_COMPONENT_ID,
test_prop_name="stageParameters",
test_prop_value=json.dumps(stage_config),
prop_value_type="dict",
validation_fn=lambda x: json.dumps(x) == json.dumps(stage_config),
take_snapshot=True,
)
def test_dbm2001_load_mol_data(dash_duo):
app = dash.Dash(__name__)
app.layout = html.Div(
simple_app_layout(dash_bio.Molecule2dViewer(id=_COMPONENT_ID)))
def compare_nodes_links(computed_props):
given_nodes = _data['nodes']
given_links = _data['links']
computed_nodes = computed_props['nodes']
computed_links = computed_props['links']
defined_node_props = ['id', 'atom']
for i in range(len(given_nodes)):
for key in defined_node_props:
if given_nodes[i][key] != computed_nodes[i][key]:
return False
defined_link_props = ['bond', 'strength', 'distance']
for i in range(len(given_links)):
for key in defined_link_props:
if given_links[i][key] != computed_links[i][key]:
return False
if given_links[i]['source'] != \
computed_links[i]['source']['id']:
return False
if given_links[i]['target'] != \
computed_links[i]['target']['id']:
return False
return True
simple_app_callback(app,
dash_duo,
component_id=_COMPONENT_ID,
test_prop_name='modelData',
test_prop_value=json.dumps(_data),
prop_value_type='dict',
validation_fn=lambda x: compare_nodes_links(x))
def test_dbop001_background_color(dash_duo):
app = dash.Dash(__name__)
app.layout = html.Div(
simple_app_layout(dash_bio.OncoPrint(id=_COMPONENT_ID, data=_data)))
simple_app_callback(app,
dash_duo,
component_id=_COMPONENT_ID,
test_prop_name='backgroundcolor',
test_prop_value='rgb(25, 211, 243)',
prop_value_type='string',
take_snapshot=True)
background = dash_duo.find_elements(
'g.cartesianlayer g.plot g.trace.bars:nth-child(1) g.point > path')
for point in background:
match = re.search(r'.*fill: ([\w\s,\(\)]+);.*',
point.get_attribute('style'))
assert match.group(1) == 'rgb(25, 211, 243)'
def test_sacCer3(dash_duo):
app = dash.Dash(__name__)
app.layout = html.Div(simple_app_layout(
dash_bio.Igv(
id=_COMPONENT_ID,
reference={
"id": "sacCer3",
"name": "S. cerevisiae (sacCer3)",
"fastaURL": "https://s3.dualstack.us-east-1.amazonaws.com/igv.org.genomes/sacCer3/sacCer3.fa",
"indexURL": "https://s3.dualstack.us-east-1.amazonaws.com/igv.org.genomes/sacCer3/sacCer3.fa.fai",
"tracks": [
{
"name": "Ensembl Genes",
"type": "annotation",
"format": "ensgene",
"displayMode": "EXPANDED",
"url": "https://s3.dualstack.us-east-1.amazonaws.com/igv.org.genomes/sacCer3/ensGene.txt.gz",
"indexed": False,
"supportsWholeGenome": False
}
]
},
minimumBases=100,
style=igvStyle
),
))
dash_duo.start_server(app)
# Check that the genome loaded
dash_duo.wait_for_text_to_equal('#igv-current_genome', 'sacCer3')
# Check that track(s) loaded
tracks = dash_duo.find_elements('.igv-track-label')
assert len(tracks) == 1
assert tracks[0].text == 'Ensembl Genes'
def test_dbpu001_reference(dash_duo):
app = dash.Dash(__name__)
TWOBIT_URL = os.path.join(app.get_asset_url(''), "pileup",
"chr17_little.2bit")
pileup_label = 'bam file'
feature_label = 'features'
tracks = [{
'viz': 'scale',
'label': 'Scale'
}, {
'viz': 'location',
'label': 'Location'
}, {
'viz': 'genes',
'label': 'genes',
'source': 'bigBed',
'sourceOptions': {
'url': 'http://www.biodalliance.org/datasets/ensGene.bb'
}
}, {
'viz': 'variants',
'label': 'variants',
'source': 'vcf',
'sourceOptions': {
'url': os.path.join(app.get_asset_url(''), "pileup",
"snv.chr17.vcf")
}
}, {
'viz': 'pileup',
'label': pileup_label,
'source': 'bam',
'sourceOptions': {
'url':
os.path.join(app.get_asset_url(''), "pileup",
"synth3.normal.17.7500000-7515000.bam"),
'indexUrl':
os.path.join(app.get_asset_url(''), "pileup",
"synth3.normal.17.7500000-7515000.bam.bai")
}
}, {
'viz': 'features',
'label': feature_label,
'source': 'bigBed',
'sourceOptions': {
'url':
os.path.join(app.get_asset_url(''), "pileup",
"chr17.22.10000-21000.bb")
}
}]
app.layout = html.Div(
simple_app_layout(
dash_bio.Pileup(id=_COMPONENT_ID,
range={
"contig": 'chr17',
"start": 7512284,
"stop": 7512644
},
reference={
"label": _GENOME,
"url": TWOBIT_URL
},
tracks=tracks), ))
dash_duo.start_server(app)
# Check that the genome loaded
dash_duo.wait_for_text_to_equal('.reference>.track-label', _GENOME)
# Check that reference track loaded
tracks = dash_duo.find_elements('.reference')
assert len(tracks) == 1 # track-label and track-content
assert tracks[0].text == _GENOME
# check dropdown menu
tracks = dash_duo.find_elements('.controls')
assert "chr17" in tracks[0].text
# Check that pileup track loaded
tracks = dash_duo.find_elements('.pileup')
assert len(tracks) == 1 # track-label and track-content
# gear and track name should be printed
assert pileup_label in tracks[0].text
assert _GEAR_ICON in tracks[0].text
# Take a Percy snapshot to check that tracks are rendered correctly
dash_duo.percy_snapshot('test-pileup_reference', convert_canvases=True)
# Check that feature track loaded
tracks = dash_duo.find_elements('.features')
assert len(tracks) == 1 # track-label and track-content
# gear and track name should be printed
assert feature_label in tracks[0].text
assert _GEAR_ICON in tracks[0].text
def test_dbnp001_needle_style(dash_duo):
app = dash.Dash(__name__)
app.layout = html.Div(simple_app_layout(
dash_bio.NeedlePlot(
id=_COMPONENT_ID,
mutationData=_data
)
))
new_needle_style = {
'stemConstHeight': True,
'stemColor': 'rgb(99, 110, 250)',
'stemThickness': 4,
'headColor': 'rgb(239, 85, 59)',
'headSize': 10
}
simple_app_callback(
app,
dash_duo,
component_id=_COMPONENT_ID,
test_prop_name='needleStyle',
test_prop_value=json.dumps(new_needle_style),
prop_value_type='dict',
validation_fn=lambda x: json.dumps(x) == json.dumps(new_needle_style),
take_snapshot=True
)
# points should all be at the same height (y-value)
points = dash_duo.find_elements('g.trace.scatter > g.points > path')
lines = dash_duo.find_elements('g.trace.scatter > g.errorbars > g.errorbar > path')
y_location = points[0].get_attribute('transform').strip(
'translate(').strip(
')').split(',')[1]
for point in points[1:]:
point_y_location = point.get_attribute('transform').strip(
'translate').strip(
'(').strip(')').split(',')[1]
assert point_y_location == y_location
match = re.search(
r'.*fill: ([\w\s,\(\)]+);.*',
point.get_attribute('style')
)
assert match.group(1) == 'rgb(239, 85, 59)'
for line in lines:
match = re.search(
r'.*stroke: ([\w\s,\(\)]+);.*',
line.get_attribute('style')
)
assert match.group(1) == 'rgb(99, 110, 250)'
match = re.search(
r'.*stroke-width: ([\w]+);.*',
line.get_attribute('style')
)
assert match.group(1) == '4px'
def test_dbsv001_coverage(dash_duo):
app = dash.Dash(__name__)
app.layout = html.Div(simple_app_layout(
dash_bio.SequenceViewer(
id=_COMPONENT_ID,
sequence=_data
)
))
new_coverage = [
{'start': 0, 'end': 10, 'color': 'rgb(255, 0, 0)',
'bgcolor': 'rgb(0, 0, 255)', 'underscore': True,
'tooltip': 'Coverage one'},
{'start': 45, 'end': 80, 'color': 'rgb(200, 150, 150)',
'bgcolor': 'rgb(0, 0, 0)', 'underscore': False}
]
simple_app_callback(
app,
dash_duo,
component_id=_COMPONENT_ID,
test_prop_name='coverage',
test_prop_value=json.dumps(new_coverage),
prop_value_type='list',
validation_fn=lambda x: json.dumps(x) == json.dumps(new_coverage),
take_snapshot=True
)
coverage_1 = dash_duo.find_element(
'.sequenceBody .fastaSeq span:nth-child(1)')
match = re.search(
r'.*color:\s*([\w\s,\(\)]+);.*',
coverage_1.get_attribute('style')
)
assert match.group(1) == new_coverage[0]['color']
match = re.search(
r'.*background:\s*([\w\s,\(\)]+);.*',
coverage_1.get_attribute('style')
)
assert match.group(1) == new_coverage[0]['bgcolor']
assert coverage_1.get_attribute('title') == new_coverage[0]['tooltip']
assert coverage_1.get_attribute('innerHTML').replace(
' ', '').replace('<br>', '') == \
_data[new_coverage[0]['start']:new_coverage[0]['end']]
coverage_2 = dash_duo.find_element(
'.sequenceBody .fastaSeq span:nth-child(3)')
match = re.search(
r'.*color:\s*([\w\s,\(\)]+);.*',
coverage_2.get_attribute('style')
)
assert match.group(1) == new_coverage[1]['color']
match = re.search(
r'.*background:\s*([\w\s,\(\)]+);.*',
coverage_2.get_attribute('style')
)
assert match.group(1) == new_coverage[1]['bgcolor']
assert coverage_2.get_attribute('title') == ''
assert coverage_2.get_attribute('innerHTML').replace(
' ', '').replace('<br>', '') == \
_data[new_coverage[1]['start']:new_coverage[1]['end']]
