def test_embed_data_two_widgets(self):
feature_track = pileup.Track(
viz="features",
label="myFeatures",
source=pileup.sources.GA4GHFeatureJson('{}'))
variant_track = pileup.Track(
viz="variants",
label="myVariants",
source=pileup.sources.GA4GHVariantJson('{}'))
w1 = pileup.PileupViewer(chrom="chr17",
start=1,
stop=250,
reference="hg19",
tracks=[feature_track])
w2 = pileup.PileupViewer(chrom="chr17",
start=1,
stop=250,
reference="hg19",
tracks=[variant_track])
jslink((w1, 'reference'), (w2, 'reference'))
state = dependency_state([w1, w2], drop_defaults=True)
data = embed_data(views=[w1, w2], drop_defaults=True, state=state)
state = data['manager_state']['state']
views = data['view_specs']
assert len(views) == 2
model_names = [s['model_name'] for s in state.values()]
widget_names = list(
filter(lambda x: x == 'PileupViewerModel', model_names))
assert len(widget_names) == 2
def test_track_invalid_viz_features(self):
pileup.Track(viz="features", label="myFeatures", source=pileup.sources.BigBedDataSource("fakeFile.bb"))
with self.assertRaises(RuntimeError) as context:
# viz features with incompatible GA4GHVariantJson source
pileup.Track(viz="features", label="myFeatures", source=pileup.sources.GA4GHVariantJson("{}"))
self.assertTrue('Invalid data source variantJson for track features' in context.exception)
def test_track_invalid_viz_coverage(self):
pileup.Track(viz="coverage", label="myCoverage", source=pileup.sources.BamDataSource("fakeFile.bam"))
with self.assertRaises(RuntimeError) as context:
# viz coverage with incompatible TwoBit source
pileup.Track(viz="coverage", label="myReads", source=pileup.sources.TwoBitDataSource("fakeFile.2bit"))
self.assertTrue('Invalid data source twoBit for track coverage' in context.exception)
def test_track_invalid_viz_location(self):
pileup.Track(viz="location", label="location")
with self.assertRaises(RuntimeError) as context:
# viz location with incompatible any source
pileup.Track(viz="location", label="location", source=pileup.sources.BamDataSource("fakeFile.bam"))
self.assertTrue('Invalid data source bam for track location' in context.exception)
def test_track_invalid_viz_genes(self):
pileup.Track(viz="genes", label="myGenes", source=pileup.sources.BigBedDataSource("fakeFile.bb"))
with self.assertRaises(RuntimeError) as context:
# viz genes with incompatible bam data source
pileup.Track(viz="genes", label="myGenes", source=pileup.sources.BamDataSource("fakeFile.bam"))
self.assertTrue('Invalid data source bam for track genes' in context.exception)
def test_track_invalid_viz_variants(self):
pileup.Track(viz="variants", label="myVariants", source=pileup.sources.GA4GHVariantSource("www.fakeEndpoint.com", "readGroup"))
with self.assertRaises(RuntimeError) as context:
# viz variants with incompatible GA4GHAlignmentSource source
pileup.Track(viz="variants", label="myVariants", source=pileup.sources.GA4GHAlignmentSource("www.fakeEndpoint.com", "readGroup"))
self.assertTrue('Invalid data source GAReadAlignment for track variants' in context.exception)
def test_track_invalid_viz_genome(self):
pileup.Track(viz="genome", label="myReference", source=pileup.sources.TwoBitDataSource("fakeFile.2bit"))
with self.assertRaises(RuntimeError) as context:
# viz genome with incompatible GA4GHFeatureJson source
pileup.Track(viz="genome", label="myReference", source=pileup.sources.GA4GHFeatureJson("{}"))
self.assertTrue('Invalid data source featureJson for track genome' in context.exception)
def test_track_invalid_viz_location(self):
pileup.Track(viz="location", label="location")
with self.assertRaises(ValueError) as context:
# viz location with incompatible any source
pileup.Track(viz="location",
label="location",
source=pileup.sources.BamDataSource("fakeFile.bam"))
self.assertTrue("Invalid viz 'location'" in str(context.exception))
self.assertTrue("Valid viz tracks include: coverage, pileup." in str(
context.exception))
def test_track_invalid_viz_genome(self):
pileup.Track(viz="genome",
label="myReference",
source=pileup.sources.TwoBitDataSource("fakeFile.2bit"))
with self.assertRaises(ValueError) as context:
# viz genome with incompatible GA4GHFeatureJson source
pileup.Track(viz="genome",
label="myReference",
source=pileup.sources.GA4GHFeatureJson("{}"))
self.assertTrue("Invalid viz 'genome'" in str(context.exception))
self.assertTrue("Valid viz tracks include: coverage, features." in str(
context.exception))
def test_track_invalid_viz_features(self):
pileup.Track(viz="features",
label="myFeatures",
source=pileup.sources.BigBedDataSource("fakeFile.bb"))
with self.assertRaises(ValueError) as context:
# viz features with incompatible GA4GHVariantJson source
pileup.Track(viz="features",
label="myFeatures",
source=pileup.sources.GA4GHVariantJson("{}"))
self.assertTrue("Invalid viz 'features'" in str(context.exception))
self.assertTrue("Valid viz tracks include: variants, genotypes." in
str(context.exception))
def test_track_invalid_viz_genes(self):
# should work
pileup.Track(viz="genes",
label="myGenes",
source=pileup.sources.BigBedDataSource("fakeFile.bb"))
with self.assertRaises(ValueError) as context:
# viz genes with incompatible bam data source
pileup.Track(viz="genes",
label="myGenes",
source=pileup.sources.BamDataSource("fakeFile.bam"))
self.assertTrue("Invalid viz 'genes'" in str(context.exception))
self.assertTrue("Valid viz tracks include: coverage, pileup." in str(
context.exception))
def test_track_invalid_viz_coverage(self):
pileup.Track(viz="coverage",
label="myCoverage",
source=pileup.sources.BamDataSource("fakeFile.bam"))
with self.assertRaises(ValueError) as context:
# viz coverage with incompatible TwoBit source
pileup.Track(
viz="coverage",
label="myReads",
source=pileup.sources.TwoBitDataSource("fakeFile.2bit"))
self.assertTrue("Invalid viz 'coverage'" in str(context.exception))
self.assertTrue(
"Valid viz tracks include: genome." in str(context.exception))
def test_track_invalid_viz_variants(self):
pileup.Track(viz="variants",
label="myVariants",
source=pileup.sources.GA4GHVariantSource(
"www.fakeEndpoint.com", "readGroup"))
with self.assertRaises(ValueError) as context:
# viz variants with incompatible GA4GHAlignmentSource source
pileup.Track(viz="variants",
label="myVariants",
source=pileup.sources.GA4GHAlignmentSource(
"www.fakeEndpoint.com", "readGroup"))
self.assertTrue("Invalid viz 'variants'" in str(context.exception))
self.assertTrue(
"Valid viz tracks include: pileup." in str(context.exception))
def test_tracks_serialization(self):
sourceOptions = {
'url': 'http://www.biodalliance.org/datasets/ensGene.bb'
}
gene_track=pileup.Track(viz="genes", label="myGenes", source=pileup.sources.BigBedDataSource(sourceOptions))
pileup_track = pileup.Track(viz="pileup", label="myReads", source=pileup.sources.GA4GHAlignmentJson(str))
tracks = [pileup_track, gene_track]
serialized_tracks = tracks_to_json(tracks, any)
assert(len(serialized_tracks) == 2)
deserialized_tracks = tracks_from_json(serialized_tracks, any)
assert(len(deserialized_tracks) == 2)
assert(deserialized_tracks[0].viz == 'pileup')
assert(deserialized_tracks[1].viz == 'genes')
def test_pileup(self):
track = pileup.Track(viz="pileup",
label="myReads",
source=pileup.sources.GA4GHAlignmentJson('{}'))
x = pileup.PileupViewer(locus="chr17:1-250",
reference="hg19",
tracks=[track])
assert (x.reference == 'hg19')
assert (x.tracks[0] == track)
def test_variants(self):
track = pileup.Track(viz="variants",
label="myVariants",
source=pileup.sources.GA4GHVariantJson('{}'))
x = pileup.PileupViewer(locus="chr17:1-250",
reference="hg19",
tracks=[track])
assert (x.reference == 'hg19')
assert (x.tracks[0] == track)
def test_genotypes(self):
track = pileup.Track(viz="genotypes",
label="myGenotypes",
source=pileup.sources.VcfDataSource('{}'))
x = pileup.PileupViewer(locus="chr22:21340030-21340150",
reference="hg19",
tracks=[track])
assert (x.reference == 'hg19')
assert (x.tracks[0] == track)
def test_toSVG(self):
track = pileup.Track(
viz="genes",
label="myGenes",
source=pileup.sources.BigBedDataSource('fakeGenes.bb'))
x = pileup.PileupViewer(chrom="chr17",
start=1,
stop=250,
reference="hg19",
tracks=[track])
x.getSVG()
def test_genes(self):
track = pileup.Track(
viz="genes",
label="myGenes",
source=pileup.sources.BigBedDataSource('fakeGenes.bb'))
x = pileup.PileupViewer(locus="chr17:1-250",
reference="hg19",
tracks=[track])
assert (x.reference == 'hg19')
assert (x.tracks[0] == track)
def test_features(self):
track = pileup.Track(viz="features",
label="myFeatures",
source=pileup.sources.GA4GHFeatureJson('{}'))
x = pileup.PileupViewer(chrom="chr17",
start=1,
stop=250,
reference="hg19",
tracks=[track])
assert (x.reference == 'hg19')
assert (x.tracks[0] == track)
def test_minimal_pileup_html(self):
track = pileup.Track(viz="pileup",
label="myReads",
source=pileup.sources.GA4GHAlignmentJson('{}'))
w = pileup.PileupViewer(locus="chr17:1-250",
reference="hg19",
tracks=[track])
output = StringIO()
state = dependency_state(w, drop_defaults=True)
embed_minimal_html(output, views=w, drop_defaults=True, state=state)
content = output.getvalue()
assert content.splitlines()[0] == '<!DOCTYPE html>'
def test_snippet(self):
class Parser(HTMLParser):
state = 'initial'
states = []
def handle_starttag(self, tag, attrs):
attrs = dict(attrs)
if tag == 'script' and attrs.get(
'type',
'') == "application/vnd.jupyter.widget-state+json":
self.state = 'widget-state'
self.states.append(self.state)
elif tag == 'script' and attrs.get(
'type',
'') == "application/vnd.jupyter.widget-view+json":
self.state = 'widget-view'
self.states.append(self.state)
def handle_endtag(self, tag):
self.state = 'initial'
def handle_data(self, data):
if self.state == 'widget-state':
manager_state = json.loads(data)['state']
assert len(manager_state) == 2
self.states.append('check-widget-state')
elif self.state == 'widget-view':
view = json.loads(data)
assert isinstance(view, dict)
self.states.append('check-widget-view')
track = pileup.Track(viz="variants",
label="myVariants",
source=pileup.sources.GA4GHVariantJson('{}'))
w = pileup.PileupViewer(chrom="chr17",
start=1,
stop=250,
reference="hg19",
tracks=[track])
state = dependency_state(w, drop_defaults=True)
snippet = embed_snippet(views=w, drop_defaults=True, state=state)
parser = Parser()
parser.feed(snippet)
assert parser.states == [
'widget-state', 'check-widget-state', 'widget-view',
'check-widget-view'
]
def test_track_serialization(self):
pileup_track = pileup.Track(viz="pileup", label="myReads", source=pileup.sources.GA4GHAlignmentJson(str))
# serialize track
serialized_track = track_to_json(pileup_track, any)
assert(serialized_track['viz'] == pileup_track.viz)
assert(serialized_track['source'] == pileup_track.source)
assert(serialized_track['sourceOptions'] == pileup_track.sourceOptions)
assert(serialized_track['label'] == pileup_track.label)
# deserialize_track
deserialized_track = track_from_json(serialized_track, any)
assert(deserialized_track.viz == pileup_track.viz)
assert(deserialized_track.source == pileup_track.source)
assert(deserialized_track.sourceOptions == pileup_track.sourceOptions)
assert(deserialized_track.label == pileup_track.label)
def test_embed_pileup(self):
track = pileup.Track(viz="features",
label="myFeatures",
source=pileup.sources.GA4GHFeatureJson('{}'))
w = pileup.PileupViewer(locus="chr17:1-250",
reference="hg19",
tracks=[track])
state = dependency_state(w, drop_defaults=True)
data = embed_data(views=w, drop_defaults=True, state=state)
state = data['manager_state']['state']
views = data['view_specs']
assert len(views) == 1
model_names = [s['model_name'] for s in state.values()]
assert 'PileupViewerModel' in model_names
