class TestUpload(object): def setup(self): self.hub = Hub( hub='example_hub', short_label='example hub', long_label='an example hub for testing', email='*****@*****.**') self.genomes_file = GenomesFile() self.genome = Genome('dm3') self.trackdb = TrackDb() self.tracks = [ Track( name='track1', tracktype='bam', local_fn='data/track1.bam' ), Track( name='track2', tracktype='bigWig', local_fn='data/track2.bigwig', ), ] self.hub.add_genomes_file(self.genomes_file) self.genomes_file.add_genome(self.genome) self.genome.add_trackdb(self.trackdb) self.trackdb.add_tracks(self.tracks) @unittest.skipUnless(os.path.exists('data/track1.bam'), 'No test data') def test_upload(self): self.hub.remote_fn = os.path.join( 'uploaded_version', self.hub.remote_fn) self.hub.render() upload.upload_hub( 'localhost', None, self.hub, symlink=True, symlink_dir='staging', run_local=True,) for t, level in self.hub.leaves(Track): upload.upload_track( track=t, host='localhost', user=None, run_local=True) def test_render(self): trackdb = str(self.trackdb) # make sure some of the trackdb rendered correctly assert 'track track1' in trackdb assert 'bigDataUrl track1.bam' in trackdb
class TestUpload(object): def setup(self): self.hub = Hub(hub='example_hub', short_label='example hub', long_label='an example hub for testing', email='*****@*****.**') self.genomes_file = GenomesFile() self.genome = Genome('dm3') self.trackdb = TrackDb() self.tracks = [ Track(name='track1', tracktype='bam', local_fn='data/track1.bam'), Track( name='track2', tracktype='bigWig', local_fn='data/track2.bigwig', ), ] self.hub.add_genomes_file(self.genomes_file) self.genomes_file.add_genome(self.genome) self.genome.add_trackdb(self.trackdb) self.trackdb.add_tracks(self.tracks) @unittest.skipUnless(os.path.exists('data/track1.bam'), 'No test data') def test_upload(self): self.hub.remote_fn = os.path.join('uploaded_version', self.hub.remote_fn) self.hub.render() upload.upload_hub( 'localhost', None, self.hub, symlink=True, symlink_dir='staging', run_local=True, ) for t, level in self.hub.leaves(Track): upload.upload_track(track=t, host='localhost', user=None, run_local=True) def test_render(self): trackdb = str(self.trackdb) # make sure some of the trackdb rendered correctly assert 'track track1' in trackdb assert 'bigDataUrl track1.bam' in trackdb
class TestUpload(object): def setup(self): self.hub = Hub( hub='example_hub', short_label='example hub', long_label='an example hub for testing', email='*****@*****.**') self.genomes_file = GenomesFile() self.genome = Genome('dm3') self.trackdb = TrackDb() self.tracks = [ Track( name='track1', tracktype='bam', local_fn='data/track1.bam' ), Track( name='track2', tracktype='bigWig', local_fn='data/track2.bigwig', ), ] self.hub.add_genomes_file(self.genomes_file) self.genomes_file.add_genome(self.genome) self.genome.add_trackdb(self.trackdb) self.trackdb.add_tracks(self.tracks) def test_upload(self): self.hub.remote_fn = os.path.join( 'uploaded_version', self.hub.remote_fn) self.hub.render() upload.upload_hub( 'localhost', None, self.hub, symlink=True, symlink_dir='staging', run_local=True,) for t, level in self.hub.leaves(Track): upload.upload_track( track=t, host='localhost', user=None, run_local=True)
class TestUpload(object): def setup(self): self.hub = Hub(hub='example_hub', short_label='example hub', long_label='an example hub for testing', email='*****@*****.**') self.genomes_file = GenomesFile() self.genome = Genome('dm3') self.trackdb = TrackDb() self.tracks = [ Track(name='track1', tracktype='bam', local_fn='data/track1.bam'), Track( name='track2', tracktype='bigWig', local_fn='data/track2.bigwig', ), ] self.hub.add_genomes_file(self.genomes_file) self.genomes_file.add_genome(self.genome) self.genome.add_trackdb(self.trackdb) self.trackdb.add_tracks(self.tracks) def test_upload(self): self.hub.remote_fn = os.path.join('uploaded_version', self.hub.remote_fn) self.hub.render() upload.upload_hub( 'localhost', None, self.hub, symlink=True, symlink_dir='staging', run_local=True, ) for t, level in self.hub.leaves(Track): upload.upload_track(track=t, host='localhost', user=None, run_local=True)