def test_case_sensitive(self):
flt = FilterString("name",
FilterString.Equal,
"Aardvark",
case_sensitive=True)
self.assertFalse(flt(self.inst))
flt = FilterString("name",
FilterString.Equal,
"Aardvark",
case_sensitive=False)
self.assertTrue(flt(self.inst))
def setUpClass(cls):
super().setUpClass()
cls.data = Table("https://datasets.biolab.si/sc/aml-1k.tab.gz")
genes_path = serverfiles.localpath_download(
"marker_genes", "panglao_gene_markers.tab")
filter_ = FilterString("Organism", FilterString.Equal, "Human")
cls.genes = Values([filter_])(Table(genes_path))
cls.iris = Table("iris")
def setUpClass(cls):
super().setUpClass()
Variable._clear_all_caches()
cls._init_data()
cls.signal_name = "Reference Data"
cls.signal_data = cls.data
cls.same_input_output_domain = False
genes_path = serverfiles.localpath_download("marker_genes", "panglao_gene_markers.tab")
filter_ = FilterString("Organism", FilterString.Equal, "Human")
cls.genes = Values([filter_])(Table(genes_path))
cls.genes.attributes[TAX_ID] = "9606"
def test_reprs(self):
flid = IsDefined(negate=True)
flhc = HasClass()
flr = Random()
fld = FilterDiscrete(self.attr_disc, None)
flsv = SameValue(self.attr_disc, self.value_disc, negate=True)
flc = FilterContinuous(self.vs[0], FilterContinuous.Less, 5)
flc2 = FilterContinuous(self.vs[1], FilterContinuous.Greater, 3)
flv = Values([flc, flc2], conjunction=False, negate=True)
flvf = ValueFilter(self.attr_disc)
fls = FilterString("name", FilterString.Equal, "Aardvark", case_sensitive=False)
flsl = FilterStringList("name", ["Aardvark"], case_sensitive=False)
flrx = FilterRegex("name", "^c...$")
filters = [flid, flhc, flr, fld, flsv, flc, flv, flvf, fls, flsl, flrx]
for f in filters:
repr_str = repr(f)
new_f = eval(repr_str)
self.assertEqual(repr(new_f), repr_str)
def test_operators(self):
flt = FilterString("name", FilterString.Equal, "aardvark")
self.assertTrue(flt(self.inst))
flt = FilterString("name", FilterString.Equal, "bass")
self.assertFalse(flt(self.inst))
flt = FilterString("name", FilterString.NotEqual, "bass")
self.assertTrue(flt(self.inst))
flt = FilterString("name", FilterString.NotEqual, "aardvark")
self.assertFalse(flt(self.inst))
flt = FilterString("name", FilterString.Less, "bass")
self.assertTrue(flt(self.inst))
flt = FilterString("name", FilterString.Less, "aa")
self.assertFalse(flt(self.inst))
flt = FilterString("name", FilterString.LessEqual, "bass")
self.assertTrue(flt(self.inst))
flt = FilterString("name", FilterString.LessEqual, "aardvark")
self.assertTrue(flt(self.inst))
flt = FilterString("name", FilterString.LessEqual, "aa")
self.assertFalse(flt(self.inst))
flt = FilterString("name", FilterString.Greater, "aa")
self.assertTrue(flt(self.inst))
flt = FilterString("name", FilterString.Greater, "aardvark")
self.assertFalse(flt(self.inst))
flt = FilterString("name", FilterString.GreaterEqual, "aa")
self.assertTrue(flt(self.inst))
flt = FilterString("name", FilterString.GreaterEqual, "aardvark")
self.assertTrue(flt(self.inst))
flt = FilterString("name", FilterString.GreaterEqual, "bass")
self.assertFalse(flt(self.inst))
flt = FilterString("name", FilterString.Between, "aa", "aardvark")
self.assertTrue(flt(self.inst))
flt = FilterString("name", FilterString.Between, "a", "aa")
self.assertFalse(flt(self.inst))
flt = FilterString("name", FilterString.Outside, "aaz", "bass")
self.assertTrue(flt(self.inst))
flt = FilterString("name", FilterString.Outside, "aardvark", "bass")
self.assertFalse(flt(self.inst))
flt = FilterString("name", FilterString.Contains, "ard")
self.assertTrue(flt(self.inst))
flt = FilterString("name", FilterString.Contains, "ra")
self.assertFalse(flt(self.inst))
flt = FilterString("name", FilterString.StartsWith, "aar")
self.assertTrue(flt(self.inst))
flt = FilterString("name", FilterString.StartsWith, "ard")
self.assertFalse(flt(self.inst))
flt = FilterString("name", FilterString.EndsWith, "aardvark")
self.assertTrue(flt(self.inst))
flt = FilterString("name", FilterString.EndsWith, "aard")
self.assertFalse(flt(self.inst))
flt = FilterString("name", FilterString.IsDefined)
self.assertTrue(flt(self.inst))
for s in ["?", "nan"]:
self.inst["name"] = s
flt = FilterString("name", FilterString.IsDefined)
self.assertTrue(flt(self.inst))
self.inst["name"] = ""
flt = FilterString("name", FilterString.IsDefined)
self.assertFalse(flt(self.inst))
def onDeleteWidget(self):
self.shutdown()
super().onDeleteWidget()
if __name__ == "__main__":
from Orange.projection import PCA
from orangecontrib.bioinformatics.utils import serverfiles
data_path = "https://datasets.orange.biolab.si/sc/aml-1k.tab.gz"
table_data = Table(data_path)
table_data.attributes[TAX_ID] = "9606"
ref_data = table_data[::2]
pca = PCA(n_components=2)
pca_model = pca(ref_data)
proj = pca_model(ref_data)
new_dom = Domain(
ref_data.domain.attributes, ref_data.domain.class_vars, chain(ref_data.domain.metas, proj.domain.attributes)
)
ref_data = ref_data.transform(new_dom)
genes_path = serverfiles.localpath_download("marker_genes", "panglao_gene_markers.tab")
filter_ = FilterString("Organism", FilterString.Equal, "Human")
table_genes = Values([filter_])(Table(genes_path))
table_genes.attributes[TAX_ID] = "9606"
WidgetPreview(OWAnnotateProjection).run(
set_data=ref_data, set_secondary_data=table_data[1:200:2], set_genes=table_genes
)
